ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics

accSDA

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘rARPACK’ ‘sparseLDA’ All declared Imports should be used.

adapr

Version: 1.0.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘plotly’ ‘shinydashboard’ All declared Imports should be used.

affycoretools

Version: 1.48.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘oligo’

afmToolkit

Version: 0.0.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DBI’ ‘assertthat’ ‘tibble’ All declared Imports should be used.

aire.zmvm

Version: 0.5.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:

testthat results ================================================================ OK: 58 SKIPPED: 0 FAILED: 9 1. Failure: .convert_time correctly parses string (@test_data.R#7) 2. Failure: .convert_time correctly parses string (@test_data.R#11) 3. Failure: .convert_time correctly parses string (@test_data.R#13) 4. Failure: .convert_time correctly parses string (@test_data.R#16) 5. Failure: .convert_time correctly parses string (@test_data.R#20) 6. Failure: .convert_time correctly parses string (@test_data.R#23) 7. Failure: .convert_time correctly parses string (@test_data.R#26) 8. Failure: .convert_time correctly parses string (@test_data.R#30) 9. Failure: .convert_time correctly parses string (@test_data.R#33)

Error: testthat unit tests failed Execution halted ```
checking data for non-ASCII characters ... NOTE Note: found 38 marked UTF-8 strings

ameco

Version: 0.2.8

checking installed package size ... NOTE installed size is 15.7Mb sub-directories of 1Mb or more: data 15.6Mb

ampliQueso

Version: 1.14.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘rnaSeqMap’ ‘knitr’ ‘rgl’ ‘ggplot2’ ‘gplots’ ‘parallel’ ‘doParallel’ ‘foreach’ ‘VariantAnnotation’ ‘genefilter’ ‘statmod’ ‘xtable’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘samr’ All declared Imports should be used. Packages in Depends field not imported from: ‘VariantAnnotation’ ‘doParallel’ ‘foreach’ ‘genefilter’ ‘ggplot2’ ‘gplots’ ‘knitr’ ‘parallel’ ‘rgl’ ‘statmod’ ‘xtable’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘rnaSeqMap:::newSeqReads’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... compareCoverages: no visible global function definition for ‘read.table’ getCountTable: no visible global function definition for ‘read.table’ runAQReport: no visible global function definition for ‘read.table’ runAQReport: no visible global function definition for ‘rowttests’ runAQReport: no visible global function definition for ‘p.adjust’ runAQReport: no visible global function definition for ‘%do%’ runAQReport: no visible global function definition for ‘foreach’ runAQReport: no visible global function definition for ‘aggregate’ runAQReport: no visible global function definition for ‘knit’ Undefined global functions or variables: %do% %dopar% aggregate combn detectCores end foreach hasArg knit makeCluster p.adjust permp qual ranges read.table readVcf ref registerDoParallel rowttests seqnames start stopCluster str strand width Consider adding importFrom("methods", "hasArg") importFrom("stats", "aggregate", "end", "p.adjust", "start") importFrom("utils", "combn", "read.table", "str") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

AnalysisPageServer

Version: 1.10.0

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘Rook’ ‘fork’ ‘FastRWeb’
checking for portable file names ... NOTE ``` ... AnalysisPageServer/inst/doc/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/marionettejs/backbone.marionette@2.4.4 AnalysisPageServer/inst/htdocs/client/dist-aps/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/marionettejs/backbone.marionette@2.4.4 AnalysisPageServer/inst/htdocs/client/dist-apss/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/itemview AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServer/Pages/Landing/ToolOverview/show/layoutview AnalysisPageServer/inst/htdocs/client/src/AnalysisPageServerStatic/Pages/Datasets/show/collectionview AnalysisPageServer/vignettes/static-example/jspm_packages/github/marionettejs/backbone.marionette@2.4.4 AnalysisPageServer/vignettes/static-example/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts AnalysisPageServer/vignettes/static-example2/jspm_packages/github/marionettejs/backbone.marionette@2.4.4 AnalysisPageServer/vignettes/static-example2/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts AnalysisPageServer/vignettes/static-example3/jspm_packages/github/marionettejs/backbone.marionette@2.4.4 AnalysisPageServer/vignettes/static-example3/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts AnalysisPageServer/vignettes/static-example4/jspm_packages/github/marionettejs/backbone.marionette@2.4.4 AnalysisPageServer/vignettes/static-example4/jspm_packages/github/t0m/select2-bootstrap-css@1.4.6/_jekyll/fonts

Tarballs are only required to store paths of up to 100 bytes and cannot store those of more than 256 bytes, with restrictions including to 100 bytes for the final component. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. ```
checking installed package size ... NOTE installed size is 41.8Mb sub-directories of 1Mb or more: doc 31.5Mb htdocs 8.6Mb
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘FastRWeb’ ‘RUnit’ ‘fork’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘log4r:::INFO’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... ‘printTextProtocol’ uniquify.ids.in.svg.files: no visible global function definition for ‘setNames’ validate.compound.param.value: no visible global function definition for ‘setNames’ Undefined global functions or variables: App FILES GET POST SERVER WebResult all.pages analysis analysis.id brand capture.output checkEquals clean.tmpdir defineTestSuite dev.cur dev.list dev.off events file.params handler handlers head in.analysis is.textarea.wrap.request no.rook.fork.msg packageVersion page.params params parse.multipart plot plot.file png printTextProtocol process.response request resources retrieve runTestSuite sendBin server.pid sessionInfo setContentType setHeader setNames status str svg temp.plot.file Consider adding importFrom("grDevices", "dev.cur", "dev.list", "dev.off", "png", "svg") importFrom("graphics", "plot") importFrom("stats", "setNames") importFrom("utils", "capture.output", "head", "packageVersion", "sessionInfo", "str") to your NAMESPACE file.
checking installed files from ‘inst/doc’ ... NOTE ``` The following directories should probably not be installed: ‘images’, ‘img’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. ```
checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.

Anaquin

Version: 1.2.0

checking examples ... ERROR ``` ... > title <- 'Assembly Plot' > xlab <- 'Input Concentration (log2)' > ylab <- 'Sensitivity' > > # Sequin names > seqs <- row.names(UserGuideData_5.4.5.1) > > # Input concentration > input <- log2(UserGuideData_5.4.5.1$InputConcent) > > # Measured sensitivity > measured <- UserGuideData_5.4.5.1$Sn > > anaquin <- AnaquinData(analysis='PlotLogistic',
- seqs=seqs,
- input=input,
- measured=measured)
  
  plotLogistic(anaquin, title=title, xlab=xlab, ylab=ylab, showLOA=TRUE) Error: !is.null(minX) is not TRUE Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/tPlotLODR.R’ failed. Last 13 lines of output: [1] "Estmating LODR for 2" [1] "Estmating LODR for 3" [1] "Estmating LODR for 4"

| | Ratio| LODR| |:--|-----:|--------:| |2 | 1| 3.617511| |3 | 2| 5.673070| |4 | 3| 2.584553| |5 | 4| 3.896317| Error: !is.null(minX) is not TRUE In addition: Warning message: Transformation introduced infinite values in continuous y-axis Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 114-127 (Anaquin.Rmd) Error: processing vignette 'Anaquin.Rmd' failed with diagnostics: !is.null(minX) is not TRUE Execution halted

checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘ggplot2’ A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE RnaQuin.genes: no visible binding for global variable ‘RnaQuinMixtureA’ RnaQuin.isoforms: no visible binding for global variable ‘RnaQuinMixtureA’ Undefined global functions or variables: RnaQuinMixtureA

AneuFinder

Version: 1.4.0

checking whether package ‘AneuFinder’ can be installed ... ERROR Installation failed. See ‘/home/muelleki/git/R/ggplot2/revdep/checks/AneuFinder/new/AneuFinder.Rcheck/00install.out’ for details.

* installing *source* package ‘AneuFinder’ ...
** libs
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c loghmm.cpp -o loghmm.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_interface.cpp -o R_interface.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utility.cpp -o utility.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scalehmm.cpp -o scalehmm.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c densities.cpp -o densities.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/usr/lib/R/lib -lR
installing to /home/muelleki/git/R/ggplot2/revdep/checks/AneuFinder/new/AneuFinder.Rcheck/AneuFinder/libs
** R
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/muelleki/git/R/ggplot2/revdep/library/AneuFinder/bamsignals/libs/bamsignals.so':
  libhts.so.0: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘AneuFinder’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/AneuFinder/new/AneuFinder.Rcheck/AneuFinder’

* installing *source* package ‘AneuFinder’ ...
** libs
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scalehmm.cpp -o scalehmm.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utility.cpp -o utility.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_interface.cpp -o R_interface.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c loghmm.cpp -o loghmm.o
g++  -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c densities.cpp -o densities.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o AneuFinder.so R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -L/usr/lib/R/lib -lR
installing to /home/muelleki/git/R/ggplot2/revdep/checks/AneuFinder/old/AneuFinder.Rcheck/AneuFinder/libs
** R
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/muelleki/git/R/ggplot2/revdep/library/AneuFinder/bamsignals/libs/bamsignals.so':
  libhts.so.0: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘AneuFinder’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/AneuFinder/old/AneuFinder.Rcheck/AneuFinder’

annotatr

Version: 1.2.1

checking re-building of vignette outputs ... WARNING ... Building CpG islands... loading from cache '/home/muelleki//.AnnotationHub/5086' Building CpG shores... Building CpG shelves... Building inter-CpG-islands... Annotating... Randomizing regions... `summarise_each()` is deprecated. Use `summarise_all()`, `summarise_at()` or `summarise_if()` instead. To map `funs` over a selection of variables, use `summarise_at()` Warning in subset_order_tbl(tbl = annotated_random, col = "annot.type", : There are elements in col_order that are not present in the corresponding column. Check for typos, or this could be a result of 0 tallies. Warning in bind_rows_(x, .id) : Unequal factor levels: coercing to character Warning in bind_rows_(x, .id) : binding character and factor vector, coercing into character vector Warning in bind_rows_(x, .id) : binding character and factor vector, coercing into character vector Error: processing vignette 'annotatr-vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking R code for possible problems ... NOTE plot_coannotations: no visible binding for global variable ‘.’ plot_numerical_coannotations: no visible binding for global variable ‘.’ Undefined global functions or variables: .

anomalyDetection

Version: 0.2.4

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘caret’ All declared Imports should be used.

aoristic

Version: 0.6

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... ‘slot’ aoristic.grid: no visible global function definition for ‘browseURL’ aoristic.shp: no visible global function definition for ‘aggregate’ aoristic.shp: no visible global function definition for ‘slot’ aoristic.shp : <anonymous>: no visible global function definition for ‘as’ aoristic.shp : <anonymous>: no visible global function definition for ‘slot’ aoristic.shp: no visible global function definition for ‘browseURL’ Undefined global functions or variables: aggregate as browseURL colorRampPalette contourLines dev.off image par png quantile slot Consider adding importFrom("grDevices", "colorRampPalette", "contourLines", "dev.off", "png") importFrom("graphics", "image", "par") importFrom("methods", "as", "slot") importFrom("stats", "aggregate", "quantile") importFrom("utils", "browseURL") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

apsimr

Version: 1.2

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘sensitivity’, ‘APSIMBatch’

ArchaeoPhases

Version: 1.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘DT’ All declared Imports should be used.

archetypes

Version: 2.2-0

checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘MASS’ ‘TSP’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... xyplot.stepArchetypes: no visible global function definition for ‘gray’ xyplot.stepArchetypes: no visible global function definition for ‘plot’ xyplot.stepArchetypes: no visible global function definition for ‘points’ xyplot.stepArchetypes: no visible global function definition for ‘lines’ xyplot.weightedArchetypes: no visible binding for global variable ‘gray’ Undefined global functions or variables: TSP abline arrows axis box chull cmdscale combn dist ecdf ginv gray head history layout lines matlines matplot median mtext optim par plot points polygon rgb rnorm sd solve_TSP symbols tail text Consider adding importFrom("grDevices", "chull", "gray", "rgb") importFrom("graphics", "abline", "arrows", "axis", "box", "layout", "lines", "matlines", "matplot", "mtext", "par", "plot", "points", "polygon", "symbols", "text") importFrom("stats", "cmdscale", "dist", "ecdf", "median", "optim", "rnorm", "sd") importFrom("utils", "combn", "head", "history", "tail") to your NAMESPACE file.

archivist

Version: 2.1.2

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘archivist.github’
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘rmarkdown’, ‘archivist.github’

ARPobservation

Version: 1.1

checking R code for possible problems ... NOTE ... reported_observations: no visible global function definition for ‘aggregate’ reported_observations: no visible binding for global variable ‘var’ rgamma_eq : <anonymous>: no visible global function definition for ‘uniroot’ rgamma_eq: no visible global function definition for ‘runif’ rgamma_mix_eq : <anonymous>: no visible global function definition for ‘uniroot’ rgamma_mix_eq: no visible global function definition for ‘runif’ rweibull_eq : <anonymous>: no visible global function definition for ‘uniroot’ rweibull_eq: no visible global function definition for ‘runif’ smooth_cov: no visible global function definition for ‘dist’ Undefined global functions or variables: aggregate dist integrate nobs pgamma qnorm quantile rbinom rexp rgamma rnorm runif rweibull uniroot var Consider adding importFrom("stats", "aggregate", "dist", "integrate", "nobs", "pgamma", "qnorm", "quantile", "rbinom", "rexp", "rgamma", "rnorm", "runif", "rweibull", "uniroot", "var") to your NAMESPACE file.

asremlPlus

Version: 2.0-12

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘asreml’

asVPC

Version: 1.0.2

checking R code for possible problems ... NOTE ... VPC.graph : findQuantile: no visible global function definition for ‘quantile’ VPC.graph : findQuantileCI : <anonymous>: no visible global function definition for ‘quantile’ asVPC.binW: no visible global function definition for ‘median’ asVPC.binW : <anonymous>: no visible global function definition for ‘quantile’ asVPC.binW: no visible global function definition for ‘quantile’ asVPC.distanceW: no visible global function definition for ‘median’ asVPC.distanceW : <anonymous>: no visible global function definition for ‘quantile’ asVPC.distanceW: no visible global function definition for ‘quantile’ makeCOVbin: no visible global function definition for ‘quantile’ makeCOVbin: no visible global function definition for ‘median’ read_Simdata: no visible global function definition for ‘read.table’ Undefined global functions or variables: median quantile read.table Consider adding importFrom("stats", "median", "quantile") importFrom("utils", "read.table") to your NAMESPACE file.

autoimage

Version: 2.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘akima’

automap

Version: 1.0-14

checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘ggplot2’ ‘gpclib’ ‘maptools’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... ‘geom_point’ posPredictionInterval: no visible global function definition for ‘median’ posPredictionInterval: no visible global function definition for ‘qnorm’ summary.autoKrige.cv: no visible global function definition for ‘cor’ summary.autoKrige.cv: no visible global function definition for ‘sd’ summary.autoKrige.cv: no visible global function definition for ‘IQR’ Undefined global functions or variables: IQR aes_string as.formula chull coord_equal cor facet_wrap fortify geom_path geom_point ggplot grey is median modifyList qnorm quantile scale_color_gradient2 scale_size_continuous scale_x_continuous scale_y_continuous sd Consider adding importFrom("grDevices", "chull", "grey") importFrom("methods", "is") importFrom("stats", "IQR", "as.formula", "cor", "median", "qnorm", "quantile", "sd") importFrom("utils", "modifyList") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

BaalChIP

Version: 1.2.0

checking re-building of vignette outputs ... WARNING ``` ...

Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: Rsamtools Loading required package: Biostrings Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':
```
strsplit
```
-samplesheet checks: OK! -samplesheet checks: OK! -no filters applied yet -detected readlengths323436

Error: processing vignette 'BaalChIP.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE installed size is 198.6Mb sub-directories of 1Mb or more: data 95.8Mb test 101.9Mb
checking R code for possible problems ... NOTE applyBayes: no visible binding for global variable ‘SNP_id’ plot.filt.barplot: no visible binding for global variable ‘cellname’ plot.filt.barplot: no visible binding for global variable ‘value’ plot.filt.barplot: no visible binding for global variable ‘variable’ plot.filt.boxplot: no visible binding for global variable ‘variable’ plot.filt.boxplot: no visible binding for global variable ‘value’ plot.filt.boxplot: no visible binding for global variable ‘coltype’ plot.filt.pie: no visible binding for global variable ‘variable’ plot.filt.pie: no visible binding for global variable ‘value.mean’ plot.simul: no visible binding for global variable ‘readslen’ plot.simul: no visible binding for global variable ‘perc_right’ plotadjustment: no visible binding for global variable ‘value’ plotadjustment: no visible binding for global variable ‘variable’ Undefined global functions or variables: SNP_id cellname coltype perc_right readslen value value.mean variable

BacArena

Version: 1.6

checking package dependencies ... NOTE Package suggested but not available for checking: ‘sybilSBML’
checking installed package size ... NOTE installed size is 8.4Mb sub-directories of 1Mb or more: data 3.6Mb libs 3.7Mb

backShift

Version: 0.1.4.2

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’

bacon

Version: 1.4.0

checking R code for possible problems ... NOTE .hist: no visible binding for global variable ‘..density..’ .qq: no visible binding for global variable ‘column’ Undefined global functions or variables: ..density.. column

ballr

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘XML’ ‘devtools’ ‘ggplot2’ ‘scales’ All declared Imports should be used.

BatchMap

Version: 1.0.2.0

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: libs 4.2Mb

bayesAB

Version: 1.1.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
1. Failure: Success (@test-generics.R#43) -------------------------------------- print(plot(x, rep(0.5, 4))) produced warnings.
testthat results ================================================================ OK: 132 SKIPPED: 0 FAILED: 4 1. Failure: Success (@test-generics.R#37) 2. Failure: Success (@test-generics.R#38) 3. Failure: Success (@test-generics.R#42) 4. Failure: Success (@test-generics.R#43)

Error: testthat unit tests failed Execution halted ```

bayesDP

Version: 1.2.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

bayesplot

Version: 1.4.0

checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: R 1.6Mb doc 3.6Mb

BCEA

Version: 2.2-5

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’

Bclim

Version: 3.1.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

bcp

Version: 4.0.0

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: libs 5.1Mb

bcrm

Version: 0.4.6

checking examples ... ERROR ``` ... 75% 0.8931515 0.9480442 97.5% 0.9278585 0.9652638

Posterior distribution of the model parameter using rjags

post.rjags<-Posterior.rjags(tox,notox,sdose,ff,prior.alpha + ,burnin.itr=2000,production.itr=2000) print(mean(post.rjags)) [1] 0.6712911 hist(post.rjags)

Posterior distribution of the model parameter using BRugs (Windows and i386 Linux only)

if(Sys.info()["sysname"] %in% c("Windows","Linux")){ + post.BRugs<-Posterior.BRugs(tox,notox,sdose,ff,prior.alpha + ,burnin.itr=2000,production.itr=2000) + print(mean(post.BRugs)) + hist(post.BRugs) + } Error in loadNamespace(name) : there is no package called ‘BRugs’ Calls: Posterior.BRugs ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘BRugs’

bde

Version: 1.0.1

checking R code for possible problems ... NOTE ... rsample,BoundedDensity: no visible global function definition for ‘runif’ setNormalizationConst,MacroBetaChen99Kernel: no visible global function definition for ‘integrate’ setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global function definition for ‘integrate’ setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global function definition for ‘integrate’ setNormalizationConstants,MicroBetaChen99Kernel : density.kernelFunction: no visible global function definition for ‘dbeta’ setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no visible global function definition for ‘integrate’ show,BoundedDensity: no visible global function definition for ‘str’ show,KernelDensity: no visible global function definition for ‘str’ Undefined global functions or variables: dbeta integrate runif str Consider adding importFrom("stats", "dbeta", "integrate", "runif") importFrom("utils", "str") to your NAMESPACE file.

bea.R

Version: 1.0.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’ ‘yaml’ All declared Imports should be used.

beadarray

Version: 2.26.1

checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘Nozzle.R1’ ‘affy’ ‘ggbio’ ‘hwriter’ ‘lumi’ ‘vsn’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘ggplot2’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: ‘BeadDataPackR:::combineFiles’ ‘BeadDataPackR:::readHeader’ ‘Biobase:::assayDataStorageMode’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘illuminaForeground_6x6’ ‘locsIndicesToGrid’ ‘obtainLocs’ ‘simpleXMLparse’
checking foreign function calls ... NOTE Foreign function call to a different package: .Call("roundLocsFileValues", ..., PACKAGE = "BeadDataPackR") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... geom_hline geom_point geom_tile geom_vline ggplot ggsave ggtitle hwrite hwriteImage is jpeg loess lowess lumiHumanIDMapping_dbconn lumiMouseIDMapping_dbconn lumiRatIDMapping_dbconn lumiT menu metaTemplate model.matrix new newCustomReport newFigure newParagraph newSection newTable normalize.invariantset normalize.qspline openPage opts p.adjust packageDescription pdf platformSigs plotIdeogram png predict qplot rainbow read.csv read.table rgb rsn runif scale_fill_discrete scale_fill_gradient setTxtProgressBar stat_binhex theme theme_blank theme_bw tracks txtProgressBar value value.1 vsn2 write.csv write.table writeReport xlab ylab Consider adding importFrom("grDevices", "col2rgb", "dev.off", "jpeg", "pdf", "png", "rainbow", "rgb") importFrom("methods", "as", "callNextMethod", "is", "new") importFrom("stats", "aggregate", "approx", "density", "loess", "lowess", "model.matrix", "p.adjust", "predict", "runif") importFrom("utils", "data", "menu", "packageDescription", "read.csv", "read.table", "setTxtProgressBar", "txtProgressBar", "write.csv", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

benchmark

Version: 0.3-6

checking dependencies in R code ... NOTE 'library' or 'require' call to ‘multcomp’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... ‘algorithms’ stripchart.AlgorithmPerformance: no visible binding for global variable ‘value’ stripchart.AlgorithmPerformance: no visible binding for global variable ‘samples’ Undefined global functions or variables: abline addEdge agopen algorithms as.formula axis barplot box cancor characteristics col2rgb getDefaultAttrs gray is layout legend lines lm median mi.plugin mtext na.omit new par points predict rect relation_is_strict_weak_order reshape rgb samples segments terms theme_text value Consider adding importFrom("grDevices", "col2rgb", "gray", "rgb") importFrom("graphics", "abline", "axis", "barplot", "box", "layout", "legend", "lines", "mtext", "par", "points", "rect", "segments") importFrom("methods", "is", "new") importFrom("stats", "as.formula", "cancor", "lm", "median", "na.omit", "predict", "reshape", "terms") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

benchr

Version: 0.2.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 184 SKIPPED: 0 FAILED: 10
1. Failure: Boxplot ggplot without log (@test-plot.R#39)
2. Failure: Boxplot ggplot without log (@test-plot.R#40)
3. Failure: Boxplot ggplot with log and horizontal (@test-plot.R#53)
4. Failure: Boxplot ggplot with log and horizontal (@test-plot.R#54)
5. Failure: Boxplot ggplot with violin geom (@test-plot.R#67)
6. Failure: Boxplot ggplot with violin geom (@test-plot.R#68)
7. Failure: Scatter plot ggplot with log (@test-plot.R#83)
8. Failure: Scatter plot ggplot with log (@test-plot.R#84)
9. Failure: Scatter plot ggplot without log (@test-plot.R#99)
10. Failure: Scatter plot ggplot without log (@test-plot.R#100)
Error: testthat unit tests failed Execution halted ```

bife

Version: 0.4

checking installed package size ... NOTE installed size is 5.7Mb sub-directories of 1Mb or more: data 2.1Mb libs 3.3Mb

bigKRLS

Version: 2.0.4

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: libs 4.8Mb

BIGL

Version: 1.1.0

checking re-building of vignette outputs ... WARNING ... Warning: Transformation introduced infinite values in continuous x-axis Warning: Transformation introduced infinite values in continuous y-axis Warning: Transformation introduced infinite values in continuous x-axis Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 199 rows containing non-finite values (stat_contour). Warning in is.na(verts[, 2]) : is.na() applied to non-(list or vector) of type 'NULL' Warning in is.na(verts[, 3]) : is.na() applied to non-(list or vector) of type 'NULL' Warning in is.na(verts[, 1]) : is.na() applied to non-(list or vector) of type 'NULL' Warning in is.na(verts[, 3]) : is.na() applied to non-(list or vector) of type 'NULL' Warning in is.na(verts[, 1]) : is.na() applied to non-(list or vector) of type 'NULL' Warning in is.na(verts[, 2]) : is.na() applied to non-(list or vector) of type 'NULL' Quitting from lines 240-243 (analysis.Rmd) Error: processing vignette 'analysis.Rmd' failed with diagnostics: there is no package called 'webshot' Execution halted

bigstatsr

Version: 0.2.2

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 'dimnames' applied to non-array 1: sparseSVM::sparseSVM(X2, y.factor, alpha = alpha, lambda.min = lambda.min, penalty.factor = m) at testthat/test-spSVM.R:32
1. Error: equality with sparseSVM with only half the data (@test-spSVM.R#68) --- 'dimnames' applied to non-array 1: sparseSVM::sparseSVM(X2[ind, ], y.factor[ind], alpha = alpha, lambda.min = lambda.min, penalty.factor = m) at testthat/test-spSVM.R:68
testthat results ================================================================ OK: 1629 SKIPPED: 0 FAILED: 2 1. Error: equality with sparseSVM with all data (@test-spSVM.R#32) 2. Error: equality with sparseSVM with only half the data (@test-spSVM.R#68)

Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE installed size is 12.7Mb sub-directories of 1Mb or more: extdata 2.3Mb libs 9.6Mb

binom

Version: 1.1-1

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘ggplot2’ ‘lattice’ ‘polynom’ ‘tcltk’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... definition for ‘tkdestroy’ var.probit: no visible global function definition for ‘qnorm’ var.probit: no visible global function definition for ‘dnorm’ Undefined global functions or variables: abline aes_string aggregate approx axis binomial box col.whitebg current.panel.limits dbeta dbinom dnorm facet_wrap find geom_polygon ggplot heat.colors integral legend lines llines lpoints lpolygon ltext optim panel.abline panel.levelplot panel.xyplot pbeta plot pnorm polynomial predict qbeta qnorm rbinom reorder spline tclObj tclVar theme_bw tkbutton tkcheckbutton tkdestroy tkframe tklabel tkpack tkradiobutton tkscale tktoplevel tkwm.title trellis.par.get trellis.par.set uniroot xlab xlim xyplot ylab ylim Consider adding importFrom("grDevices", "heat.colors") importFrom("graphics", "abline", "axis", "box", "legend", "lines", "plot") importFrom("stats", "aggregate", "approx", "binomial", "dbeta", "dbinom", "dnorm", "optim", "pbeta", "pnorm", "predict", "qbeta", "qnorm", "rbinom", "reorder", "spline", "uniroot") importFrom("utils", "find") to your NAMESPACE file.

biobroom

Version: 1.8.0

checking dependencies in R code ... NOTE 'library' or 'require' call to ‘DESeq2’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing or unexported object: ‘dplyr::tbl_dt’
checking R code for possible problems ... NOTE ... for ‘colData’ tidy.deSet: no visible global function definition for ‘exprs<-’ tidy.deSet: no visible binding for global variable ‘value’ tidy.deSet: no visible binding for global variable ‘gene’ tidy.deSet: no visible global function definition for ‘pData’ tidy.qvalue: no visible binding for global variable ‘smoothed’ tidy.qvalue: no visible binding for global variable ‘pi0’ tidy.qvalue: no visible binding for global variable ‘lambda’ tidy_matrix: no visible binding for global variable ‘value’ tidy_matrix: no visible binding for global variable ‘gene’ Undefined global functions or variables: . DGEList calcNormFactors colData counts design end estimate estimateSizeFactors exprs<- fData<- gene gr is lambda model.matrix p.adjust pData pData<- pi0 protein rowRanges sample.id seqnames setNames smoothed start tbl_dt term value voom voomWithQualityWeights Consider adding importFrom("methods", "is") importFrom("stats", "end", "model.matrix", "p.adjust", "setNames", "start") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

bioCancer

Version: 1.4.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'bioCancer.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘magrittr’ ‘ggplot2’ ‘lubridate’ ‘tidyr’ ‘cgdsr’ ‘RCurl’ ‘XML’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 22.3Mb sub-directories of 1Mb or more: base 6.9Mb bioCancer 3.1Mb doc 2.8Mb quant 7.7Mb

biogas

Version: 1.8.1

checking re-building of vignette outputs ... WARNING `` Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'biogas_quick_start.tex' failed. LaTeX errors: ! LaTeX Error: Filemhchem.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.58 \usepackage [colorlinks = true, urlcolor = blue]{hyperref} % Must be loa... ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

biogram

Version: 1.4

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘seqinr’

biomod2

Version: 3.3-7

checking examples ... ERROR ``` ...
```
> Projecting GuloGulo_AllData_RUN1_RF ...
> Projecting GuloGulo_AllData_RUN2_RF ...
```
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Done -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

4. Creating the ensemble projections

BIOMOD_EnsembleForecasting( projection.output = myBiomodProjection, + EM.output = myBiomodEM)

-=-=-=-=-=-=-=-=-=-=-=-= Do Ensemble Models Projections -=-=-=-=-=-=-=-=-=-=-=-=
```
> Projecting GuloGulo_EMmeanByTSS_RF_mergedRun_mergedData ...Error in calc(formal_predictions, function(x) { :
```
unused arguments (function(x) { m <- mean(x) if (on_0_1000) m <- round(m) return(m) }, filename = filename, overwrite = TRUE) Calls: BIOMOD_EnsembleForecasting ... .local -> .predict.EMmean_biomod2_model.RasterStack Execution halted ```
checking whether package ‘biomod2’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘raster::calc’ by ‘ggplot2::calc’ when loading ‘biomod2’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/biomod2/new/biomod2.Rcheck/00install.out’ for details.
checking R code for possible problems ... NOTE ... as.numeric(predict.maxent(get_formal_model(object), x.no.na)[, "1"]) proj.out[-attr(x.no.na, "na.action")] <- proj.not.na } return(proj.out) }) .predict.MAXENT.Tsuruoka_biomod2_model.RasterStack: possible error in return(proj.out): unused argument (function(x) { proj.out <- rep(NA, nrow(x)) x.no.na <- na.omit(x) if (nrow(x.no.na)) { proj.not.na <- as.numeric(predict.maxent(get_formal_model(object), x.no.na)[, "1"]) proj.out[-attr(x.no.na, "na.action")] <- proj.not.na } return(proj.out) }) .predict.MAXENT.Tsuruoka_biomod2_model.RasterStack: possible error in }): unused argument (function(x) { proj.out <- rep(NA, nrow(x)) x.no.na <- na.omit(x) if (nrow(x.no.na)) { proj.not.na <- as.numeric(predict.maxent(get_formal_model(object), x.no.na)[, "1"]) proj.out[-attr(x.no.na, "na.action")] <- proj.not.na } return(proj.out) }) BinaryTransformation,RasterStack: possible error in calc(data, function(x) {: unused argument (function(x) { x >= threshold }) BinaryTransformation,RasterStack: possible error in x >= threshold: unused argument (function(x) { x >= threshold }) BinaryTransformation,RasterStack: possible error in }): unused argument (function(x) { x >= threshold })

checking package dependencies ... NOTE Package suggested but not available for checking: ‘ecospat’
checking DESCRIPTION meta-information ... NOTE BugReports field is not a suitable URL but contains an email address which will be used as from R 3.4.0

bioplots

Version: 0.0.1

checking files in ‘vignettes’ ... NOTE Package has no Sweave vignette sources and no VignetteBuilder field.

BioStatR

Version: 2.0.0

checking R code for possible problems ... NOTE ... cvar: no visible global function definition for ‘sd’ eta2: no visible global function definition for ‘lm’ eta2: no visible global function definition for ‘as.formula’ gg_qqplot: no visible binding for global variable ‘qnorm’ gg_qqplot: no visible global function definition for ‘quantile’ panel.hist: no visible global function definition for ‘par’ panel.hist: no visible global function definition for ‘hist’ panel.hist: no visible global function definition for ‘rect’ plotcdf2: no visible global function definition for ‘colorRampPalette’ plotcdf2 : jet.colors: no visible global function definition for ‘gray’ plotcdf2: no visible global function definition for ‘persp’ poi.ci: no visible global function definition for ‘qchisq’ Undefined global functions or variables: as.formula colorRampPalette gray hist lm par persp qchisq qf qnorm quantile rect sd Consider adding importFrom("grDevices", "colorRampPalette", "gray") importFrom("graphics", "hist", "par", "persp", "rect") importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm", "quantile", "sd") to your NAMESPACE file.

biotmle

Version: 1.0.4

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Matrix’ ‘SuperLearner’ ‘biotmleData’ All declared Imports should be used.

blandr

Version: 0.4.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘knitr’ All declared Imports should be used.

blastula

Version: 0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rJava’ All declared Imports should be used.

blkbox

Version: 1.0

checking package dependencies ... NOTE Package suggested but not available for checking: ‘bigrf’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’ ‘rmarkdown’ ‘shinyjs’ All declared Imports should be used. Missing or unexported object: ‘xgboost::predict’

bmlm

Version: 1.3.3

checking installed package size ... NOTE installed size is 32.9Mb sub-directories of 1Mb or more: libs 32.6Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used.

bmmix

Version: 0.1-2

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE bmmix : LL.y: no visible global function definition for ‘dmultinom’ bmmix : LL.x : <anonymous>: no visible global function definition for ‘dmultinom’ bmmix : LPrior.alpha: no visible global function definition for ‘dexp’ bmmix : alpha.move: no visible global function definition for ‘rnorm’ bmmix : alpha.move: no visible global function definition for ‘runif’ bmmix : phi.move: no visible global function definition for ‘rnorm’ bmmix : phi.move: no visible global function definition for ‘runif’ bmmix: no visible global function definition for ‘read.table’ Undefined global functions or variables: dexp dmultinom read.table rnorm runif Consider adding importFrom("stats", "dexp", "dmultinom", "rnorm", "runif") importFrom("utils", "read.table") to your NAMESPACE file.

bodenmiller

Version: 0.1

checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: data 8.7Mb

bomrang

Version: 0.0.8

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: [2019] "IDE00437.201711210540.tif" "IDE00437.201711210550.tif" [2021] "IDE00437.201711210600.tif" "IDE00437.201711210610.tif" [2023] "IDE00437.201711210620.tif" "IDE00437.201711210630.tif" [2025] "IDE00437.201711210640.tif" "IDE00437.201711210650.tif" [2027] "IDE00437.201711210700.tif" "IDE00437.201711210710.tif" [2029] "IDE00437.201711210720.tif" "IDE00437.201711210730.tif" trying URL 'ftp://ftp.bom.gov.au/anon/gen/gms/IDE00425.201711210730.tif' Content type 'unknown' length 18648256 bytes (17.8 MB) ================================================== testthat results ================================================================ OK: 102 SKIPPED: 0 FAILED: 1
1. Error: caching utils list files in cache and delete when asked (@test-check_cache.R#47)
Error: testthat unit tests failed Execution halted ```

bossMaps

Version: 0.1.0

checking whether package ‘bossMaps’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘bossMaps’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/bossMaps/new/bossMaps.Rcheck/00install.out’ for details.

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘rgdal’ ‘tidyr’ All declared Imports should be used.

BradleyTerryScalable

Version: 0.1.0

checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: libs 6.1Mb

BrailleR

Version: 0.26.0

checking package dependencies ... NOTE Package suggested but not available for checking: ‘installr’

brainGraph

Version: 1.0.0

checking whether package ‘brainGraph’ can be installed ... ERROR Installation failed. See ‘/home/muelleki/git/R/ggplot2/revdep/checks/brainGraph/new/brainGraph.Rcheck/00install.out’ for details.

* installing *source* package ‘brainGraph’ ...
** package ‘brainGraph’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
R session is headless; GTK+ not initialized.

(R:37582): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Error: package or namespace load failed for ‘cairoDevice’:
 .onLoad failed in loadNamespace() for 'cairoDevice', details:
  call: fun(libname, pkgname)
  error: GDK display not found - please make sure X11 is running
Error : package ‘cairoDevice’ could not be loaded
ERROR: lazy loading failed for package ‘brainGraph’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/brainGraph/new/brainGraph.Rcheck/brainGraph’

* installing *source* package ‘brainGraph’ ...
** package ‘brainGraph’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
R session is headless; GTK+ not initialized.

(R:37542): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Error: package or namespace load failed for ‘cairoDevice’:
 .onLoad failed in loadNamespace() for 'cairoDevice', details:
  call: fun(libname, pkgname)
  error: GDK display not found - please make sure X11 is running
Error : package ‘cairoDevice’ could not be loaded
ERROR: lazy loading failed for package ‘brainGraph’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/brainGraph/old/brainGraph.Rcheck/brainGraph’

brazilmaps

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘sp’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ggthemes’

breathtestcore

Version: 0.4.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘breathteststan’

breathteststan

Version: 0.4.0

checking installed package size ... NOTE installed size is 28.9Mb sub-directories of 1Mb or more: libs 28.7Mb

brms

Version: 1.10.2

R CMD check timed out

checking re-building of vignette outputs ... WARNING ... Start sampling Compiling the C++ model Start sampling Using 10 posterior samples for ppc type 'dens_overlay' by default. Using 10 posterior samples for ppc type 'dens_overlay' by default. Warning: Found 1 observations with a pareto_k > 0.7 in model 'fit1'. It is recommended to set 'reloo = TRUE' in order to calculate the ELPD without the assumption that these observations are negligible. This will refit the model 1 times to compute the ELPDs for the problematic observations directly. Warning: Found 1 observations with a pareto_k > 0.7 in model 'fit2'. It is recommended to set 'reloo = TRUE' in order to calculate the ELPD without the assumption that these observations are negligible. This will refit the model 1 times to compute the ELPDs for the problematic observations directly. Compiling the C++ model Start sampling Compiling the C++ model Start sampling Compiling the C++ model Start sampling Compiling the C++ model Start sampling Warning in file(file, "r") : cannot open file 'C:/Users/paulb/Dropbox/Psychologie/Paper/2015_Bayesian_Regression_Models/Models/MCMCglmm/phylo.nex': No such file or directory Quitting from lines 35-40 (brms_phylogenetics.Rmd) Error: processing vignette 'brms_phylogenetics.Rmd' failed with diagnostics: cannot open the connection Execution halted
checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: R 2.2Mb doc 2.4Mb

broom

Version: 0.4.2

checking examples ... ERROR ``` ...
- f2 <- Finance[1:300, "hml"] - rf
- f3 <- Finance[1:300, "smb"] - rf
- h <- cbind(f1, f2, f3)
- res2 <- gmm(z ~ f1 + f2 + f3, x = h)
- td2 <- tidy(res2, conf.int = TRUE)
- td2
- coefficient plot
- td2 %>%
- mutate(variable = reorder(variable, estimate)) %>%
- ggplot(aes(estimate, variable)) +
- geom_point() +
- geom_errorbarh(aes(xmin = conf.low, xmax = conf.high)) +
- facet_wrap(~ term) +
- geom_vline(xintercept = 0, color = "red", lty = 2)
- } Error in colnames<-(*tmp*, value = c("conf.low", "conf.high")) : attempt to set 'colnames' on an object with less than two dimensions Calls: tidy -> tidy.gmm -> process_lm -> colnames<- Execution halted ```
checking tests ... ERROR Running the tests in ‘tests/test-all.R’ failed. Complete output: > library(testthat) > test_check("broom") Loading required package: broom Error in lahman_df() : could not find function "lahman_df" Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> tbl testthat results ================================================================ OK: 621 SKIPPED: 0 FAILED: 0 Execution halted

brotli

Version: 1.0

checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: bin 2.3Mb doc 1.2Mb libs 2.2Mb

bsam

Version: 1.1.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘rworldxtra’ ‘sp’ All declared Imports should be used.

bssm

Version: 0.1.1-1

checking installed package size ... NOTE installed size is 29.4Mb sub-directories of 1Mb or more: libs 28.5Mb

btergm

Version: 1.9.0

checking whether package ‘btergm’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/btergm/new/btergm.Rcheck/00install.out’ for details.

BTSPAS

Version: 2014.0901

checking package dependencies ... NOTE Package suggested but not available for checking: ‘BRugs’
checking R code for possible problems ... NOTE ... trace_plot: no visible global function definition for ‘text’ trace_plot: no visible global function definition for ‘close.screen’ visualize.muTT.prior: no visible global function definition for ‘rnorm’ visualize.muTT.prior: no visible global function definition for ‘stack’ visualize.muTT.prior: no visible global function definition for ‘boxplot’ Undefined global functions or variables: abline acf approx boxplot chisq.test close.screen dbinom density dev.off dmultinom flush.console lines lm matplot median par pdf plot pnorm points quantile rbinom rmultinom rnorm runif screen sd segments spline split.screen stack text var write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "abline", "boxplot", "close.screen", "lines", "matplot", "par", "plot", "points", "screen", "segments", "split.screen", "text") importFrom("stats", "acf", "approx", "chisq.test", "dbinom", "density", "dmultinom", "lm", "median", "pnorm", "quantile", "rbinom", "rmultinom", "rnorm", "runif", "sd", "spline", "var") importFrom("utils", "flush.console", "stack", "write.table") to your NAMESPACE file.

BubbleTree

Version: 2.6.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in get_engine(options$engine) : Unknown language engine 'rr' (must be registered via knit_engines$set()). Warning in get_engine(options$engine) : Unknown language engine 'rr' (must be registered via knit_engines$set()). Warning in get_engine(options$engine) : Unknown language engine 'rr' (must be registered via knit_engines$set()). Error: processing vignette 'BubbleTree-vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking installed package size ... NOTE installed size is 25.4Mb sub-directories of 1Mb or more: data 22.9Mb doc 2.2Mb
checking R code for possible problems ... NOTE annoByOverlap,Annotate: no visible binding for global variable 'queryHits' Undefined global functions or variables: queryHits

CAFE

Version: 1.12.0

checking whether package ‘CAFE’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/CAFE/new/CAFE.Rcheck/00install.out’ for details.
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... facetPlot: no visible global function definition for 'dev.off' facetPlot: no visible global function definition for 'na.omit' fisher.method: no visible global function definition for 'pchisq' fisherExact: no visible global function definition for 'fisher.test' makelevels: no visible global function definition for 'na.omit' rawPlot: no visible global function definition for 'png' rawPlot: no visible global function definition for 'dev.off' rawPlot: no visible global function definition for 'data' slidPlot: no visible global function definition for 'png' slidPlot: no visible global function definition for 'dev.off' slidPlot: no visible global function definition for 'data' Undefined global functions or variables: chisq.test data dev.off download.file fisher.test na.omit p.adjust pchisq png read.table setTxtProgressBar txtProgressBar Consider adding importFrom("grDevices", "dev.off", "png") importFrom("stats", "chisq.test", "fisher.test", "na.omit", "p.adjust", "pchisq") importFrom("utils", "data", "download.file", "read.table", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file.

caffsim

Version: 0.2.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘markdown’ All declared Imports should be used.

CAnD

Version: 1.8.0

checking R code for possible problems ... NOTE CAnD : pairedTtest: no visible global function definition for ‘t.test’ barPlotAncest: no visible binding for global variable ‘id’ barPlotAncest: no visible binding for global variable ‘value’ barPlotAncest: no visible binding for global variable ‘variable’ calc_combP: no visible binding for global variable ‘var’ calc_combP: no visible global function definition for ‘pchisq’ plotPvals: no visible binding for global variable ‘numPs’ plotPvals: no visible binding for global variable ‘pval’ Undefined global functions or variables: id numPs pchisq pval t.test value var variable Consider adding importFrom("stats", "pchisq", "t.test", "var") to your NAMESPACE file.

caret

Version: 6.0-77

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: data 1.5Mb models 2.4Mb

caretEnsemble

Version: 2.0.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ^~~~~~ tests/testthat/test-theme.r:325:49: style: Only use double-quotes. axis.line.y.right = element_line(colour = 'yellow') ^~~~~~~~ tests/testthat/test-viridis.R:16:1: style: Trailing whitespace is superfluous.

^~

testthat results ================================================================ OK: 733 SKIPPED: 1 FAILED: 1 1. Failure: Code Lint (@test-lintr.R#25)

Error: testthat unit tests failed Execution halted ```

CATALYST

Version: 1.1.1

checking installed package size ... NOTE installed size is 11.2Mb sub-directories of 1Mb or more: data 2.3Mb doc 8.5Mb

cate

Version: 1.0.4

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'cate-vignette.tex' failed. BibTeX errors: The top-level auxiliary file: cate-vignette.aux I couldn't open style file chicago.bst ---line 40 of file cate-vignette.aux : \bibstyle{chicago : } I'm skipping whatever remains of this command I found no style file---while reading file cate-vignette.aux Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted

Causata

Version: 4.2-0

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking R code for possible problems ... NOTE ... PredictivePowerCv: no visible global function definition for ‘sd’ ReadCausataCsv: no visible global function definition for ‘read.csv’ ToPmml.GlmnetModelDefinition: no visible global function definition for ‘coef’ ToPmml.GlmnetModelDefinition: no visible global function definition for ‘terms.formula’ ValidateModel: no visible global function definition for ‘predict’ predict.GlmnetModelDefinition: no visible global function definition for ‘model.matrix’ predict.GlmnetModelDefinition: no visible binding for global variable ‘contrasts’ predict.GlmnetModelDefinition: no visible global function definition for ‘predict’ Undefined global functions or variables: coef contrasts dbGetQuery median model.matrix na.omit predict quantile read.csv sd terms.formula Consider adding importFrom("stats", "coef", "contrasts", "median", "model.matrix", "na.omit", "predict", "quantile", "sd", "terms.formula") importFrom("utils", "read.csv") to your NAMESPACE file.

cda

Version: 2.0.0

checking installed package size ... NOTE installed size is 7.9Mb sub-directories of 1Mb or more: libs 7.6Mb

cellHTS2

Version: 2.40.0

checking Rd cross-references ... WARNING Unknown package ‘cellHTS’ in Rd xrefs
checking running R code from vignettes ... ``` ‘cellhts2.Rnw’ ... OK ‘cellhts2Complete.Rnw’ ... failed ‘twoChannels.Rnw’ ... OK ‘twoWay.Rnw’ ... OK WARNING Errors in running code in vignettes: when running code in ‘cellhts2Complete.Rnw’ ... > categs <- cateGOry(genes, unlist(goids, use.names = FALSE)) Loading required namespace: GO.db Failed with error: ‘there is no package called ‘GO.db’’

When sourcing ‘cellhts2Complete.R’: Error: use 'biocLite("GO.db")' to install the GO.db package recover called non-interactively; frames dumped, use debugger() to view

proc.time() user system elapsed 35.220 0.300 42.684 ```
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘RColorBrewer’ ‘Biobase’ ‘genefilter’ ‘splots’ ‘vsn’ ‘hwriter’ ‘locfit’ ‘grid’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: KcViab 2.0Mb doc 1.6Mb
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘genefilter’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘Biobase:::.showAnnotatedDataFrame’ See the note in ?`:::` about the use of this operator.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘GO.db’ ‘KEGG.db’

cellity

Version: 1.4.0

checking re-building of vignette outputs ... WARNING ``` ... Loading required package: Biobase Welcome to Bioconductor
```
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
```
Loading required package: IRanges Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':
```
expand.grid
```
Loading required package: GO.db Loading required package: lattice Error: processing vignette 'cellity_vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

CellNOptR

Version: 1.22.0

checking examples ... ERROR ``` Running examples in ‘CellNOptR-Ex.R’ failed The error most likely occurred in:

Name: CNOdata

Title: Get data from a CellNOpt data repository

Aliases: CNOdata

** Examples

readSIF(CNOdata("PKN-ToyMMB.sif")) Error in matrix(sif, ncol = 3, byrow = TRUE) : 'data' must be of a vector type, was 'NULL' Calls: readSIF -> matrix Execution halted ```
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘RBGL’ ‘graph’ ‘hash’ ‘ggplot2’ ‘RCurl’ ‘Rgraphviz’ ‘XML’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘RBGL’ ‘RCurl’ ‘Rgraphviz’ ‘XML’ ‘hash’ Please remove these calls from your code. 'library' or 'require' call to ‘igraph’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘RCurl’ ‘Rgraphviz’ ‘XML’ ‘ggplot2’ ‘hash’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... Undefined global functions or variables: aes arrows axis close.screen combn count.fields dev.new dev.off element_rect element_text facet_grid geom_line geom_point getURL ggplot has.key hash heat.colors igraph.from.graphNEL image installed.packages layoutGraph lines new par pdf plot.new png points read.csv read.table rect renderGraph rgb rnorm runif screen segments split.screen svg tail text theme theme_bw toDot values var write.table xlab xmlApply xmlChildren xmlGetAttr xmlRoot xmlTreeParse ylab ylim Consider adding importFrom("grDevices", "dev.new", "dev.off", "heat.colors", "pdf", "png", "rgb", "svg") importFrom("graphics", "arrows", "axis", "close.screen", "image", "lines", "par", "plot.new", "points", "rect", "screen", "segments", "split.screen", "text") importFrom("methods", "new") importFrom("stats", "rnorm", "runif", "var") importFrom("utils", "combn", "count.fields", "installed.packages", "read.csv", "read.table", "tail", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

cellWise

Version: 1.0.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Loading required package: ggplot2 Loading required package: perry Loading required package: parallel Loading required package: robustbase Quitting from lines 121-205 (DDC_examples.Rmd) Error: processing vignette 'DDC_examples.Rmd' failed with diagnostics: unused argument (range = c(0, 1)) Execution halted

Census2016

Version: 0.2.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘data.table’ All declared Imports should be used.

ChannelAttributionApp

Version: 1.1

checking DESCRIPTION meta-information ... NOTE Checking should be performed on sources prepared by ‘R CMD build’.

ChemmineR

Version: 2.28.3

checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘ChemmineOB’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘ChemmineDrugs’ ‘ChemmineOB’ ‘RPostgreSQL’ ‘RSQLite’ ‘fmcsR’ ‘png’ ‘snow’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘BiocGenerics’ All declared Imports should be used.
checking R code for possible problems ... NOTE ... smartsSearchOB: no visible global function definition for ‘smartsSearch_OB’ smile2sdfFile: no visible global function definition for ‘convertFormatFile’ smiles2sdf: no visible global function definition for ‘convertFormat’ smiles2sdfOB: no visible global function definition for ‘convertFormat’ write.SMI: no visible global function definition for ‘write.table’ Undefined global functions or variables: AW C1 C1.1 C2 C2.1 browseURL canonicalNumbering_OB clusterApplyLB clusterExport combn convertFormat convertFormatFile data dev.off error exactMass_OB fingerprint_OB fmcs forEachMol pdf postgresqlCopyInDataframe postgresqlQuoteId postgresqlTableRef postgresqlgetResult postgresqlpqExec postscript prop_OB rainbow read.delim read.table readPNG rgb smartsSearch_OB str string write.table Consider adding importFrom("grDevices", "dev.off", "pdf", "postscript", "rainbow", "rgb") importFrom("utils", "browseURL", "combn", "data", "read.delim", "read.table", "str", "write.table") to your NAMESPACE file.
checking compiled code ... NOTE ``` File ‘ChemmineR/libs/ChemmineR.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Objects: ‘desc.o’, ‘formats.o’, ‘script.o’ Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++) Object: ‘cluster.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

childsds

Version: 0.6.7

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gamlss.dist’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 20 marked UTF-8 strings

ChIPQC

Version: 1.12.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘S4Vectors:::tabulate2’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘makeFripPlot’ ‘mergeMetadata’
checking foreign function calls ... NOTE Foreign function call to a different package: .Call("rle_sum_any", ..., PACKAGE = "chipseq") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... makeRegiPlot: no visible binding for global variable ‘Sample’ makeRegiPlot: no visible binding for global variable ‘GenomicIntervals’ makeRegiPlot: no visible binding for global variable ‘log2_Enrichment’ makeSSDPlot: no visible binding for global variable ‘Sample’ makeSSDPlot: no visible binding for global variable ‘SSD’ makeSSDPlot: no visible global function definition for ‘geom_point’ sampleQC: no visible global function definition for ‘seqlevels<-’ plotCC,ChIPQCexperiment: no visible binding for global variable ‘Sample’ plotCC,list: no visible binding for global variable ‘Sample’ plotPeakProfile,ChIPQCexperiment: no visible binding for global variable ‘Sample’ plotPeakProfile,list: no visible binding for global variable ‘Sample’ Undefined global functions or variables: CC_Score CountsInPeaks Depth Distance FRIBL FRIP GenomicIntervals Reads SSD Sample Shift_Size Signal TxDb.Hsapiens.UCSC.hg38.knownGene geom_point log10_bp log2_Enrichment seqlengths seqlengths<- seqlevels<- Consider adding importFrom("stats", "SSD") to your NAMESPACE file.
checking data for non-ASCII characters ... NOTE Error in .requirePackage(package) : unable to find required package 'ChIPQC' Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage Execution halted

ChIPseeker

Version: 1.12.1

checking re-building of vignette outputs ... WARNING ``` ... DOSE v3.2.0 For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite: Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

clusterProfiler v3.4.4 For help: https://guangchuangyu.github.io/clusterProfiler

If you use clusterProfiler in published research, please cite: Guangchuang Yu., Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. ReactomePA v1.20.2 For help: https://guangchuangyu.github.io/ReactomePA

If you use ReactomePA in published research, please cite: Guangchuang Yu, Qing-Yu He. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479 ChIPseeker v1.12.1 For help: https://guangchuangyu.github.io/ChIPseeker

If you use ChIPseeker in published research, please cite: Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383 'select()' returned 1:many mapping between keys and columns Error: processing vignette 'ChIPseeker.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

ChocoLattes

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘knitr’ ‘tools’ All declared Imports should be used.

choroplethr

Version: 3.6.1

checking examples ... ERROR ``` ...

Name: calculate_percent_change

Title: Calculate the percentage change between two choroplethr

dataframes.

Aliases: calculate_percent_change

** Examples

load median age estimates from 2010 and 2015

data(df_state_age_2010) data(df_state_age_2015)

df_age_diff = calculate_percent_change(df_state_age_2010, df_state_age_2015) state_choropleth(df_age_diff, + title = "Percent Change in Median Age, 2010-2015", + legend = "Percent Change", + num_colors = 0) Theme element panel.border missing Error in if (theme$panel.ontop) { : argument is of length zero Calls: state_choropleth ... ggplotGrob -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```

choroplethrAdmin1

Version: 1.1.1

checking installed package size ... NOTE installed size is 18.0Mb sub-directories of 1Mb or more: data 17.9Mb

chromstaR

Version: 1.2.0

checking whether package ‘chromstaR’ can be installed ... ERROR Installation failed. See ‘/home/muelleki/git/R/ggplot2/revdep/checks/chromstaR/new/chromstaR.Rcheck/00install.out’ for details.

* installing *source* package ‘chromstaR’ ...
** libs
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utility.cpp -o utility.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c densities.cpp -o densities.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_interface.cpp -o R_interface.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scalehmm.cpp -o scalehmm.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/usr/lib/R/lib -lR
installing to /home/muelleki/git/R/ggplot2/revdep/checks/chromstaR/new/chromstaR.Rcheck/chromstaR/libs
** R
** data
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/muelleki/git/R/ggplot2/revdep/library/chromstaR/bamsignals/libs/bamsignals.so':
  libhts.so.0: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘chromstaR’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/chromstaR/new/chromstaR.Rcheck/chromstaR’

* installing *source* package ‘chromstaR’ ...
** libs
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c densities.cpp -o densities.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utility.cpp -o utility.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.cpp -o init.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_interface.cpp -o R_interface.o
g++  -I/usr/share/R/include -DNDEBUG     -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scalehmm.cpp -o scalehmm.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o chromstaR.so R_interface.o densities.o init.o scalehmm.o utility.o -fopenmp -L/usr/lib/R/lib -lR
installing to /home/muelleki/git/R/ggplot2/revdep/checks/chromstaR/old/chromstaR.Rcheck/chromstaR/libs
** R
** data
** inst
** preparing package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/home/muelleki/git/R/ggplot2/revdep/library/chromstaR/bamsignals/libs/bamsignals.so':
  libhts.so.0: cannot open shared object file: No such file or directory
ERROR: lazy loading failed for package ‘chromstaR’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/chromstaR/old/chromstaR.Rcheck/chromstaR’

chron

Version: 2.3-51

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘zoo’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘zoo’

CINNA

Version: 1.1.2

checking re-building of vignette outputs ... WARNING ``` ... ...

Attaching package: 'igraph'

The following objects are masked from 'package:stats':
```
decompose, spectrum
```
The following object is masked from 'package:base':
```
union
```
Loading required namespace: circlize Failed with error: 'there is no package called 'circlize'' Quitting from lines 290-293 (CINNA.Rmd) Error: processing vignette 'CINNA.Rmd' failed with diagnostics: The 'circlize' package is not installed on your system. You first need to run: install.packages('circlize') before you can use the circlize_dendrogram function. Execution halted ```

CINOEDV

Version: 2.0

checking R code for possible problems ... NOTE ... NormalizationEffect: no visible global function definition for ‘layout’ NormalizationEffect: no visible global function definition for ‘plot’ NormalizationEffect: no visible global function definition for ‘lines’ PSOSearch: no visible global function definition for ‘combn’ PSOSearch: no visible global function definition for ‘runif’ PlotTopEffects: no visible global function definition for ‘dev.new’ PlotTopEffects: no visible global function definition for ‘par’ PlotTopEffects: no visible global function definition for ‘layout’ PlotTopEffects: no visible global function definition for ‘barplot’ PlotTopEffects: no visible global function definition for ‘rainbow’ PlotTopEffects: no visible global function definition for ‘title’ Undefined global functions or variables: barplot combn dev.new graphics.off hist install.packages layout lines par plot rainbow runif title Consider adding importFrom("grDevices", "dev.new", "graphics.off", "rainbow") importFrom("graphics", "barplot", "hist", "layout", "lines", "par", "plot", "title") importFrom("stats", "runif") importFrom("utils", "combn", "install.packages") to your NAMESPACE file.

classifierplots

Version: 1.3.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

classify

Version: 1.3

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking R code for possible problems ... NOTE classify.bug: no visible global function definition for ‘txtProgressBar’ classify.bug: no visible global function definition for ‘setTxtProgressBar’ plot.scores: no visible binding for global variable ‘quantile’ plot.scores: no visible global function definition for ‘runif’ plot.scores: no visible binding for global variable ‘median’ scores.gpcm.bug: no visible global function definition for ‘txtProgressBar’ scores.gpcm.bug: no visible global function definition for ‘setTxtProgressBar’ across.reps,classification: no visible global function definition for ‘sd’ Undefined global functions or variables: median quantile runif sd setTxtProgressBar txtProgressBar Consider adding importFrom("stats", "median", "quantile", "runif", "sd") importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file.

ClassifyR

Version: 1.10.2

checking re-building of vignette outputs ... WARNING ``` ...

Loading required package: BiocParallel Loading required package: affy stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. stat_bindot() using bins = 30. Pick better value with binwidth. Error: processing vignette 'ClassifyR.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE ... ‘combn’ samplesMetricMap,list: no visible binding for global variable ‘Class’ samplesMetricMap,list: no visible binding for global variable ‘name’ samplesMetricMap,list: no visible binding for global variable ‘type’ samplesMetricMap,list: no visible binding for global variable ‘Metric’ selectionPlot,list: no visible binding for global variable ‘Freq’ selectionPlot,list: no visible global function definition for ‘reformulate’ subtractFromLocation,ExpressionSet: no visible binding for global variable ‘median’ Undefined global functions or variables: ..density.. Class Freq Metric bartlett.test capture.output classes combn density dlda dnorm expr featureValues ks.test largerClass mad median model.matrix na.omit name predict reformulate sd splinefun type var Consider adding importFrom("stats", "bartlett.test", "density", "dnorm", "ks.test", "mad", "median", "model.matrix", "na.omit", "predict", "reformulate", "sd", "splinefun", "var") importFrom("utils", "capture.output", "combn") to your NAMESPACE file.

classyfire

Version: 0.1-2

checking R code for possible problems ... NOTE .boxRadial: no visible global function definition for ‘predict’ .radialSVM: no visible global function definition for ‘predict’ cfPredict: no visible global function definition for ‘predict’ getPerm5Num: no visible global function definition for ‘median’ getPerm5Num: no visible global function definition for ‘quantile’ ggClassPred: no visible global function definition for ‘ftable’ ggEnsHist: no visible global function definition for ‘sd’ ggPermHist: no visible global function definition for ‘sd’ Undefined global functions or variables: ftable median predict quantile sd Consider adding importFrom("stats", "ftable", "median", "predict", "quantile", "sd") to your NAMESPACE file.

cleanEHR

Version: 0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘stats’ All declared Imports should be used.

clusterfly

Version: 0.4

checking examples ... ERROR ``` Running examples in ‘clusterfly-Ex.R’ failed The error most likely occurred in:

Name: cfly_show

Title: Show in ggobi. Opens an instance ggobi for this dataset (if not

already open), and colours the points according the cluster

assignment.

Aliases: cfly_show

Keywords: dynamic

** Examples

o <- olive_example() cfly_show(o, 1)

(R:42504): Gtk-WARNING **: cannot open display: ```
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘ggplot2’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... hierfly: no visible global function definition for ‘dist’ olive_example: no visible binding for global variable ‘kmeans’ print.hierfly: no visible global function definition for ‘str’ rescaler : <anonymous>: no visible global function definition for ‘sd’ rescaler : <anonymous>: no visible global function definition for ‘median’ rescaler : <anonymous>: no visible global function definition for ‘mad’ som_iterate: no visible global function definition for ‘quantile’ som_iterate: no visible global function definition for ‘unit.distances’ summary.somiter : interesting: no visible global function definition for ‘sd’ Undefined global functions or variables: aes_string cutree dist facet_grid facet_wrap geom_density geom_line geom_tile ggplot hclust kmeans mad median qf quantile rnorm scale_x_discrete scale_y_discrete sd step str theme unit.distances var Consider adding importFrom("stats", "cutree", "dist", "hclust", "kmeans", "mad", "median", "qf", "quantile", "rnorm", "sd", "step", "var") importFrom("utils", "str") to your NAMESPACE file.

ClusterR

Version: 1.0.8

checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: libs 6.4Mb

ClusterSignificance

Version: 1.4.1

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

clustRcompaR

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tidyr’ All declared Imports should be used.

CNEr

Version: 1.12.1

checking compiled code ... WARNING ``` File ‘CNEr/libs/CNEr.so’: Found ‘abort’, possibly from ‘abort’ (C) Object: ‘ucsc/errabort.o’ Found ‘exit’, possibly from ‘exit’ (C) Objects: ‘ucsc/errabort.o’, ‘ucsc/pipeline.o’ Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Object: ‘ucsc/pipeline.o’ Found ‘rand’, possibly from ‘rand’ (C) Object: ‘ucsc/obscure.o’ Found ‘stderr’, possibly from ‘stderr’ (C) Objects: ‘ucsc/axt.o’, ‘ucsc/errabort.o’, ‘ucsc/obscure.o’, ‘ucsc/verbose.o’, ‘ucsc/os.o’ Found ‘stdout’, possibly from ‘stdout’ (C) Objects: ‘ucsc/common.o’, ‘ucsc/errabort.o’, ‘ucsc/verbose.o’, ‘ucsc/os.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
checking re-building of vignette outputs ... WARNING ``` ... Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: Biostrings Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:CNEr':
```
N50
```
The following object is masked from 'package:base':
```
strsplit
```
Loading required package: rtracklayer Loading required package: grid Error: processing vignette 'CNEr.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE installed size is 18.3Mb sub-directories of 1Mb or more: extdata 15.9Mb libs 1.1Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘S4Vectors:::make_zero_col_DataFrame’ See the note in ?`:::` about the use of this operator.

CNPBayes

Version: 1.6.1

checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'labelSwitching': labelSwitching Code: function(object, ...) Docs: function(object, merge = TRUE) Argument names in code not in docs: ... Argument names in docs not in code: merge Mismatches in argument names: Position: 2 Code: ... Docs: merge
checking installed package size ... NOTE installed size is 12.7Mb sub-directories of 1Mb or more: libs 10.6Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘GenomicRanges’ A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE consensusRegion: no visible global function definition for ‘elementLengths’ Undefined global functions or variables: elementLengths

CNVPanelizer

Version: 1.6.0

checking re-building of vignette outputs ... WARNING ``` ...
```
expand.grid
```
Loading required package: IRanges Loading required package: GenomeInfoDb Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'CNVPanelizer.tex' failed. LaTeX errors: ! LaTeX Error: File `biblatex.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.66 \usepackage [T1]{fontenc}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

CNVrd2

Version: 1.14.0

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DNAcopy’ ‘Rsamtools’ All declared Imports should be used. Packages in Depends field not imported from: ‘VariantAnnotation’ ‘ggplot2’ ‘gridExtra’ ‘methods’ ‘parallel’ ‘rjags’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... definition for ‘as’ segmentSamplesUsingPopInformation,CNVrd2: no visible global function definition for ‘fitted’ segmentSamplesUsingPopInformation,CNVrd2: no visible global function definition for ‘lm’ Undefined global functions or variables: GRanges Hsapiens Quantile ScanBamParam TabixFile abline aes alphabetFrequency as axis chisq.test coda.samples coord_cartesian countBam dnorm fisher.test fitted geno geom_line geom_rect geom_text ggplot grid.arrange hist jags.model kmeans label lines lm mclapply objectCNVrd2 p.adjust par plot readDNAStringSet readVcf rect text theme unmasked write.table x x1 x2 xmax xmin y ylab ymax ymin Consider adding importFrom("graphics", "abline", "axis", "hist", "lines", "par", "plot", "rect", "text") importFrom("methods", "as") importFrom("stats", "chisq.test", "dnorm", "fisher.test", "fitted", "kmeans", "lm", "p.adjust") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

cobalt

Version: 3.1.0

checking examples ... ERROR ``` Running examples in ‘cobalt-Ex.R’ failed The error most likely occurred in:

Name: bal.tab.weightit

Title: Balance Statistics for WeightIt Objects

Aliases: bal.tab.weightit

** Examples

library(WeightIt); data("lalonde", package = "cobalt") Error in library(WeightIt) : there is no package called ‘WeightIt’ Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Note: estimand and s.d.denom not specified; assuming ATT and treated. Note: estimand and s.d.denom not specified; assuming ATT and treated. Note: estimand and s.d.denom not specified; assuming ATT and treated. Note: estimand and s.d.denom not specified; assuming ATT and treated. Note: estimand and s.d.denom not specified; assuming ATT and treated. Note: estimand and s.d.denom not specified; assuming ATE and pooled.

Attaching package: 'MatchIt'

The following object is masked by '.GlobalEnv':
```
lalonde
```
The following object is masked from 'package:cobalt':
```
lalonde
```
Quitting from lines 241-252 (cobalt_basic_use.Rmd) Error: processing vignette 'cobalt_basic_use.Rmd' failed with diagnostics: there is no package called 'WeightIt' Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘WeightIt’

cocoreg

Version: 0.1.1

checking R code for possible problems ... NOTE mapping_rf: Error while checking: there is no package called ‘randomForest’

codingMatrices

Version: 0.3.1

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 478-486 (codingMatrices.Rnw) Error: processing vignette 'codingMatrices.Rnw' failed with diagnostics: xtable not installed. Execution halted

coefplot

Version: 1.2.4

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘glmnet’ ‘maxLik’

CoGAPS

Version: 2.10.0

checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: libs 7.2Mb
checking R code for possible problems ... NOTE GWCoGAPS: no visible binding for global variable ‘i’ patternMatcher : <anonymous>: no visible binding for global variable ‘Samples’ patternMatcher : <anonymous>: no visible binding for global variable ‘value’ patternMatcher : <anonymous>: no visible binding for global variable ‘BySet’ Undefined global functions or variables: BySet Samples i value

cogena

Version: 1.10.0

checking whether package ‘cogena’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/cogena/new/cogena.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: doc 1.9Mb extdata 3.1Mb
checking R code for possible problems ... NOTE ... corInCluster,cogena: no visible global function definition for ‘cor’ heatmapCluster,cogena: no visible global function definition for ‘topo.colors’ heatmapCluster,cogena: no visible global function definition for ‘rainbow’ heatmapCluster,cogena: no visible global function definition for ‘par’ heatmapCluster,cogena: no visible global function definition for ‘legend’ Undefined global functions or variables: abline as.dist axis cor data density dist hist image layout legend lines median mtext order.dendrogram p.adjust par phyper plot.new rainbow rect reorder sd text title topo.colors Consider adding importFrom("grDevices", "rainbow", "topo.colors") importFrom("graphics", "abline", "axis", "hist", "image", "layout", "legend", "lines", "mtext", "par", "plot.new", "rect", "text", "title") importFrom("stats", "as.dist", "cor", "density", "dist", "median", "order.dendrogram", "p.adjust", "phyper", "reorder", "sd") importFrom("utils", "data") to your NAMESPACE file.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘clValid’

CollapseLevels

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘magrittr’ All declared Imports should be used.

coloc

Version: 2.3-1

checking R code for possible problems ... NOTE ... pcs.prepare: no visible global function definition for ‘prcomp’ prepare.df: no visible global function definition for ‘cor’ sdY.est: no visible global function definition for ‘lm’ sdY.est: no visible global function definition for ‘coef’ p.value,coloc: no visible global function definition for ‘pchisq’ plot,colocPCs-missing: no visible binding for global variable ‘object’ plot,colocPCs-missing: no visible global function definition for ‘abline’ Undefined global functions or variables: abline arrows as.formula axis box coef coefficients col.summary combn cor glm impute.snps integrate lm object optimize pchisq pf points polygon prcomp qnorm segments single.snp.tests snp.imputation var vcov Consider adding importFrom("graphics", "abline", "arrows", "axis", "box", "points", "polygon", "segments") importFrom("stats", "as.formula", "coef", "coefficients", "cor", "glm", "integrate", "lm", "optimize", "pchisq", "pf", "prcomp", "qnorm", "var", "vcov") importFrom("utils", "combn") to your NAMESPACE file.

colorpatch

Version: 0.1.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘grid’ ‘gridExtra’ All declared Imports should be used.

coMET

Version: 1.8.0

checking whether package ‘coMET’ can be installed ... WARNING Found the following significant warnings: WARNING: omitting pointless dependence on 'R' without a version requirement See ‘/home/muelleki/git/R/ggplot2/revdep/checks/coMET/new/coMET.Rcheck/00install.out’ for details.
checking data for ASCII and uncompressed saves ... WARNING Error in if (dep$op != ">=") next : argument is of length zero Calls: <Anonymous> Execution halted
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘grid’ ‘biomaRt’ ‘Gviz’ ‘psych’ ‘ggbio’ ‘trackViewer’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 17.3Mb sub-directories of 1Mb or more: data 9.7Mb doc 2.6Mb extdata 4.5Mb
checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file.
checking R code for possible problems ... NOTE ... eQTL_GTEx: no visible binding for global variable 'snp_pos' eQTL_GTEx: no visible binding for global variable 'snp_chrom' eQTL_GTEx: no visible binding for global variable 'gene_start' eQTL_GTEx: no visible binding for global variable 'gene_stop' eQTL_GTEx: no visible binding for global variable 'gene_chr' geneExpression_GTEx: no visible global function definition for 'as' metQTL: no visible binding for global variable 'chromosome_stop' metQTL: no visible binding for global variable 'chromosome_start' metQTL: no visible binding for global variable 'chromosome_name' psiQTL_GTEx: no visible binding for global variable 'pos_snp' psiQTL_GTEx: no visible binding for global variable 'chr_snp' psiQTL_GTEx: no visible binding for global variable 'pos_middle_exon' psiQTL_GTEx: no visible binding for global variable 'chr_exon' Undefined global functions or variables: as chr_exon chr_snp chromosome_name chromosome_start chromosome_stop gene_chr gene_start gene_stop pos_middle_exon pos_snp snp_chrom snp_pos Consider adding importFrom("methods", "as") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

CommT

Version: 0.1.1

checking R code for possible problems ... NOTE CommT.anova: no visible global function definition for ‘aov’ CommT.legendpos: no visible global function definition for ‘quantile’ CommT.plotcolors: no visible global function definition for ‘hcl’ Undefined global functions or variables: aov hcl quantile Consider adding importFrom("grDevices", "hcl") importFrom("stats", "aov", "quantile") to your NAMESPACE file.

compcodeR

Version: 1.12.0

checking whether package ‘compcodeR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/compcodeR/new/compcodeR.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘rpanel’ ‘DSS’
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘rpanel’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... ‘packageVersion’ voom.limma.createRmd: no visible global function definition for ‘packageVersion’ voom.ttest.createRmd: no visible global function definition for ‘packageVersion’ vst.limma.createRmd: no visible global function definition for ‘packageVersion’ vst.ttest.createRmd: no visible global function definition for ‘packageVersion’ show,compData: no visible global function definition for ‘head’ Undefined global functions or variables: as.dist axis cor hclust head heat.colors legend lines loess median na.omit packageVersion par predict rexp rnbinom rpois runif sd title Consider adding importFrom("grDevices", "heat.colors") importFrom("graphics", "axis", "legend", "lines", "par", "title") importFrom("stats", "as.dist", "cor", "hclust", "loess", "median", "na.omit", "predict", "rexp", "rnbinom", "rpois", "runif", "sd") importFrom("utils", "head", "packageVersion") to your NAMESPACE file.

CompGO

Version: 1.12.0

checking R code for possible problems ... NOTE ... ‘nodeRenderInfo<-’ plotZScores: no visible global function definition for ‘complete.cases’ plotZScores: no visible global function definition for ‘setNames’ plotZScores: no visible global function definition for ‘cor’ slidingJaccard: no visible binding for global variable ‘useRawPvals’ zTransformDirectory: no visible global function definition for ‘read.table’ zTransformDirectory: no visible global function definition for ‘complete.cases’ zTransformDirectory: no visible binding for global variable ‘var’ Undefined global functions or variables: Term Var1 Var2 Z complete.cases cor dev.off dist goDag hclust nodeRenderInfo<- nodes p.adjust par png pnorm read.table setNames text useRawPvals value var Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "par", "text") importFrom("stats", "complete.cases", "cor", "dist", "hclust", "p.adjust", "pnorm", "setNames", "var") importFrom("utils", "read.table") to your NAMESPACE file.

CONFESS

Version: 1.4.0

checking package dependencies ... ERROR ``` Package required but not available: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

confidence

Version: 1.1-2

checking whether package ‘confidence’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/confidence/new/confidence.Rcheck/00install.out’ for details.

congressbr

Version: 0.1.1

checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

consensusSeekeR

Version: 1.4.0

checking re-building of vignette outputs ... WARNING ``` ... is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: IRanges Loading required package: S4Vectors Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':
```
expand.grid
```
Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: BiocParallel Error: processing vignette 'consensusSeekeR.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

contiBAIT

Version: 1.4.0

checking examples ... WARNING ``` Found the following significant warnings:

Warning: 'switch' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: extdata 3.4Mb
checking R code for possible problems ... NOTE ... definition for ‘boxplot’ plotWCdistribution,StrandFreqMatrix: no visible global function definition for ‘lines’ plotWCdistribution,StrandFreqMatrix: no visible global function definition for ‘text’ show,ContigOrdering: no visible global function definition for ‘head’ show,ContigOrdering: no visible global function definition for ‘tail’ show,LibraryGroupList: no visible global function definition for ‘head’ show,LibraryGroupList: no visible global function definition for ‘tail’ show,LinkageGroupList: no visible global function definition for ‘head’ show,LinkageGroupList: no visible global function definition for ‘tail’ show,StrandStateList: no visible global function definition for ‘head’ show,StrandStateList: no visible global function definition for ‘tail’ Undefined global functions or variables: boxplot head hist legend lines lm queryHits rbinom runif subjectHits tail text unstrand Consider adding importFrom("graphics", "boxplot", "hist", "legend", "lines", "text") importFrom("stats", "lm", "rbinom", "runif") importFrom("utils", "head", "tail") to your NAMESPACE file.

coseq

Version: 1.0.1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ******
1. Failure: compareARI (@test-coseq.R#45) -------------------------------------- compareARI(obj2) did not throw an error.
coseq analysis: Normal approach & logMedianRef transformation K = 2 to 4

testthat results ================================================================ OK: 30 SKIPPED: 0 FAILED: 1 1. Failure: compareARI (@test-coseq.R#45)

Error: testthat unit tests failed Execution halted ```

cosinor

Version: 1.1

checking R code for possible problems ... NOTE ... cosinor_analyzer : <anonymous>: no visible global function definition for ‘as.formula’ ggplot.cosinor.lm: no visible global function definition for ‘predict’ predict.cosinor.lm: no visible global function definition for ‘fitted’ predict.cosinor.lm: no visible global function definition for ‘predict’ simulate_cosinor: no visible global function definition for ‘runif’ simulate_cosinor: no visible global function definition for ‘rbinom’ simulate_cosinor: no visible global function definition for ‘rnorm’ summary.cosinor.lm: no visible global function definition for ‘vcov’ summary.cosinor.lm: no visible global function definition for ‘qnorm’ summary.cosinor.lm: no visible global function definition for ‘pnorm’ test_cosinor: no visible global function definition for ‘pchisq’ test_cosinor: no visible global function definition for ‘pnorm’ Undefined global functions or variables: as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm runif terms vcov vitamind Consider adding importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq", "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif", "terms", "vcov") to your NAMESPACE file.

cosinor2

Version: 0.1.0

checking examples ... ERROR ``` ... 25 26 27 28 29 30 1.6250000 1.3815789 1.2894737 1.3333333 1.1710526 0.8088235

$cosinors[[17]]$fitted.values [1] 0.9751600 1.3201375 1.6020512 1.6086144 1.3348849 0.9869865 0.8268939 [8] 0.9751600 1.3201375 1.6020512 1.6086144 1.3348849 0.9869865 0.8268939

$cosinors[[17]]$residuals 17 18 19 20 21 22 0.372062185 -0.099549245 -0.129828980 0.030274467 0.408536153 0.061624562 23 24 25 26 27 28 -0.368560591 -0.113317932 0.304862520 -0.220472255 -0.319140737 -0.001551566 29 30 0.184066083 -0.018070395

$plots $plots[[1]] Error: Column y must be a 1d atomic vector or a list Execution halted ```

CosmoPhotoz

Version: 0.1

checking R code for possible problems ... NOTE CosmoPhotoZestimator: no visible global function definition for ‘predict’ computeCombPCA: no visible global function definition for ‘prcomp’ computeDiagPhotoZ: no visible global function definition for ‘sd’ computeDiagPhotoZ: no visible global function definition for ‘median’ computeDiagPhotoZ: no visible global function definition for ‘mad’ glmPredictPhotoZ: no visible global function definition for ‘predict’ glmTrainPhotoZ: no visible global function definition for ‘glm’ glmTrainPhotoZ: no visible global function definition for ‘Gamma’ glmTrainPhotoZ: no visible global function definition for ‘inverse.gaussian’ plotDiagPhotoZ: no visible global function definition for ‘median’ plotDiagPhotoZ: no visible global function definition for ‘mad’ Undefined global functions or variables: Gamma glm inverse.gaussian mad median prcomp predict sd Consider adding importFrom("stats", "Gamma", "glm", "inverse.gaussian", "mad", "median", "prcomp", "predict", "sd") to your NAMESPACE file.

CountClust

Version: 1.3.0

checking whether package ‘CountClust’ can be installed ... ERROR Installation failed. See ‘/home/muelleki/git/R/ggplot2/revdep/checks/CountClust/new/CountClust.Rcheck/00install.out’ for details.

* installing *source* package ‘CountClust’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : object ‘switch_axis_position’ is not exported by 'namespace:cowplot'
ERROR: lazy loading failed for package ‘CountClust’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/CountClust/new/CountClust.Rcheck/CountClust’

* installing *source* package ‘CountClust’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Error : object ‘switch_axis_position’ is not exported by 'namespace:cowplot'
ERROR: lazy loading failed for package ‘CountClust’
* removing ‘/home/muelleki/git/R/ggplot2/revdep/checks/CountClust/old/CountClust.Rcheck/CountClust’

countyfloods

Version: 0.1.0

checking re-building of vignette outputs ... WARNING ``` ... The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
stat_bin() using bins = 30. Pick better value with binwidth. To use this package, you must install the hurricaneexposuredata package. To install that package, run install.packages('hurricaneexposuredata', repos='https://geanders.github.io/drat/', type='source'). See the hurricaneexposure vignette for more details. To use this function, you must have the hurricaneexposuredata package installed. See the hurricaneexposure package vignette for more details. Quitting from lines 311-313 (countyflood.Rmd) Error: processing vignette 'countyflood.Rmd' failed with diagnostics: there is no package called 'hurricaneexposuredata' Execution halted ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘maps’ All declared Imports should be used.

countytimezones

Version: 1.0.0

checking re-building of vignette outputs ... WARNING ``` ...

Attaching package: 'dplyr'

The following object is masked from 'package:acs':
```
combine
```
The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Theme element panel.border missing Quitting from lines 111-123 (countytimezones.Rmd) Error: processing vignette 'countytimezones.Rmd' failed with diagnostics: argument is of length zero Execution halted ```

countyweather

Version: 0.1.0

checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

covafillr

Version: 0.4.1

checking installed package size ... NOTE installed size is 9.7Mb sub-directories of 1Mb or more: libs 9.1Mb

cowbell

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ggplot2’ ‘misc3d’ All declared Imports should be used.

cowplot

Version: 0.9.1

checking package dependencies ... NOTE Package suggested but not available for checking: ‘magick’

cpvSNP

Version: 1.8.0

checking dependencies in R code ... NOTE 'library' or 'require' call to ‘GSEABase’ which was already attached by Depends. Please remove these calls from your code.
checking R code for possible problems ... NOTE ... createArrayData: no visible global function definition for ‘elementMetadata<-’ geneToSNPList: no visible global function definition for ‘findOverlaps’ glossiMarginal: no visible global function definition for ‘pgamma’ plotPvals: no visible binding for global variable ‘df’ plotPvals: no visible binding for global variable ‘pval’ simulate_chisq: no visible global function definition for ‘rnorm’ vegasMarginal: no visible global function definition for ‘rbinom’ vegasMarginal: no visible global function definition for ‘qchisq’ vegasPrep: no visible global function definition for ‘elementMetadata’ show,VEGASResult: no visible global function definition for ‘var’ Undefined global functions or variables: GRanges IRanges Rle col2rgb density df elementMetadata elementMetadata<- findOverlaps legend lines pgamma plot points polygon pval qchisq rbinom rgb rnorm var Consider adding importFrom("grDevices", "col2rgb", "rgb") importFrom("graphics", "legend", "lines", "plot", "points", "polygon") importFrom("stats", "density", "df", "pgamma", "qchisq", "rbinom", "rnorm", "var") to your NAMESPACE file.

crawl

Version: 2.1.1

checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: libs 6.5Mb

cricketr

Version: 0.0.14

checking whether package ‘cricketr’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::autolayer’ by ‘forecast::autolayer’ when loading ‘cricketr’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/cricketr/new/cricketr.Rcheck/00install.out’ for details.

crossmeta

Version: 1.2.0

checking for code/documentation mismatches ... WARNING ``` Data with usage in documentation object 'gs.names' but not in code: gs.names

Data with usage in documentation object 'gslist' but not in code: gslist ```
checking dependencies in R code ... NOTE Missing or unexported objects: ‘crossmeta::gs.names’ ‘crossmeta::gslist’
checking R code for possible problems ... NOTE explore_paths : server: no visible binding for global variable ‘gslist’ explore_paths : server: no visible binding for global variable ‘gs.names’ Undefined global functions or variables: gs.names gslist
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘PADOG’, ‘GeneMeta’

Crossover

Version: 0.1-17

checking re-building of vignette outputs ... WARNING ``` ...

The following object is masked from 'package:MASS':
```
geyser
```
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'Crossover.tex' failed. LaTeX errors: ! LaTeX Error: File `algorithmic.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.68 \usepackage {algorithm}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

csabounds

Version: 1.0.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘qte’ All declared Imports should be used.

csp

Version: 0.1.0

checking installed package size ... NOTE installed size is 11.0Mb sub-directories of 1Mb or more: data 10.9Mb
checking data for non-ASCII characters ... NOTE Note: found 59670 marked Latin-1 strings Note: found 16 marked UTF-8 strings

ctsGE

Version: 1.2.0

checking re-building of vignette outputs ... WARNING ``` ...
```
html_document, md_document, pdf_document
```
Attaching package: 'dplyr'

The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Using tags as id variables Using tags as id variables Using tags as id variables Using tags as id variables Error: processing vignette 'ctsGE.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

cummeRbund

Version: 2.18.0

checking examples ... ERROR ... Warning in rsqlite_fetch(res@ptr, n = n) : Don't need to call dbFetch() for statements, only for queries Warning in rsqlite_fetch(res@ptr, n = n) : Don't need to call dbFetch() for statements, only for queries Reading Run Info File /home/muelleki/git/R/ggplot2/revdep/checks/cummeRbund/new/cummeRbund.Rcheck/cummeRbund/extdata/run.info Writing runInfo Table Warning: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data). Warning: Factors converted to character Warning in rsqlite_fetch(res@ptr, n = n) : Don't need to call dbFetch() for statements, only for queries Reading Read Group Info /home/muelleki/git/R/ggplot2/revdep/checks/cummeRbund/new/cummeRbund.Rcheck/cummeRbund/extdata/read_groups.info Warning: RSQLite::make.db.names() is deprecated, please switch to DBI::dbQuoteIdentifier(). Writing replicates Table Warning: Factors converted to character Warning in rsqlite_fetch(res@ptr, n = n) : Don't need to call dbFetch() for statements, only for queries Reading /home/muelleki/git/R/ggplot2/revdep/checks/cummeRbund/new/cummeRbund.Rcheck/cummeRbund/extdata/genes.fpkm_tracking Checking samples table... Populating samples table... Error: Column name mismatch. Execution halted
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘BiocGenerics’ ‘RSQLite’ ‘ggplot2’ ‘reshape2’ ‘fastcluster’ ‘rtracklayer’ ‘Gviz’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: doc 1.6Mb extdata 5.6Mb
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocGenerics’ ‘plyr’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: 'NMFN' 'cluster' 'rjson' 'stringr' Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: 'Gviz' 'RSQLite' 'fastcluster' 'ggplot2' 'reshape2' 'rtracklayer' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... geom_hline geom_line geom_point geom_rect geom_rug geom_segment geom_smooth geom_text geom_tile geom_vline ggplot guides hasAxis<- hclust ids import labs log2_fold_change make.db.names makeTxDb mean_cl_boot melt nnmf obsnames order.dendrogram p.adjust p_value pam plot plotIdeogram plotTracks position_dodge prcomp quant_status ranges read.delim read.table rowInd sample_1 sample_2 sample_name scale_color_gradient scale_color_hue scale_color_manual scale_colour_manual scale_fill_continuous scale_fill_gradient scale_fill_gradient2 scale_fill_hue scale_x_continuous scale_x_discrete scale_x_log10 scale_y_continuous scale_y_discrete scale_y_log10 seqnames significant stat_density stat_smooth stat_sum stat_summary stdev str_split_fixed strand theme theme_bw toJSON tracking_id tracks unit v1 v2 value variable varnames write.table x xlab xlim y ylab Consider adding importFrom("graphics", "plot") importFrom("stats", "as.dendrogram", "as.dist", "as.formula", "cmdscale", "dist", "hclust", "order.dendrogram", "p.adjust", "prcomp") importFrom("utils", "read.delim", "read.table", "write.table") to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE ``` ... Loading required package: grid

Attaching package: 'cummeRbund'

The following object is masked from 'package:GenomicRanges':
```
promoters
```
The following object is masked from 'package:IRanges':
```
promoters
```
The following object is masked from 'package:BiocGenerics':
```
conditions
```
Error: processing vignette 'cummeRbund-example-workflow.Rnw' failed with diagnostics: chunk 4 (label = model_fit_1) Error in rsqlite_send_query(conn@ptr, statement) : near ")": syntax error Execution halted ```

curatedBreastData

Version: 2.4.0

checking installed package size ... NOTE installed size is 283.1Mb sub-directories of 1Mb or more: data 282.7Mb

curatedMetagenomicData

Version: 1.2.2

checking re-building of vignette outputs ... WARNING ``` ... The data you have provided does not have any singletons. This is highly suspicious. Results of richness estimates (for example) are probably unreliable, or wrong, if you have already trimmed low-abundance taxa from the data.

We recommended that you find the un-trimmed data and retry. Warning in graphics:::plotHclust(n1, merge, height, order(x$order), hang, : "method" is not a graphical parameter Warning in graphics:::plotHclust(n1, merge, height, order(x$order), hang, : "method" is not a graphical parameter Warning in axis(2, at = pretty(range(height)), ...) : "method" is not a graphical parameter Warning in title(main = main, sub = sub, xlab = xlab, ylab = ylab, ...) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Warning in replayPlot(x) : "method" is not a graphical parameter Error: processing vignette 'curatedMetagenomicData.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘dplyr’ ‘phyloseq’ ‘Biobase’ ‘ExperimentHub’ ‘AnnotationHub’ ‘magrittr’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: help 7.9Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘BiocInstaller’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocInstaller’ All declared Imports should be used.
checking R code for possible problems ... NOTE ExpressionSet2MRexperiment: no visible global function definition for ‘AnnotatedDataFrame’ ExpressionSet2MRexperiment: no visible global function definition for ‘phenoData’ curatedMetagenomicData : <anonymous>: no visible global function definition for ‘exprs<-’ Undefined global functions or variables: AnnotatedDataFrame exprs<- phenoData
checking Rd files ... NOTE prepare_Rd: HMP_2012.Rd:540-542: Dropping empty section \seealso prepare_Rd: KarlssonFH_2013.Rd:90-92: Dropping empty section \seealso prepare_Rd: LeChatelierE_2013.Rd:86-88: Dropping empty section \seealso prepare_Rd: LomanNJ_2013_Hi.Rd:82-84: Dropping empty section \seealso prepare_Rd: LomanNJ_2013_Mi.Rd:82-84: Dropping empty section \seealso prepare_Rd: NielsenHB_2014.Rd:94-96: Dropping empty section \seealso prepare_Rd: Obregon_TitoAJ_2015.Rd:94-96: Dropping empty section \seealso prepare_Rd: OhJ_2014.Rd:86-88: Dropping empty section \seealso prepare_Rd: QinJ_2012.Rd:106-108: Dropping empty section \seealso prepare_Rd: QinN_2014.Rd:94-96: Dropping empty section \seealso prepare_Rd: RampelliS_2015.Rd:90-92: Dropping empty section \seealso prepare_Rd: TettAJ_2016.Rd:184-186: Dropping empty section \seealso prepare_Rd: ZellerG_2014.Rd:94-96: Dropping empty section \seealso

cutoffR

Version: 1.0

checking R code for possible problems ... NOTE Cut: no visible global function definition for ‘cor’ MissSimulation: no visible global function definition for ‘rbinom’ cutoff: no visible global function definition for ‘cor’ Undefined global functions or variables: cor rbinom Consider adding importFrom("stats", "cor", "rbinom") to your NAMESPACE file.

CVE

Version: 1.2.0

checking data for ASCII and uncompressed saves ... WARNING ```

Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress WGCNAmelanoma_extension.RData 2.4Mb 2.1Mb xz crcCase.RData 1.1Mb 676Kb xz melanomaCase.RData 654Kb 473Kb xz ```
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... gdac.broadinstitute.org_COAD.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/gdac.broadinstitute.org_COAD.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz' Content type 'application/x-gzip' length 80929 bytes (79 KB) ================================================== downloaded 79 KB

gdac.broadinstitute.org_COAD.Clinical_Pick_Tier1.Level_4.2016012800.0.0 gdac.broadinstitute.org_COAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz trying URL 'http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/COAD/20160128/gdac.broadinstitute.org_COAD.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz' Content type 'application/x-gzip' length 2675595 bytes (2.6 MB) ================================================== downloaded 2.6 MB

Error: processing vignette 'CVE_tutorial.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘shiny’ ‘ConsensusClusterPlus’ ‘RColorBrewer’ ‘gplots’ ‘plyr’ ‘ggplot2’ ‘jsonlite’ ‘ape’ ‘WGCNA’ ‘RTCGAToolbox’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘RTCGAToolbox’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.

cvxclustr

Version: 1.1.1

checking R code for possible problems ... NOTE create_clustering_problem: no visible global function definition for ‘rnorm’ Undefined global functions or variables: rnorm Consider adding importFrom("stats", "rnorm") to your NAMESPACE file.
checking line endings in Makefiles ... NOTE Found the following Makefile(s) without a final LF: src/Makevars Some ‘make’ programs ignore lines not ending in LF.

Cyclops

Version: 1.3.0

checking installed package size ... NOTE installed size is 23.2Mb sub-directories of 1Mb or more: libs 22.5Mb

cytofkit

Version: 1.8.4

checking whether package ‘cytofkit’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/cytofkit/new/cytofkit.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: doc 2.1Mb extdata 3.6Mb
checking R code for possible problems ... NOTE cytof_clusterPlot: no visible global function definition for ‘geom_text’ cytof_progressionPlot: no visible global function definition for ‘aes’ cytof_progressionPlot: no visible binding for global variable ‘Pseudotime’ cytof_progressionPlot: no visible binding for global variable ‘cluster’ cytofkitShinyAPP : <anonymous> : C_ScatterPlotInput: no visible global function definition for ‘scatterPlot’ cytofkitShinyAPP : <anonymous>: no visible global function definition for ‘heatMap’ cytofkitShinyAPP : <anonymous> : M_markerExpressionPlotInput: no visible global function definition for ‘scatterPlot’ cytofkitShinyAPP : <anonymous> : M_stackDensityPlotInput: no visible global function definition for ‘stackDenistyPlot’ cytofkitShinyAPP : <anonymous> : P_markerPlotInput: no visible global function definition for ‘cytof_expressionTrends’ Undefined global functions or variables: Pseudotime aes cluster cytof_expressionTrends geom_text heatMap scatterPlot stackDenistyPlot

dada2

Version: 1.4.0

checking installed package size ... NOTE installed size is 8.4Mb sub-directories of 1Mb or more: doc 1.3Mb libs 5.9Mb
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘ShortRead:::.set_omp_threads’ See the note in ?`:::` about the use of this operator.
checking foreign function calls ... NOTE Foreign function call to a different package: .Call(ShortRead:::.set_omp_threads, ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... plotComplementarySubstitutions: no visible binding for global variable ‘Quality’ plotErrors: no visible binding for global variable ‘Qual’ plotErrors: no visible binding for global variable ‘Observed’ plotErrors: no visible binding for global variable ‘Estimated’ plotErrors: no visible binding for global variable ‘Input’ plotErrors: no visible binding for global variable ‘Nominal’ plotQualityProfile: no visible binding for global variable ‘Cycle’ plotQualityProfile: no visible binding for global variable ‘Score’ plotQualityProfile: no visible binding for global variable ‘Count’ plotQualityProfile: no visible binding for global variable ‘Mean’ plotQualityProfile: no visible binding for global variable ‘Q25’ plotQualityProfile: no visible binding for global variable ‘Q50’ plotQualityProfile: no visible binding for global variable ‘Q75’ plotQualityProfile: no visible binding for global variable ‘minScore’ plotQualityProfile: no visible binding for global variable ‘label’ Undefined global functions or variables: Count Cycle Direction Estimated Forward Input Mean Nominal Observed Q25 Q50 Q75 Qual Quality Reverse Score Sub1 Sub2 SubGrp Substitution abundance accept allMismatch als1 als2 indel label minScore mismatch n0F n0R prefer seqF seqR
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

DaMiRseq

Version: 1.0.0

checking tests ... ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Loading required package: ggplot2 > > test_check("DaMiRseq") 10 Predictors have been selected for classification 3 Predictors have been selected for classification 100 Highly correlated features have been discarded for classification. 0 Features remained. 100 Highly correlated features have been discarded for classification. 0 Features remained. Error in array(STATS, dims[perm]) : 'dims' cannot be of length 0 Calls: test_check ... DaMiR.FSelect -> bve_pls -> VIP -> apply -> sweep -> aperm -> array In addition: There were 50 or more warnings (use warnings() to see the first 50) testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 0 Execution halted

checking re-building of vignette outputs ... WARNING ``` ...

The following objects are masked from 'package:Biobase':
```
anyMissing, rowMedians
```
Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':
```
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
```
The following object is masked from 'package:base':
```
apply
```
Loading required package: ggplot2 Quitting from lines 334-338 (DaMiRseq.Rnw) Error: processing vignette 'DaMiRseq.Rnw' failed with diagnostics: 'dims' cannot be of length 0 Execution halted ```
checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: data 5.5Mb
checking R code for possible problems ... NOTE DaMiR.Allplot: warning in pheatmap(sampleDistMatrix, clustering_distance_rows = mydist, clustering_distance_cols = mydist, col = colors, breaks = seque, annotation_col = df): partial argument match of 'col' to 'color' DaMiR.Clustplot: warning in pheatmap(count_data, clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale = "row", col = colors, annotation_col = df): partial argument match of 'col' to 'color' DaMiR.Allplot: no visible binding for global variable ‘X1’ DaMiR.Allplot: no visible binding for global variable ‘X2’ DaMiR.EnsembleLearning: no visible binding for global variable ‘Predictors’ DaMiR.EnsembleLearning: no visible binding for global variable ‘Accuracy’ DaMiR.MDSplot: no visible binding for global variable ‘X1’ DaMiR.MDSplot: no visible binding for global variable ‘X2’ Undefined global functions or variables: Accuracy Predictors X1 X2

DAPAR

Version: 1.8.7

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
1. Failure: corrMatrixD (@test_descriptiveStatistics.R#174) -------------------- t$data[[1]] inherits from factor not data.frame.
Procedure of Benjamini-Hochberg is used. pi0 is fixed to 1. testthat results ================================================================ OK: 176 SKIPPED: 0 FAILED: 4 1. Failure: wrapper.corrMatrixD (@test_descriptiveStatistics.R#161) 2. Failure: wrapper.corrMatrixD (@test_descriptiveStatistics.R#162) 3. Failure: corrMatrixD (@test_descriptiveStatistics.R#173) 4. Failure: corrMatrixD (@test_descriptiveStatistics.R#174)

Error: testthat unit tests failed Execution halted ```

checking for missing documentation entries ... WARNING Undocumented data sets: ‘testWithoutNA’ ‘test’ ‘UPSpep25’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking package dependencies ... NOTE Package suggested but not available for checking: ‘Prostar’

darksky

Version: 1.3.0

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:
- }
- Error: the API call works (@test-darksky.R#6) ------------------------------- Please set env var DARKSKY_API_KEY to your Dark Sky API key 1: get_current_forecast(43.2672, -70.8617) at testthat/test-darksky.R:6 2: sprintf("https://api.darksky.net/forecast/%s/%s,%s", darksky_api_key(), latitude, longitude) 3: darksky_api_key() 4: stop("Please set env var DARKSKY_API_KEY to your Dark Sky API key", call. = FALSE)
testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 1 1. Error: the API call works (@test-darksky.R#6)

Error: testthat unit tests failed Execution halted ```

dartR

Version: 0.93

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’ All declared Imports should be used.

data.table

Version: 1.10.4-3

checking tests ... ``` ERROR Running the tests in ‘tests/main.R’ failed. Last 13 lines of output: > x = names(print(ggplot(DT) + geom_hex(aes(b, f)) + facet_wrap(~grp)))[c(1, 3)] [1] "data" "scales" > y = c("data", "plot") [1] "data" "plot" 1 string mismatch Don't know how to automatically pick scale for object of type ITime. Defaulting to continuous. Don't know how to automatically pick scale for object of type ITime. Defaulting to continuous. Tests 1441-1444 not run. If required install the 'fr_FR.utf8' locale.

Running test id 1696 Error in eval(exprs[i], envir) : 2 errors out of 5939 (lastID=1751, endian==little, sizeof(long double)==16, sizeof(pointer)==8) in inst/tests/tests.Rraw on Tue Nov 21 12:27:40 2017. Search tests.Rraw for test numbers: 167, 167.2. Calls: test.data.table -> sys.source -> eval -> eval Execution halted ```

DataExplorer

Version: 0.4.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > library(testthat) > library(DataExplorer) > > test_check("DataExplorer")
1. Failure: test if quiet is working for GenerateReport (@test-generate-report.r#8) GenerateReport(...) produced warnings.
testthat results ================================================================ OK: 58 SKIPPED: 0 FAILED: 1 1. Failure: test if quiet is working for GenerateReport (@test-generate-report.r#8)

Error: testthat unit tests failed Execution halted ```

datarobot

Version: 2.7.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘curl’ All declared Imports should be used.

DChIPRep

Version: 1.6.2

checking re-building of vignette outputs ... WARNING ``` ... anyMissing, rowMedians

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':
```
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
```
The following object is masked from 'package:base':
```
apply
```
gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates geom_smooth() using method = 'gam' and formula 'y ~ s(x, bs = "cs")' Error: processing vignette 'DChIPRepVignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.

dcmr

Version: 1.0

checking R code for possible problems ... NOTE ... ‘combn’ SampleParameterEstimates: no visible global function definition for ‘rnorm’ plot,attribute.class-missing: no visible binding for global variable ‘attr.number’ plot,attribute.class-missing: no visible binding for global variable ‘mean.attr’ plot,attribute.profile.class-missing: no visible binding for global variable ‘attr.profile.number’ plot,attribute.profile.class-missing: no visible binding for global variable ‘mean.attr.profile’ summary,attribute.class: no visible binding for global variable ‘value’ summary,attribute.profile.class: no visible binding for global variable ‘max.class’ Undefined global functions or variables: attr.number attr.profile.number combn max.class mean.attr mean.attr.profile rmultinom rnorm runif value Consider adding importFrom("stats", "rmultinom", "rnorm", "runif") importFrom("utils", "combn") to your NAMESPACE file.

debrowser

Version: 1.4.5

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'DEBrowser.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ Execution halted
checking installed package size ... NOTE installed size is 8.9Mb sub-directories of 1Mb or more: doc 6.3Mb extdata 2.1Mb
checking R code for possible problems ... NOTE ... scatterZoom: no visible binding for global variable ‘size.hover’ scatterZoom: no visible binding for global variable ‘key’ startDEBrowser: no visible binding for global variable ‘.startdebrowser.called’ volcanoPlot: no visible global function definition for ‘:=’ volcanoPlot: no visible binding for global variable ‘size’ volcanoPlot: no visible binding for global variable ‘size.hover’ volcanoPlot: no visible binding for global variable ‘fillOpacity’ volcanoPlot: no visible binding for global variable ‘fillOpacity.hover’ volcanoPlot: no visible binding for global variable ‘fill.brush’ volcanoPlot: no visible binding for global variable ‘opacity’ volcanoPlot: no visible binding for global variable ‘key’ volcanoZoom: no visible global function definition for ‘:=’ volcanoZoom: no visible binding for global variable ‘size’ volcanoZoom: no visible binding for global variable ‘size.hover’ volcanoZoom: no visible binding for global variable ‘key’ Undefined global functions or variables: .startdebrowser.called := NUL align baseline biocLite conds debrowser demodata fill fill.brush fillOpacity fillOpacity.hover fit fontSize get_user_info googleAuth googleAuthUI initStore key opacity samples searched size size.hover stroke updateStore with_shiny

DeconRNASeq

Version: 1.18.0

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: data 6.5Mb
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘grid’ which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: ‘ggplot2’ ‘grid’ ‘pcaMethods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... condplot: no visible global function definition for ‘plot’ condplot: no visible global function definition for ‘rainbow’ condplot: no visible global function definition for ‘lines’ condplot: no visible global function definition for ‘axis’ condplot: no visible global function definition for ‘title’ decon.bootstrap: no visible global function definition for ‘t.test’ multiplot: no visible global function definition for ‘grid.newpage’ multiplot: no visible global function definition for ‘pushViewport’ multiplot: no visible global function definition for ‘viewport’ multiplot: no visible global function definition for ‘grid.layout’ multiplot : vplayout: no visible global function definition for ‘viewport’ Undefined global functions or variables: R2cum aes axis geom_abline geom_point ggplot grid.layout grid.newpage labs lines pca plot prep pushViewport rainbow t.test title viewport xlab ylab Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "axis", "lines", "plot", "title") importFrom("stats", "t.test") to your NAMESPACE file.

Deducer

Version: 0.7-9

checking whether the namespace can be unloaded cleanly ... WARNING ... 7f302349c000-7f30234c2000 r-xp 00000000 08:01 16865 /lib/x86_64-linux-gnu/ld-2.23.so 7f30234c2000-7f30234c4000 r--s 00001000 08:01 1025768 /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/dnsns.jar 7f30234c4000-7f30234ca000 r--s 0003a000 08:01 1025763 /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/sunjce_provider.jar 7f30234ca000-7f30234cb000 r--s 00010000 08:01 1025760 /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/zipfs.jar 7f30234cb000-7f30234cc000 r--s 0000a000 08:01 1025767 /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/jaccess.jar 7f30234cc000-7f30234ce000 r--s 00008000 08:01 1025764 /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/sunec.jar 7f30234ce000-7f30236ae000 rw-p 00000000 00:00 0 7f30236ae000-7f30236b6000 rw-s 00000000 08:01 1292559 /tmp/hsperfdata_muelleki/43455 7f30236b6000-7f30236b7000 rw-p 00000000 00:00 0 7f30236b7000-7f30236b8000 r--p 00000000 00:00 0 7f30236b8000-7f30236bf000 r--s 00000000 08:01 27320 /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache 7f30236bf000-7f30236c1000 rw-p 00000000 00:00 0 7f30236c1000-7f30236c2000 r--p 00025000 08:01 16865 /lib/x86_64-linux-gnu/ld-2.23.so 7f30236c2000-7f30236c3000 rw-p 00026000 08:01 16865 /lib/x86_64-linux-gnu/ld-2.23.so 7f30236c3000-7f30236c4000 rw-p 00000000 00:00 0 7fff29fbc000-7fff29fbf000 ---p 00000000 00:00 0 7fff29fbf000-7fff2a7bc000 rw-p 00000000 00:00 0 [stack] 7fff2a7e2000-7fff2a7e4000 r--p 00000000 00:00 0 [vvar] 7fff2a7e4000-7fff2a7e6000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] Aborted (core dumped)

DeepBlueR

Version: 1.2.10

checking examples ... ERROR ``` ...
- experiment_names = deepblue_extract_names(experiments_list)
- histones_datasets[[epigenetic_marks[[i]]]] = experiment_names
- } Called method: deepblue_list_experiments Reported status was: okay Called method: deepblue_list_experiments Reported status was: okay Called method: deepblue_list_experiments Reported status was: okay
  
  deepblue_enrich_region_overlap(
- query_id=filtered_query_id,
- background_query=rg_10kb_tilling,
- datasets=histones_datasets,
- genome="grch38") Called method: deepblue_enrich_region_overlap Reported status was: error Error in deepblue_enrich_region_overlap(query_id = filtered_query_id, : Command enrich_region_overlap does not exists. Execution halted ```

DEGreport

Version: 1.12.0

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... ‘plotCounts’ degPlotWide: no visible binding for global variable ‘gene’ degPlotWide: no visible binding for global variable ‘count’ degPlotWide: no visible binding for global variable ‘treatment’ degResults: no visible global function definition for ‘assay’ degResults: no visible global function definition for ‘rlog’ degResults: no visible global function definition for ‘results’ degResults: no visible global function definition for ‘colData’ degResults: no visible global function definition for ‘rowMax’ degVolcano: no visible binding for global variable ‘logFC’ degVolcano: no visible binding for global variable ‘V1’ degVolcano: no visible binding for global variable ‘V2’ degVolcano: no visible binding for global variable ‘adj.P.Val’ degVolcano: no visible binding for global variable ‘x’ degVolcano: no visible binding for global variable ‘y’ degVolcano: no visible binding for global variable ‘name’ Undefined global functions or variables: MulticoreParam V1 V2 adj.P.Val assay bplapply coda.samples colData comp count enrichGO gene group jags.model keys label log2FoldChange logFC name one plotCounts results rlog rowMax simplify treatment two value variable x y

DeLorean

Version: 1.2.5

checking S3 generic/method consistency ... WARNING ``` filter: function(x, filter, method, sides, circular, init) filter.cells: function(dl, .filter, number, cells)

filter: function(x, filter, method, sides, circular, init) filter.genes: function(dl, .filter, number, genes)

See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. ```

deltaGseg

Version: 1.16.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘ggplot2’ ‘changepoint’ ‘wavethresh’ ‘tseries’ ‘pvclust’ ‘fBasics’ ‘grid’ ‘reshape’ ‘scales’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... diagnosticPlots,SegSeriesTrajectories: no visible binding for global variable ‘residuals’ diagnosticPlots,SegSeriesTrajectories: no visible global function definition for ‘acf’ diagnosticPlots,SegSeriesTrajectories: no visible global function definition for ‘qnorm’ diagnosticPlots,SegSeriesTrajectories: no visible binding for global variable ‘lag’ Undefined global functions or variables: abline acf as.dist cor cutree dist hclust identify lag layout lines locator median mtext na.omit par points qnorm quantile read.table residuals setTxtProgressBar text txtProgressBar Consider adding importFrom("graphics", "abline", "identify", "layout", "lines", "locator", "mtext", "par", "points", "text") importFrom("stats", "acf", "as.dist", "cor", "cutree", "dist", "hclust", "lag", "median", "na.omit", "qnorm", "quantile", "residuals") importFrom("utils", "read.table", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file.
checking installed files from ‘inst/doc’ ... NOTE ``` The following files should probably not be installed: ‘diagplots.png’, ‘simclust.png’, ‘simtraj.png’, ‘simtrajtr.png’, ‘simtrajtr2.png’, ‘traj1.png’, ‘traj1break.png’, ‘traj1ss0.png’, ‘traj1ss1.png’, ‘traj1tr.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. ```

demi

Version: 1.1.2

checking R code for possible problems ... NOTE ... demi.wilcox.test.fast: no visible global function definition for ‘wilcox.test’ demiequal: no visible global function definition for ‘wilcox.test’ wprob: no visible global function definition for ‘combn’ diffexp,DEMIDiff: no visible global function definition for ‘median’ diffexp,DEMIDiff: no visible global function definition for ‘p.adjust’ loadAnnotation,DEMIExperiment-environment: no visible global function definition for ‘data’ loadBlat,DEMIExperiment-environment: no visible global function definition for ‘data’ loadCytoband,DEMIExperiment-environment: no visible global function definition for ‘data’ loadPathway,DEMIExperiment-environment: no visible global function definition for ‘data’ Undefined global functions or variables: combn data dhyper median p.adjust t.test wilcox.test write.table Consider adding importFrom("stats", "dhyper", "median", "p.adjust", "t.test", "wilcox.test") importFrom("utils", "combn", "data", "write.table") to your NAMESPACE file.

dendextend

Version: 1.6.0

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘ggdendro’ ‘labeltodendro’ ‘dendroextras’ ‘Hmisc’
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘WGCNA’, ‘dendroextras’, ‘moduleColor’, ‘distory’, ‘phangorn’, ‘ggdendro’, ‘zoo’

DendroSync

Version: 0.1.0

checking examples ... ERROR ``` ... The error most likely occurred in:

Name: sync.plot

Title: Plot within- and between-group synchrony

Aliases: sync.plot

** Examples

Plot homoscedastic narrow evaluation (mNE) and unstructured model (mUN)

# synchronies for conifersIP data: data(conifersIP)

##Fit the homoscedastic set of varcov models (mBE, mNE, mCS, mUN) # using geographic grouping criteria (ie. Region) ModHm <- dendro.varcov(TRW ~ Code, varTime = "Year", varGroup = "Region", + data = conifersIP, homoscedastic = TRUE) [1] "Please wait. I am fitting the models now :)"

sync.plot(sync(ModHm, modname = "mNE")) Error: Columns ymin, ymax must be 1d atomic vectors or lists Execution halted ```

DepthProc

Version: 2.0.2

checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: libs 5.4Mb

derfinder

Version: 1.10.6

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in citation("BiocStyle") : no date field in DESCRIPTION file of package 'BiocStyle' Quitting from lines 53-115 (derfinder-quickstart.Rmd) Error: processing vignette 'derfinder-quickstart.Rmd' failed with diagnostics: package 'knitrBootstrap' not found Execution halted
checking package dependencies ... NOTE Package suggested but not available for checking: ‘derfinderPlot’
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘GenomeInfoDb:::.guessSpeciesStyle’ ‘GenomeInfoDb:::.supportedSeqnameMappings’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.smootherFstats’

derfinderPlot

Version: 1.10.0

checking re-building of vignette outputs ... WARNING ... Warning in citation("biovizBase") : no date field in DESCRIPTION file of package 'biovizBase' Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") : no date field in DESCRIPTION file of package 'TxDb.Hsapiens.UCSC.hg19.knownGene' Writing 24 Bibtex entries ... OK Results written to file 'derfinderPlotRef.bib' Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: Transformation introduced infinite values in continuous y-axis Error: processing vignette 'derfinderPlot.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘RefManageR’

DESeq2

Version: 1.16.1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check("DESeq2")
1. Error: tximport works (@test_tximport.R#12) --------------------------------- importing inferential replicates for Salmon or Sailfish requires package rjson. to skip this step, set dropInfReps=TRUE 1: tximport(files, type = "salmon", tx2gene = tx2gene) at testthat/test_tximport.R:12 2: infRepImporter(dirname(files[i])) 3: readInfRepFish(x, type) 4: stop("importing inferential replicates for Salmon or Sailfish requires package rjson.\n to skip this step, set dropInfReps=TRUE")
testthat results ================================================================ OK: 203 SKIPPED: 0 FAILED: 1 1. Error: tximport works (@test_tximport.R#12)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... reading in files with read_tsv 1 Quitting from lines 256-257 (DESeq2.Rmd) Error: processing vignette 'DESeq2.Rmd' failed with diagnostics: importing inferential replicates for Salmon or Sailfish requires package `rjson`. to skip this step, set dropInfReps=TRUE Execution halted
checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: doc 2.4Mb libs 2.6Mb

destiny

Version: 2.4.5

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘rgl’
checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 3.1Mb libs 2.4Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘scatterplot3d’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘rgl’
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'plot.DPT': ‘plot.DPT’

S3 methods shown with full name in documentation object 'plot.DiffusionMap': ‘plot.DiffusionMap’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘viridis’ 'library' or 'require' calls not declared from: ‘IRdisplay’ ‘IRkernel’ ‘base64enc’ ‘repr’ ‘xlsx’
checking re-building of vignette outputs ... NOTE Error in re-building vignettes: ... Error: processing vignette 'DPT.ipynbmeta' failed with diagnostics: Either IPython 3+ or Jupyter has to be installed, but neither could be called. Execution halted

detzrcr

Version: 0.2.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘utils’ All declared Imports should be used.

dfexplore

Version: 0.2.1

checking R code for possible problems ... NOTE simulate_dataframe : generate_dumb_answer: no visible global function definition for ‘rbinom’ simulate_dataframe : generate_dumb_answer: no visible global function definition for ‘rnorm’ simulate_dataframe : generate_initial: no visible global function definition for ‘rbinom’ simulate_dataframe: no visible binding for global variable ‘randu’ simulate_dataframe: no visible global function definition for ‘rbinom’ simulate_dataframe: no visible global function definition for ‘rnorm’ simulate_dataframe: no visible global function definition for ‘rpois’ simulate_dataframe : add_NAs: no visible global function definition for ‘rbinom’ Undefined global functions or variables: randu rbinom rnorm rpois Consider adding importFrom("datasets", "randu") importFrom("stats", "rbinom", "rnorm", "rpois") to your NAMESPACE file.

dfpk

Version: 3.4.0

checking installed package size ... NOTE installed size is 43.2Mb sub-directories of 1Mb or more: libs 42.8Mb

dggridR

Version: 2.0.1

checking installed package size ... NOTE installed size is 27.5Mb sub-directories of 1Mb or more: doc 1.9Mb libs 25.2Mb

diagis

Version: 0.1.3

checking examples ... ERROR ... > > #optimal case > set.seed(42) > s_opt <- sqrt(2) > x_opt <- rnorm(1000, sd = s_opt) > w_opt <- p(x_opt) / q(x_opt, s_opt) > weighted_mean(x_opt, w_opt) [1] -0.01223051 > weighted_var(x_opt, w_opt) [1] 0.9954861 > s_inf <- 0.25 > x_inf <- rnorm(1000, sd = s_inf) > w_inf <- p(x_inf) / q(x_inf, s_inf) > weighted_mean(x_inf, w_inf) #!! [1] 0.1281881 > weighted_var(x_inf, w_inf) #!! [1] 0.2531165 > # diagnostic plots > weight_plot(w_inf) Error: Column `y` must be a 1d atomic vector or a list Execution halted
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 73-74 (diagis.Rmd) Error: processing vignette 'diagis.Rmd' failed with diagnostics: Column `y` must be a 1d atomic vector or a list Execution halted

dielectric

Version: 0.2.3

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE L2eV: no visible binding for global variable ‘constants’ L2w: no visible binding for global variable ‘constants’ dielectric: no visible global function definition for ‘new’ dielectric2plot: no visible global function definition for ‘reshape’ eV2L: no visible binding for global variable ‘constants’ t2eV: no visible binding for global variable ‘constants’ Undefined global functions or variables: constants new reshape Consider adding importFrom("methods", "new") importFrom("stats", "reshape") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

DiffBind

Version: 2.4.8

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘rgl’ ‘XLConnect’
checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: libs 3.3Mb
checking R code for possible problems ... NOTE pv.DBAplotVolcano: no visible binding for global variable ‘Fold’ pv.DBAplotVolcano: no visible binding for global variable ‘Legend’ Undefined global functions or variables: Fold Legend

diffeR

Version: 0.0-4

checking examples ... ERROR ``` Running examples in ‘diffeR-Ex.R’ failed The error most likely occurred in:

Name: MAD

Title: Mean Absolute Deviation (MAD)

Aliases: MAD

Keywords: spatial

** Examples

old.par <- par(no.readonly = TRUE) grid1 <- raster(system.file("external/GRID1_INT.rst", package="diffeR")) grid2 <- raster(system.file("external/GRID2_INT.rst", package="diffeR")) strata <- raster(system.file("external/strata_int.rst", package="diffeR")) MAD(grid1, grid2, strata, eval="original") Error in calc(strata, fun) : unused argument (fun) Calls: MAD Execution halted ```
checking whether package ‘diffeR’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘raster::calc’ by ‘ggplot2::calc’ when loading ‘diffeR’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/diffeR/new/diffeR.Rcheck/00install.out’ for details.
checking R code for possible problems ... NOTE MAD: possible error in calc(strata, fun): unused argument (fun) MAD: possible error in calc(strataM2, fun1): unused argument (fun1) MAD: possible error in calc(tmp1, fun2): unused argument (fun2) MAD: possible error in calc(strataM, sum): unused argument (sum)

diffloop

Version: 1.4.0

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

directlabels

Version: 2017.03.31

checking examples ... ERROR ``` ... The error most likely occurred in:

Name: normal.l2.cluster

Title: Clustering of some normal data in 2d with the l2 clusterpath

Aliases: normal.l2.cluster

Keywords: datasets

** Examples

data(normal.l2.cluster) if(require(ggplot2)){ + p <- ggplot(normal.l2.cluster$path,aes(x,y))+ + geom_path(aes(group=row),colour="grey")+ + geom_point(aes(size=lambda),colour="grey")+ + geom_point(aes(colour=class),data=normal.l2.cluster$pts)+ + coord_equal() + print(direct.label(p)) + } Loading required package: ggplot2 Error: Column colour must have a unique name Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/ggplot.R’ failed. Last 13 lines of output:
- stopifnot(result$hide %in% L$hide)
- stopifnot(length(result$hide) == length(L$hide))
- stopifnot(L$colour == result$colour)
- label it and check for different legends.
- dl <- direct.label(L$plot)
- after <- legends2hide(dl)
- stopifnot(is.null(after))
- }
- }
- } Loading required package: ggplot2 Error in loadNamespace(name) : there is no package called 'dplyr' Calls: geom_point ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted ```

diveRsity

Version: 1.9.90

checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: libs 5.9Mb

DLMtool

Version: 5.0

checking whether package ‘DLMtool’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/DLMtool/new/DLMtool.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: libs 4.6Mb

dMod

Version: 0.4

checking package dependencies ... NOTE Package suggested but not available for checking: ‘rPython’

DMRScan

Version: 1.0.0

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 4.9Mb

doBy

Version: 4.5-15

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘gdata’

dodgr

Version: 0.0.3

checking installed package size ... NOTE installed size is 9.7Mb sub-directories of 1Mb or more: doc 3.4Mb libs 6.1Mb

DOSE

Version: 3.2.0

checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...

DOSE v3.2.0 For help: https://guangchuangyu.github.io/DOSE

If you use DOSE in published research, please cite: Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

Error: processing vignette 'DOSE.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 3.0Mb doc 2.5Mb

dotwhisker

Version: 0.3.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘arm’

dplyr

Version: 0.7.4

checking installed package size ... NOTE installed size is 33.0Mb sub-directories of 1Mb or more: libs 31.0Mb
checking data for non-ASCII characters ... NOTE Note: found 4 marked UTF-8 strings

dr4pl

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘devtools’ ‘drc’ ‘testthat’ All declared Imports should be used.

DRIMSeq

Version: 1.4.1

checking examples ... ERROR ``` ... 3 FBgn0259735 0.9383577 2 6.255157e-01 7.744480e-01 4 FBgn0032785 3.4718633 2 1.762359e-01 3.143951e-01 5 FBgn0040297 6.0769622 4 1.934739e-01 3.143951e-01 6 FBgn0032979 1.7139224 1 1.904773e-01 3.143951e-01 > > ## Plot feature proportions for a top DTU gene > res <- results(d) > res <- res[order(res$pvalue, decreasing = FALSE), ] > > top_gene_id <- res$gene_id[1] > > plotProportions(d, gene_id = top_gene_id, group_variable = "group") > > plotProportions(d, gene_id = top_gene_id, group_variable = "group",
- plot_type = "lineplot")
  
  plotProportions(d, gene_id = top_gene_id, group_variable = "group",
- plot_type = "ribbonplot") Coordinate system already present. Adding new coordinate system, which will replace the existing one. Error: Columns ymin, ymax must be 1d atomic vectors or lists Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 369-379 (DRIMSeq.Rnw) Error: processing vignette 'DRIMSeq.Rnw' failed with diagnostics: Columns `ymin`, `ymax` must be 1d atomic vectors or lists Execution halted

dSimer

Version: 1.2.0

checking re-building of vignette outputs ... WARNING ... finding first neighbours of the disease-related genes.. calculating shortest path of each gene pair.. this may take a while.. calculating transformed distance of each gene pair.. this may take a while.. calculating similarity of each disease pair.. done.. calculating similarity of each disease pair.. done.. calculating similarity of each disease pair.. done.. calculating similarity of each disease pair.. done.. filtering disease-gene associations.. calculating separation distance between diseases.. this may need a lot of time.. be patient.. done.. filtering disease-gene associations.. calculating separation distance between diseases.. this may need a lot of time.. be patient.. done.. Using ID as id variables Error: processing vignette 'dSimer.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: data 3.1Mb libs 3.5Mb

dsm

Version: 2.2.15

checking data for non-ASCII characters ... NOTE Error in .requirePackage(package) : unable to find required package 'sp' Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage Execution halted

dtwclust

Version: 4.1.1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 1920 SKIPPED: 0 FAILED: 11
1. Error: Pairwise proxy distances give the same result as references
2. Error: Included (valid) distances can accept multivariate series.
3. Error: Pairwise proxy distances give the same result as references
4. Error: Distance matrices calculated with families give the same results as references.
5. Error: Centroids calculated with families give the same results as references.
6. Error: A custom distance in dtwclust give the same results as references.
7. Error: CVIs give the same results as references.
8. Error: Fuzzy clustering gives the same results as references.
9. Error: Hierarchical clustering gives the same results as references.
10. ...
Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE installed size is 10.1Mb sub-directories of 1Mb or more: doc 1.9Mb libs 7.2Mb

dtwSat

Version: 0.2.3

checking whether package ‘dtwSat’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘dtwSat’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/dtwSat/new/dtwSat.Rcheck/00install.out’ for details.

checking re-building of vignette outputs ... WARNING ``` ...

Attaching package: 'caret'

The following object is masked from 'package:survival':
```
cluster
```
This is BibTeX, Version 0.99d (TeX Live 2015/Debian) The top-level auxiliary file: applying_twdtw.aux The style file: jss.bst Illegal, another \bibstyle command---line 155 of file applying_twdtw.aux : \bibstyle : {jss} I'm skipping whatever remains of this command Database file #1: references.bib.bib Warning--entry type for "Dutrieux:2014" isn't style-file defined --line 584 of file references.bib.bib (There was 1 error message) Error: processing vignette 'applying_twdtw.Rmd' failed with diagnostics: Failed to build the bibliography via bibtex Execution halted ```

DVHmetrics

Version: 0.3.6

checking re-building of vignette outputs ... WARNING `` ... Coordinate system already present. Adding new coordinate system, which will replace the existing one. Coordinate system already present. Adding new coordinate system, which will replace the existing one. Coordinate system already present. Adding new coordinate system, which will replace the existing one. Warning in getEQD2.default(D = D$dvh[, "dose"], fd = fd, ab = ab) : 'D' must be > 0 Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'DVHmetrics.tex' failed. LaTeX errors: ! LaTeX Error: Fileapacite.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.93 ^^M

! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

dynr

Version: 0.1.11-8

checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: models 4.3Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rdpack’ All declared Imports should be used.

earlywarnings

Version: 1.0.59

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... surrogates_RShiny: no visible global function definition for ‘par’ surrogates_RShiny: no visible global function definition for ‘hist’ surrogates_RShiny: no visible global function definition for ‘abline’ surrogates_RShiny: no visible global function definition for ‘points’ surrogates_RShiny: no visible global function definition for ‘title’ surrogates_ews: no visible global function definition for ‘dev.new’ surrogates_ews: no visible global function definition for ‘par’ surrogates_ews: no visible global function definition for ‘hist’ surrogates_ews: no visible global function definition for ‘abline’ surrogates_ews: no visible global function definition for ‘points’ surrogates_ews: no visible global function definition for ‘mtext’ Undefined global functions or variables: abline aes contour dev.new geom_tile grid hist labs layout legend lines mtext par plot points rainbow scale_fill_gradient stat_contour text title topo.colors xlab ylab Consider adding importFrom("grDevices", "dev.new", "rainbow", "topo.colors") importFrom("graphics", "abline", "contour", "grid", "hist", "layout", "legend", "lines", "mtext", "par", "plot", "points", "text", "title") to your NAMESPACE file.

EasyHTMLReport

Version: 0.1.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’ All declared Imports should be used. Packages in Depends field not imported from: ‘base64enc’ ‘knitr’ ‘markdown’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... .file_attachment: no visible global function definition for ‘base64encode’ .plot_attachment: no visible global function definition for ‘dev.off’ .update_list: no visible global function definition for ‘modifyList’ easyHtmlReport: no visible global function definition for ‘knit’ easyHtmlReport: no visible global function definition for ‘markdownToHTML’ mime_part.data.frame: no visible global function definition for ‘write.table’ mime_part.ggplot: no visible binding for global variable ‘pdf’ mime_part.matrix: no visible global function definition for ‘write.table’ mime_part.trellis: no visible binding for global variable ‘pdf’ simpleHtmlReport : <anonymous>: no visible global function definition for ‘write.table’ Undefined global functions or variables: base64encode dev.off knit markdownToHTML modifyList pdf write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("utils", "modifyList", "write.table") to your NAMESPACE file.

easyml

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘corrplot’ ‘scorer’ All declared Imports should be used.

ecoengine

Version: 1.11.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘magrittr’ All declared Imports should be used.

EcoGenetics

Version: 1.2.1-2

checking whether package ‘EcoGenetics’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘EcoGenetics’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/EcoGenetics/new/EcoGenetics.Rcheck/00install.out’ for details.

edge

Version: 2.8.0

checking R code for possible problems ... NOTE ... fitFDist: no visible global function definition for ‘median’ fitFDist: no visible global function definition for ‘lm.fit’ fitFDist: no visible global function definition for ‘predict’ fit_wmodels: no visible global function definition for ‘model.matrix’ fit_wmodels: no visible global function definition for ‘lm.wfit’ null: no visible global function definition for ‘model.matrix’ apply_sva,deSet: no visible global function definition for ‘as.formula’ apply_sva,deSet: no visible global function definition for ‘terms’ fit_models,deSet: no visible global function definition for ‘model.matrix’ fullModel<-,deSet: no visible global function definition for ‘model.matrix’ lrt,deSet-deFit: no visible global function definition for ‘pf’ nullModel<-,deSet: no visible global function definition for ‘model.matrix’ Undefined global functions or variables: as.formula lm.fit lm.wfit median model.matrix pf predict terms Consider adding importFrom("stats", "as.formula", "lm.fit", "lm.wfit", "median", "model.matrix", "pf", "predict", "terms") to your NAMESPACE file.

eechidna

Version: 1.1

checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: data 4.9Mb doc 1.2Mb

eegc

Version: 1.2.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 28-29 (eegc.Rnw) Error: processing vignette 'eegc.Rnw' failed with diagnostics: there is no package called 'BiocStyle' Execution halted
checking installed package size ... NOTE installed size is 11.1Mb sub-directories of 1Mb or more: data 10.5Mb
checking R code for possible problems ... NOTE ... grnPlot: no visible global function definition for ‘title’ grnPlot: no visible global function definition for ‘legend’ markerScatter: no visible global function definition for ‘colorRampPalette’ markerScatter: no visible global function definition for ‘points’ markerScatter: no visible global function definition for ‘lm’ markerScatter: no visible global function definition for ‘abline’ markerScatter: no visible global function definition for ‘text’ markerScatter: no visible global function definition for ‘legend’ Undefined global functions or variables: abline adjustcolor axis colorRampPalette control density dev.copy2pdf legend lines lm model.matrix p.adjust par phyper points quantile results text title treat Consider adding importFrom("grDevices", "adjustcolor", "colorRampPalette", "dev.copy2pdf") importFrom("graphics", "abline", "axis", "legend", "lines", "par", "points", "text", "title") importFrom("stats", "density", "lm", "model.matrix", "p.adjust", "phyper", "quantile") to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocStyle’

eeptools

Version: 1.1.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Loading required package: ggplot2 Quitting from lines 172-181 (intro.Rmd) Error: processing vignette 'intro.Rmd' failed with diagnostics: Package `maps` required for `map_data`. Please install and try again. Execution halted

EFDR

Version: 0.1.1

checking R code for possible problems ... NOTE .gdf : find_loss: no visible global function definition for ‘rnorm’ .p.values : <anonymous>: no visible global function definition for ‘pnorm’ .relist.dwt: no visible global function definition for ‘relist’ .relist.dwt: no visible global function definition for ‘as’ .std.wav.coeff : <anonymous>: no visible global function definition for ‘mad’ regrid: no visible global function definition for ‘predict’ regrid: no visible global function definition for ‘var’ regrid: no visible global function definition for ‘medpolish’ Undefined global functions or variables: as mad medpolish pnorm predict relist rnorm var Consider adding importFrom("methods", "as") importFrom("stats", "mad", "medpolish", "pnorm", "predict", "rnorm", "var") importFrom("utils", "relist") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

EGSEA

Version: 1.4.1

checking R code for possible problems ... NOTE buildGeneSetDBIdx: no visible binding for global variable ‘GOTERM’ buildMSigDBIdx: no visible binding for global variable ‘msigdb’ generateSummaryPlots: no visible binding for global variable ‘x.data’ generateSummaryPlots: no visible binding for global variable ‘y.data’ generateSummaryPlots: no visible binding for global variable ‘gsSize’ generateSummaryPlots: no visible binding for global variable ‘id’ generateSummaryPlots: no visible binding for global variable ‘sig’ loadKeggData: no visible binding for global variable ‘kegg.pathways’ plotBars,EGSEAResults: no visible global function definition for ‘abline’ Undefined global functions or variables: GOTERM abline gsSize id kegg.pathways msigdb sig x.data y.data Consider adding importFrom("graphics", "abline") to your NAMESPACE file.

ELMER

Version: 1.6.0

checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘ELMER.data’ ‘Homo.sapiens’ ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... motif.enrichment.plot: no visible binding for global variable ‘OR’ promoterMeth: no visible global function definition for ‘write.csv’ scatter: no visible binding for global variable ‘value’ schematic: no visible global function definition for ‘pdf’ schematic: no visible global function definition for ‘dev.off’ txs: no visible binding for global variable ‘Homo.sapiens’ show,MEE.data: no visible global function definition for ‘str’ show,Pair: no visible global function definition for ‘str’ summary,MEE.data: no visible global function definition for ‘str’ summary,Pair: no visible global function definition for ‘str’ Undefined global functions or variables: Homo.sapiens IlluminaHumanMethylation450kanno.ilmn12.hg19 OR coef data dev.off label lm lowerOR motif p.adjust pdf pvalue read.csv read.delim read.table str t.test upperOR value wilcox.test write.csv write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("stats", "coef", "lm", "p.adjust", "t.test", "wilcox.test") importFrom("utils", "data", "read.csv", "read.delim", "read.table", "str", "write.csv", "write.table") to your NAMESPACE file.

emdi

Version: 1.1.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘FNN’ ‘ggmap’ ‘simFrame’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 2098 marked UTF-8 strings

EMDomics

Version: 2.6.0

checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Sadhika Malladi <contact@sadhikamalladi.com> [aut, cre] Daniel Schmolze <emd@schmolze.com> [aut, cre]
checking R code for possible problems ... NOTE ... calculate_cvm : <anonymous>: no visible global function definition for ‘median’ calculate_cvm_gene: no visible global function definition for ‘combn’ calculate_emd: no visible global function definition for ‘combn’ calculate_emd : <anonymous>: no visible global function definition for ‘median’ calculate_emd_gene: no visible global function definition for ‘combn’ calculate_ks: no visible global function definition for ‘combn’ calculate_ks : <anonymous>: no visible global function definition for ‘p.adjust’ calculate_ks : <anonymous>: no visible global function definition for ‘median’ calculate_ks_gene: no visible global function definition for ‘combn’ calculate_ks_gene: no visible global function definition for ‘ks.test’ Undefined global functions or variables: combn hist ks.test median p.adjust Consider adding importFrom("graphics", "hist") importFrom("stats", "ks.test", "median", "p.adjust") importFrom("utils", "combn") to your NAMESPACE file.
checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.

emil

Version: 2.2.8

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

emmeans

Version: 0.9.1

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘CARBayes’ ‘coxme’ ‘gee’ ‘geepack’ ‘glmmADMB’ ‘MCMCglmm’ ‘MCMCpack’ ‘pscl’ ‘rstanarm’

emojifont

Version: 0.5.1

checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: emoji_fonts 6.5Mb

enrichwith

Version: 0.1

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘betareg’

EnvStats

Version: 2.3.0

checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: doc 3.3Mb help 3.4Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Hmisc’

episensr

Version: 0.9.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘llogistic’ ‘logitnorm’ All declared Imports should be used.

erccdashboard

Version: 1.10.0

checking R code for possible problems ... NOTE dynRangePlot: no visible binding for global variable ‘value’ dynRangePlot: no visible binding for global variable ‘Rep’ Undefined global functions or variables: Rep value

erma

Version: 0.8.0

checking whether the namespace can be loaded with stated dependencies ... WARNING ``` Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking installed package size ... NOTE installed size is 199.7Mb sub-directories of 1Mb or more: bed_tabix 161.3Mb data 37.1Mb
checking R code for possible problems ... NOTE Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted

esetVis

Version: 1.2.0

checking examples ... ERROR ``` ...
```
expand.grid
```
Loading required package: org.Hs.eg.db

probeIDs <- featureNames(ALL) geneInfo <- select(hgu95av2.db, probeIDs,"ENTREZID", "PROBEID") 'select()' returned 1:many mapping between keys and columns

get pathway annotation for the genes contained in the ALL dataset (can take a few minutes)

geneSets <- getGeneSetsForPlot(entrezIdentifiers = geneInfo$ENTREZID, species = "Human", + geneSetSource = 'GOBP', + useDescription = FALSE, trace = TRUE) Loading required package: GO.db Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘GO.db’ Error in as.list(GOBPANCESTOR) : object 'GOBPANCESTOR' not found Calls: getGeneSetsForPlot ... system.time -> lapply -> FUN -> getGeneSets -> as.list Timing stopped at: 23.12 0.44 32.89 Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ...

'select()' returned 1:many mapping between keys and columns Loading required package: MASS

Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':
```
select
```
Warning: Removed 5 rows containing missing values (geom_point). Warning: Removed 5 rows containing missing values (geom_point). Loading required package: GO.db Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'GO.db' Quitting from lines 382-389 (esetVis-vignette.Rmd) Timing stopped at: 21.73 0.296 32.16 Error: processing vignette 'esetVis-vignette.Rmd' failed with diagnostics: object 'GOBPANCESTOR' not found Execution halted ```
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: doc 5.6Mb
checking R code for possible problems ... NOTE esetPlotWrapper: no visible global function definition for ‘:=’ esetPlotWrapper: no visible binding for global variable ‘fill’ getMethodsInputObjectEsetVis: no visible binding for global variable ‘rowData’ getMethodsInputObjectEsetVis: no visible binding for global variable ‘colData’ getMethodsInputObjectEsetVis: no visible binding for global variable ‘assay’ getMethodsInputObjectEsetVis : <anonymous>: no visible global function definition for ‘colData’ getMethodsInputObjectEsetVis : <anonymous>: no visible global function definition for ‘rowData’ Undefined global functions or variables: := assay colData fill rowData
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘a4Base’

ESGtoolkit

Version: 0.1

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking R code for possible problems ... NOTE ... esgplotts: no visible global function definition for ‘deltat’ esgplotts: no visible global function definition for ‘xlab’ esgplotts: no visible global function definition for ‘ylab’ esgplotts: no visible global function definition for ‘theme’ simdiff: no visible global function definition for ‘ts’ simshocks: no visible global function definition for ‘ts’ simshocks: no visible global function definition for ‘qnorm’ simshocks : <anonymous>: no visible global function definition for ‘ts’ Undefined global functions or variables: abline aes colorRampPalette coord_flip cor cor.test deltat element_blank end geom_density geom_point is.ts lines matplot par plot points polygon pt qnorm qt quantile scale_color_manual scale_fill_manual sd start t.test theme time ts tsp window xlab ylab Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "abline", "lines", "matplot", "par", "plot", "points", "polygon") importFrom("stats", "cor", "cor.test", "deltat", "end", "is.ts", "pt", "qnorm", "qt", "quantile", "sd", "start", "t.test", "time", "ts", "tsp", "window") to your NAMESPACE file.

esmisc

Version: 0.0.3

checking whether package ‘esmisc’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘esmisc’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/esmisc/new/esmisc.Rcheck/00install.out’ for details.

etm

Version: 0.6-2

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... plot.clos.etm: no visible global function definition for ‘plot’ plot.clos.etm: no visible global function definition for ‘axis’ plot.clos.etm: no visible global function definition for ‘box’ plot.clos.etm: no visible global function definition for ‘lines’ plot.clos.etm: no visible global function definition for ‘close.screen’ plot.etm: no visible global function definition for ‘plot’ plot.etm: no visible global function definition for ‘lines’ plot.etmCIF: no visible global function definition for ‘plot’ plot.etmCIF: no visible global function definition for ‘lines’ plot.etmCIF: no visible global function definition for ‘segments’ print.summary.etm: no visible global function definition for ‘quantile’ print.summary.etmCIF: no visible global function definition for ‘quantile’ Undefined global functions or variables: axis box close.screen lines model.extract par plot qnorm quantile screen segments split.screen terms Consider adding importFrom("graphics", "axis", "box", "close.screen", "lines", "par", "plot", "screen", "segments", "split.screen") importFrom("stats", "model.extract", "qnorm", "quantile", "terms") to your NAMESPACE file.

evaluator

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ggalt’ ‘pander’ ‘psych’ All declared Imports should be used. Missing or unexported object: ‘purrr::by_row’

EventStudy

Version: 0.34

checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: doc 5.8Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘curl’ ‘openxlsx’ ‘stringr’ All declared Imports should be used.

evolqg

Version: 0.2-5

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

EWCE

Version: 1.3.0

checking examples ... ERROR ``` ... [1] "" [1] "oligodendrocytes" [1] 0.03 [1] "Fold enrichment: 10.8249226105033" [1] "Standard deviations from mean: 3.71155891479919" [1] "" [1] "pyramidal CA1" [1] 0.13 [1] "" [1] "pyramidal SS" [1] 0.16 [1] "" > > # Bootstrap significance testing controlling for transcript length and GC content > full_results = bootstrap.enrichment.test(sct_data=celltype_data,human.hits=human.hits,
- human.bg=human.bg,reps=reps,sub=subCellStatus,geneSizeControl=TRUE) Error in getBM(attributes = c("transcript_length", "percentage_gc_content", : Invalid attribute(s): percentage_gc_content Please use the function 'listAttributes' to get valid attribute names Calls: bootstrap.enrichment.test -> prepare.genesize.control.network -> getBM Execution halted ```
checking re-building of vignette outputs ... WARNING ... Warning: Removed 199 rows containing non-finite values (stat_boxplot). Warning: The plyr::rename operation has created duplicates for the following name(s): (`colour`) Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 221 rows containing non-finite values (stat_boxplot). Warning: The plyr::rename operation has created duplicates for the following name(s): (`colour`) Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 221 rows containing non-finite values (stat_boxplot). Warning: The plyr::rename operation has created duplicates for the following name(s): (`colour`) Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 221 rows containing non-finite values (stat_boxplot). Warning: The plyr::rename operation has created duplicates for the following name(s): (`colour`) Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 413 rows containing non-finite values (stat_boxplot). Warning: The plyr::rename operation has created duplicates for the following name(s): (`colour`) Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 335 rows containing non-finite values (stat_boxplot). Quitting from lines 238-242 (EWCE.Rmd) Error: processing vignette 'EWCE.Rmd' failed with diagnostics: Invalid attribute(s): percentage_gc_content Please use the function 'listAttributes' to get valid attribute names Execution halted
checking R code for possible problems ... NOTE ... ‘pdf’ generate.bootstrap.plots: no visible global function definition for ‘dev.off’ merged_ewce: no visible global function definition for ‘sd’ prepare.genesize.control.network: no visible global function definition for ‘aggregate’ prepare.genesize.control.network: no visible global function definition for ‘data’ prepare.genesize.control.network: no visible global function definition for ‘quantile’ read_celltype_data: no visible global function definition for ‘read.csv’ read_celltype_data: no visible global function definition for ‘aggregate’ Undefined global functions or variables: aggregate data dev.off p.adjust pdf quantile read.csv sd Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("stats", "aggregate", "p.adjust", "quantile", "sd") importFrom("utils", "data", "read.csv") to your NAMESPACE file.

ExtDist

Version: 0.6-3

checking R code for possible problems ... NOTE ... rBeta: no visible global function definition for ‘rbeta’ rBeta_ab: no visible global function definition for ‘rbeta’ rLaplace: no visible global function definition for ‘runif’ rLogistic: no visible global function definition for ‘rlogis’ rNormal: no visible global function definition for ‘rnorm’ rSSRTB: no visible global function definition for ‘runif’ rUniform: no visible global function definition for ‘runif’ vcov.eDist: no visible global function definition for ‘cov2cor’ wmle: no visible global function definition for ‘coef’ Undefined global functions or variables: abline capture.output coef cov2cor curve dbeta dlogis dnorm dunif getS3method hist median par pbeta plogis plot pnorm punif qbeta qlogis qnorm qunif rbeta rlogis rnorm runif sd uniroot var Consider adding importFrom("graphics", "abline", "curve", "hist", "par", "plot") importFrom("stats", "coef", "cov2cor", "dbeta", "dlogis", "dnorm", "dunif", "median", "pbeta", "plogis", "pnorm", "punif", "qbeta", "qlogis", "qnorm", "qunif", "rbeta", "rlogis", "rnorm", "runif", "sd", "uniroot", "var") importFrom("utils", "capture.output", "getS3method") to your NAMESPACE file.

eyetrackingR

Version: 0.1.6

checking examples ... ERROR ``` ...
- time_column = "TimeFromTrialOnset",
- trackloss_column = "TrackLoss",
- aoi_columns = c('Animate','Inanimate'),
- treat_non_aoi_looks_as_missing = TRUE ) mutate_each() is deprecated. Use mutate_all(), mutate_at() or mutate_if() instead. To map funs over a selection of variables, use mutate_at()
  
  response_window <- subset_by_window(data, window_start_time = 15500, window_end_time = 21000,
- rezero = FALSE) Avg. window length in new data will be 5500
  
  response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate",
- predictor_columns = "Sex")
  
  time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM",
- aoi = "Animate", test = "lmer",
- threshold = 1.5,
- formula = LogitAdjusted ~ Sex + (1|Trial) + (1|ParticipantName)) Error in UseMethod("analyze_time_bins") : no applicable method for 'analyze_time_bins' applied to an object of class "data.frame" Calls: make_time_cluster_data ... make_time_cluster_data.time_sequence_data -> do.call -> Execution halted ```
checking tests ... ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Computing t.test for each time bin... Computing t.test for each time bin... `mutate_each()` is deprecated. Use `mutate_all()`, `mutate_at()` or `mutate_if()` instead. To map `funs` over a selection of variables, use `mutate_at()` Avg. window length in new data will be 5500 Performing Trackloss Analysis... Will exclude trials whose trackloss proportion is greater than : 0.25 ...removed 33 trials. Error in UseMethod("make_time_cluster_data") : no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame" Calls: test_check ... source_file -> eval -> eval -> make_time_cluster_data testthat results ================================================================ OK: 38 SKIPPED: 0 FAILED: 0 Execution halted

ezsim

Version: 0.5.5

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. BugReports field is not a suitable URL but contains an email address which will be used as from R 3.4.0
checking R code for possible problems ... NOTE ... plot.ezsim: no visible global function definition for ‘tail’ plot.ezsim: no visible global function definition for ‘plot’ plot.ezsim: no visible binding for global variable ‘dnorm’ plot.ezsim: no visible binding for global variable ‘pdf’ plot.ezsim: no visible global function definition for ‘dev.off’ plot.ezsim : <anonymous>: no visible global function definition for ‘dev.new’ plot.summary.ezsim: no visible global function definition for ‘head’ plot.summary.ezsim: no visible global function definition for ‘tail’ plot.summary.ezsim: no visible binding for global variable ‘pdf’ plot.summary.ezsim: no visible global function definition for ‘dev.off’ plot.summary.ezsim : <anonymous>: no visible global function definition for ‘dev.new’ Undefined global functions or variables: as.formula dev.new dev.off dnorm head pdf plot quantile runif tail Consider adding importFrom("grDevices", "dev.new", "dev.off", "pdf") importFrom("graphics", "plot") importFrom("stats", "as.formula", "dnorm", "quantile", "runif") importFrom("utils", "head", "tail") to your NAMESPACE file.

facopy

Version: 1.10.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘cgdsr’ ‘coin’ ‘ggplot2’ ‘gridExtra’ ‘facopy.annot’ ‘grid’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘grid’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... variableSummary: no visible global function definition for ‘write.table’ Undefined global functions or variables: abline anova axis binomial chisq.test colorRampPalette combn cor.test data dev.off fisher.test formula glm grid heat.colors image kruskal.test layout legend lm mtext oneway.test p.adjust par pdf phyper plot.new plot.window points quantile read.delim read.table rect title wilcox.test write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "heat.colors", "pdf") importFrom("graphics", "abline", "axis", "grid", "image", "layout", "legend", "mtext", "par", "plot.new", "plot.window", "points", "rect", "title") importFrom("stats", "anova", "binomial", "chisq.test", "cor.test", "fisher.test", "formula", "glm", "kruskal.test", "lm", "oneway.test", "p.adjust", "phyper", "quantile", "wilcox.test") importFrom("utils", "combn", "data", "read.delim", "read.table", "write.table") to your NAMESPACE file.

factoextra

Version: 1.0.5

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘NbClust’

FAOSTAT

Version: 2.0

checking R code for possible problems ... NOTE ... Aggregation : foo: no visible global function definition for ‘weighted.mean’ Aggregation: no visible global function definition for ‘txtProgressBar’ Aggregation: no visible global function definition for ‘setTxtProgressBar’ constructSYB: no visible global function definition for ‘str’ fillCountryCode: no visible global function definition for ‘na.omit’ getFAO: no visible global function definition for ‘read.csv’ getWDImetaData: no visible global function definition for ‘write.csv’ getWDItoSYB: no visible global function definition for ‘na.omit’ lsgr: no visible global function definition for ‘na.omit’ lsgr: no visible global function definition for ‘coef’ lsgr: no visible global function definition for ‘lm’ Undefined global functions or variables: coef lm na.omit read.csv setTxtProgressBar str txtProgressBar weighted.mean write.csv Consider adding importFrom("stats", "coef", "lm", "na.omit", "weighted.mean") importFrom("utils", "read.csv", "setTxtProgressBar", "str", "txtProgressBar", "write.csv") to your NAMESPACE file.
checking data for non-ASCII characters ... NOTE Note: found 179 marked UTF-8 strings

fastR2

Version: 0.2.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘magrittr’ All declared Imports should be used.

fCCAC

Version: 1.2.0

checking R code for possible problems ... NOTE fccac: no visible binding for global variable ‘variables’ Undefined global functions or variables: variables

fdq

Version: 0.2

checking whether package ‘fdq’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/fdq/new/fdq.Rcheck/00install.out’ for details.

FField

Version: 0.1.0

checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘ggplot2’ ‘gridExtra’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE FFieldPtRepDemo: no visible global function definition for ‘ggplot’ FFieldPtRepDemo: no visible binding for global variable ‘mtcars’ FFieldPtRepDemo: no visible global function definition for ‘aes’ FFieldPtRepDemo: no visible binding for global variable ‘mpg’ FFieldPtRepDemo: no visible global function definition for ‘geom_point’ FFieldPtRepDemo: no visible global function definition for ‘geom_text’ FFieldPtRepDemo: no visible global function definition for ‘ggtitle’ FFieldPtRepDemo: no visible global function definition for ‘geom_segment’ FFieldPtRepDemo: no visible global function definition for ‘grid.arrange’ Undefined global functions or variables: aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg mtcars Consider adding importFrom("datasets", "mtcars") to your NAMESPACE file.

Fgmutils

Version: 0.9.4

checking whether package ‘Fgmutils’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/Fgmutils/new/Fgmutils.Rcheck/00install.out’ for details.

fgsea

Version: 1.2.1

checking R code for possible problems ... NOTE gmtPathways: no visible binding for global variable ‘head’ Undefined global functions or variables: head Consider adding importFrom("utils", "head") to your NAMESPACE file.

FindMyFriends

Version: 1.6.0

checking re-building of vignette outputs ... WARNING ... Found more than one class "file" in cache; using the first, from namespace 'BiocGenerics' Also defined by 'filehash' Preclustering resulted in 3326 gene groups (1.119 seconds elapsed) Grouping resulted in 3138 gene groups (10.986 seconds elapsed) Total time elapsed was 12.113 seconds Presplitting resulted in 3160 gene groups (0.046 seconds elapsed) Adding missing grouping variables: `org`, `contig` Splitting resulted in 3603 gene groups (5 minutes and 23.61 seconds elapsed) Adding missing grouping variables: `org`, `contig` Adding missing grouping variables: `org`, `contig` Adding missing grouping variables: `org`, `contig` Adding missing grouping variables: `org`, `contig` Adding missing grouping variables: `org`, `contig` Adding missing grouping variables: `org`, `contig` Adding missing grouping variables: `org`, `contig` Adding missing grouping variables: `org`, `contig` Merging resulted in 3399 gene groups (6.665 seconds elapsed) Total time elapsed was 5 minutes and 30.321 seconds Error: processing vignette 'FindMyFriends_intro.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: extdata 1.8Mb libs 5.6Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘gtable:::insert.unit’ ‘gtable:::z_arrange_gtables’ See the note in ?`:::` about the use of this operator.

fishmove

Version: 0.3-3

checking R code for possible problems ... NOTE fishmove : coefs: no visible global function definition for ‘coef’ fishmove : coefs: no visible global function definition for ‘pf’ fishmove: no visible global function definition for ‘lm’ fishmove: no visible global function definition for ‘predict.lm’ fishmove.estimate: no visible global function definition for ‘quantile’ fishmove.estimate : ddoublenorm: no visible global function definition for ‘dnorm’ fishmove.query: no visible global function definition for ‘hasArg’ fishmove.query : f: no visible global function definition for ‘pnorm’ fishmove.query: no visible global function definition for ‘uniroot’ pdk: no visible global function definition for ‘hasArg’ pdk : eq: no visible global function definition for ‘dnorm’ Undefined global functions or variables: coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot Consider adding importFrom("methods", "hasArg") importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm", "quantile", "uniroot") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

fitbitScraper

Version: 0.1.8

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 22-24 (fitbitScraper-examples.Rmd) Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics: login failed Execution halted

fitdistrplus

Version: 1.0-9

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Hmisc’

FLightR

Version: 0.4.6

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rgdal’ All declared Imports should be used.

flowCHIC

Version: 1.10.0

checking package dependencies ... ERROR ``` Package required but not available: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

fontHind

Version: 0.1.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

fontMPlus

Version: 0.1.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

forecast

Version: 8.2

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: libs 4.3Mb
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘seasonal’, ‘forecTheta’

FourCSeq

Version: 1.10.0

checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘DESeq2’ ‘GenomicRanges’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE Packages in Depends field not imported from: 'ggplot2' 'methods' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... 'keepSeqlevels' updateObject,FourC: no visible global function definition for 'callNextMethod' Undefined global functions or variables: DataFrame IRanges Rle Seqinfo SimpleList abline aes axis blues9 callNextMethod change count differentialInteraction element_blank fit fitDown fitUp formula geom_path geom_point ggplot keepSeqlevels labs legend mad median metadata mid mtext new p.adjust par peak plot pnorm points predict rel relevel scale_fill_gradient2 scale_y_continuous seqlengths seqlevels seqlevels<- subjectHits subsetByOverlaps theme theme_bw theme_set write.table Consider adding importFrom("grDevices", "blues9") importFrom("graphics", "abline", "axis", "legend", "mtext", "par", "plot", "points") importFrom("methods", "callNextMethod", "new") importFrom("stats", "formula", "mad", "median", "p.adjust", "pnorm", "predict", "relevel") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

fourierin

Version: 0.2.2

checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: libs 4.5Mb

fpp2

Version: 2.1

checking whether package ‘fpp2’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘forecast::autolayer’ by ‘ggplot2::autolayer’ when loading ‘fpp2’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/fpp2/new/fpp2.Rcheck/00install.out’ for details.

freqweights

Version: 1.0.4

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘Hmisc’

FRK

Version: 0.1.6

checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘INLA’

Package which this enhances but not available for checking: ‘dggrids’ ```
checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: data 4.8Mb doc 1.6Mb

frontiles

Version: 1.2

checking R code for possible problems ... NOTE ... alphafrontier.2d: no visible global function definition for ‘par’ alphafrontier.2d: no visible global function definition for ‘polygon’ alphafrontier.2d: no visible global function definition for ‘lines’ alphafrontier.2d: no visible global function definition for ‘points’ alphafrontier.3d: no visible global function definition for ‘layout’ alphafrontier.3d: no visible global function definition for ‘barplot’ alphafrontier.3d: no visible global function definition for ‘axis’ alphafrontier.3d: no visible global function definition for ‘lines’ alphafrontier.3d: no visible global function definition for ‘na.omit’ ordermfrontier.2d: no visible global function definition for ‘par’ ordermfrontier.2d: no visible global function definition for ‘polygon’ ordermfrontier.2d: no visible global function definition for ‘lines’ ordermfrontier.2d: no visible global function definition for ‘points’ ordermscore.boot: no visible global function definition for ‘sd’ Undefined global functions or variables: axis barplot layout legend lines mtext na.omit par points polygon sd Consider adding importFrom("graphics", "axis", "barplot", "layout", "legend", "lines", "mtext", "par", "points", "polygon") importFrom("stats", "na.omit", "sd") to your NAMESPACE file.

FSelectorRcpp

Version: 0.1.8

checking installed package size ... NOTE installed size is 11.1Mb sub-directories of 1Mb or more: doc 2.2Mb libs 8.7Mb

fSRM

Version: 0.6.4

checking whether package ‘fSRM’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/fSRM/new/fSRM.Rcheck/00install.out’ for details.

FunciSNP

Version: 1.20.0

checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘ggplot2’ A package should be listed in only one of these fields.
checking R code for possible problems ... NOTE ... bedColors: no visible global function definition for 'col2rgb' bedColors: no visible global function definition for 'png' bedColors: no visible global function definition for 'box' bedColors: no visible global function definition for 'par' bedColors: no visible global function definition for 'axis' bedColors: no visible global function definition for 'dev.off' Undefined global functions or variables: R.squared TSS.human.GRCh37 abline as.dendrogram axis box col2rgb colorRampPalette data dev.off dist distance.from.tag fisher.test hclust lincRNA order.dendrogram p.adjust par pdf plot png r.2 read.delim read.table refseqgenes sig text timestamp value variable write.table Consider adding importFrom("grDevices", "col2rgb", "colorRampPalette", "dev.off", "pdf", "png") importFrom("graphics", "abline", "axis", "box", "par", "plot", "text") importFrom("stats", "as.dendrogram", "dist", "fisher.test", "hclust", "order.dendrogram", "p.adjust") importFrom("utils", "data", "read.delim", "read.table", "timestamp", "write.table") to your NAMESPACE file.

furrowSeg

Version: 1.4.0

checking package dependencies ... ERROR ``` Package required but not available: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

fuser

Version: 1.0.0

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: libs 5.0Mb

GADMTools

Version: 2.1-1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘scales’ All declared Imports should be used.

gaiah

Version: 0.0.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’ All declared Imports should be used.

gapfill

Version: 0.9.5-3

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘raster’ ‘doParallel’ ‘doMPI’

gastempt

Version: 0.4.01

checking installed package size ... NOTE installed size is 58.6Mb sub-directories of 1Mb or more: libs 58.2Mb

gcatest

Version: 1.6.1

checking R code for possible problems ... NOTE gcat: no visible global function definition for ‘pchisq’ gcat.stat: no visible global function definition for ‘complete.cases’ gcatest: no visible global function definition for ‘pchisq’ Undefined global functions or variables: complete.cases pchisq Consider adding importFrom("stats", "complete.cases", "pchisq") to your NAMESPACE file.

gCrisprTools

Version: 1.4.0

checking installed package size ... NOTE installed size is 9.2Mb sub-directories of 1Mb or more: data 2.3Mb doc 1.1Mb

GDINA

Version: 1.4.2

checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: libs 5.7Mb

GEM

Version: 1.2.0

checking whether package ‘GEM’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/GEM/new/GEM.Rcheck/00install.out’ for details.

gender

Version: 0.5.1

checking package dependencies ... NOTE Package suggested but not available for checking: ‘genderdata’

GeneralizedUmatrix

Version: 0.9.5

checking package dependencies ... NOTE Package suggested but not available for checking: ‘ProjectionBasedClustering’

GenoGAM

Version: 1.4.0

checking R code for possible problems ... NOTE ... plot_base: no visible global function definition for ‘lines’ plot_base: no visible global function definition for ‘abline’ plot_base: no visible global function definition for ‘mtext’ writeToBroadPeaks: no visible global function definition for ‘write.table’ writeToNarrowPeaks: no visible global function definition for ‘write.table’ xsd : <anonymous>: no visible binding for global variable ‘position’ xsd: no visible binding for global variable ‘position’ Undefined global functions or variables: abline as.formula axis coefficients dev.off dnbinom estimate fdr fit gene hist id lines mtext optim p.adjust par plot png pnorm position pval pvalue region runif write.table zscore Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "abline", "axis", "hist", "lines", "mtext", "par", "plot") importFrom("stats", "as.formula", "coefficients", "dnbinom", "optim", "p.adjust", "pnorm", "runif") importFrom("utils", "write.table") to your NAMESPACE file.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'plot.GenoGAM': ‘plot.GenoGAM’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

genomation

Version: 1.8.0

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 3.6Mb extdata 1.2Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘RUnit’ All declared Imports should be used. Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’ See the note in ?`:::` about the use of this operator.
checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘cache’ Please remove from your package.

GenomicDataCommons

Version: 1.0.5

checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... Loading required package: magrittr

Attaching package: 'GenomicDataCommons'

The following object is masked from 'package:stats':
```
filter
```
sh: 1: gdc-client: not found Error: processing vignette 'overview.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE default_fields.character: no visible binding for global variable ‘defaults’ Undefined global functions or variables: defaults
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'as.data.frame.GDCResults': ‘as.data.frame.GDCResults’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

GenomicInteractions

Version: 1.10.0

checking installed package size ... NOTE installed size is 11.0Mb sub-directories of 1Mb or more: doc 2.0Mb extdata 7.9Mb

genotypeeval

Version: 1.8.0

checking for missing documentation entries ... WARNING Undocumented code objects: ‘makeHistogram’ ‘pcaPlot’ ‘tsnePlot’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.

genphen

Version: 1.4.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘randomForest’ ‘e1071’ ‘ggplot2’ ‘effsize’ ‘Biostrings’ ‘rjags’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking R code for possible problems ... NOTE ... getBayesianTtest : getDataList: no visible global function definition for ‘sd’ getBayesianTtest : getEss: no visible global function definition for ‘effectiveSize’ getBayesianTtest: no visible global function definition for ‘update’ getTTestScore: no visible global function definition for ‘t.test’ plotGenphenBayes: no visible binding for global variable ‘g.1’ plotGenphenBayes: no visible binding for global variable ‘site’ plotGenphenBayes: no visible binding for global variable ‘g.2’ plotGenphenRfSvm: no visible binding for global variable ‘ca.hdi.H’ plotGenphenRfSvm: no visible binding for global variable ‘ca.hdi.L’ plotGenphenRfSvm: no visible global function definition for ‘terrain.colors’ plotManhattan: no visible binding for global variable ‘t.test.pvalue’ Undefined global functions or variables: ca.hdi.H ca.hdi.L effectiveSize g.1 g.2 sd site t.test t.test.pvalue terrain.colors update Consider adding importFrom("grDevices", "terrain.colors") importFrom("stats", "sd", "t.test", "update") to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE `` ... Loaded modules: basemod,bugs Warning: Ignoring unknown aesthetics: x Warning: Ignoring unknown aesthetics: x Warning: Ignoring unknown aesthetics: x Warning: Ignoring unknown aesthetics: fill Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'genphenManual.tex' failed. LaTeX errors: ! LaTeX Error: Filealgorithm2e.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.7 ^^M

! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

GenVisR

Version: 1.6.3

checking re-building of vignette outputs ... WARNING ``` ...

Obtaining CDS Coordinates 'select()' returned 1:many mapping between keys and columns Obtaining UTR Coordinates 'select()' returned 1:many mapping between keys and columns Calculating transform Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Error: processing vignette 'GenVisR_intro.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE waterfall: warning in waterfall_align(genes = gene_plot, heatmap = heatmap, burden = burden_plot, clinical = clinical_plot, proportion = proportions_plot, section_heights = section_heights): partial argument match of 'proportion' to 'proportions' waterfall: warning in waterfall_align(genes = gene_plot, heatmap = heatmap, burden = burden_plot, proportion = proportions_plot, section_heights = section_heights): partial argument match of 'proportion' to 'proportions'

geofacet

Version: 0.1.5

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ~^~ tests/testthat/test-utilities.r:42:1: style: lines should not be more than 80 characters. expect_true(all(c("arg1", "arg2", "arg3") %in% names(test_fun(arg1 = 1, arg2 = 1, arg3 = 1)))) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ tests/testthat/test-viridis.R:16:1: style: Trailing whitespace is superfluous.

^~

testthat results ================================================================ OK: 14 SKIPPED: 0 FAILED: 1 1. Failure: package Style (@test-zzz-lintr.R#5)

Error: testthat unit tests failed Execution halted ```
checking data for non-ASCII characters ... NOTE Note: found 79 marked UTF-8 strings

geoknife

Version: 1.5.5

checking tests ... ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 27: eval(exprs, env) 28: source_file(path, new.env(parent = env), chdir = TRUE) 29: force(code) 30: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE) end_context() }) 31: FUN(X[[i]], ...) 32: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE) 33: force(code) 34: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE)) 35: test_files(paths, reporter = reporter, env = env, ...) 36: test_dir(test_path, reporter = reporter, env = env, filter = filter, ...) 37: with_top_env(env, { test_dir(test_path, reporter = reporter, env = env, filter = filter, ...)}) 38: run_tests(package, test_path, filter, reporter, ...) 39: test_check("geoknife") An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped)
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 360-364 (geoknife.Rmd) Error: processing vignette 'geoknife.Rmd' failed with diagnostics: need finite 'xlim' values Execution halted

GeomComb

Version: 1.0

checking whether package ‘GeomComb’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘forecast::autolayer’ by ‘ggplot2::autolayer’ when loading ‘GeomComb’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/GeomComb/new/GeomComb.Rcheck/00install.out’ for details.

geotoolsR

Version: 1.0

checking whether package ‘geotoolsR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/geotoolsR/new/geotoolsR.Rcheck/00install.out’ for details.

GERGM

Version: 0.11.2

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: libs 4.2Mb

GerminaR

Version: 1.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DT’ ‘shinydashboard’ All declared Imports should be used.

gespeR

Version: 1.8.0

checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'c,Phenotypes-method': \S4method{c}{Phenotypes} Code: function(x, ...) Docs: function(x, ..., recursive = FALSE) Argument names in docs not in code: recursive
checking R code for possible problems ... NOTE .gespeR.cv: no visible global function definition for ‘coef’ .select.model: no visible global function definition for ‘predict’ concordance: no visible global function definition for ‘cor’ lasso.rand: no visible global function definition for ‘runif’ plot.gespeR: no visible global function definition for ‘hist’ stability.selection: no visible global function definition for ‘lm’ Phenotypes,character: no visible global function definition for ‘read.delim’ Undefined global functions or variables: coef cor hist lm predict read.delim runif Consider adding importFrom("graphics", "hist") importFrom("stats", "coef", "cor", "lm", "predict", "runif") importFrom("utils", "read.delim") to your NAMESPACE file.

GetLattesData

Version: 0.8

checking examples ... ERROR ``` Running examples in ‘GetLattesData-Ex.R’ failed The error most likely occurred in:

Name: gld_get_lattes_data

Title: Downloads and reads Lattes data based on a vector of Lattes ids

Aliases: gld_get_lattes_data

** Examples

l.out <- gld_get_lattes_data(id.vec = 'K4713546D3', + field.qualis = 'ECONOMIA')

Downloading file /home/muelleki/tmp/RtmpglWMNF/K4713546D3_2017-11-20.zipWarning in utils::download.file(url = my.link, destfile = dest.file, quiet = T, : unable to resolve 'buscacv.cnpq.br' Error in utils::download.file(url = my.link, destfile = dest.file, quiet = T, : cannot open URL 'http://buscacv.cnpq.br/buscacv/rest/download/curriculo/K4713546D3' Calls: gld_get_lattes_data -> sapply -> lapply -> FUN -> Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4: identical(as.vector(object), TRUE) 5: as.vector(object) 6: gld_get_lattes_data("K4713546D3", folder.dl = "lattes files") 7: sapply(X = id.vec, FUN = gld_download_lattes_files, folder.dl = folder.dl) 8: lapply(X = X, FUN = FUN, ...) 9: FUN(X[[i]], ...) 10: utils::download.file(url = my.link, destfile = dest.file, quiet = T, mode = "wb", method = "internal")

testthat results ================================================================ OK: 1 SKIPPED: 0 FAILED: 1 1. Error: Test of main function (@test_gld.R#5)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 36-45 (gld_vignette-ReadLattes.Rmd) Error: processing vignette 'gld_vignette-ReadLattes.Rmd' failed with diagnostics: cannot open URL 'http://buscacv.cnpq.br/buscacv/rest/download/curriculo/K4713546D3' Execution halted

gettingtothebottom

Version: 3.2

checking R code for possible problems ... NOTE example.alpha: no visible global function definition for ‘rnorm’ example.quadratic.approx: no visible global function definition for ‘rnorm’ generate_nnm: no visible global function definition for ‘rnorm’ generate_nnm: no visible global function definition for ‘rgamma’ generate_nnm: no visible global function definition for ‘dnorm’ plot_nnm: no visible global function definition for ‘stack’ testmatrix: no visible global function definition for ‘rnorm’ Undefined global functions or variables: dnorm rgamma rnorm stack Consider adding importFrom("stats", "dnorm", "rgamma", "rnorm") importFrom("utils", "stack") to your NAMESPACE file.

gfer

Version: 0.1.9

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tidyr’ All declared Imports should be used.

GGally

Version: 1.3.2

checking examples ... ERROR ``` ... No edge attributes > > ggnet(n, label = TRUE, alpha = 1, color = "white", segment.color = "black") Loading required package: sna Loading required package: statnet.common

Attaching package: ‘statnet.common’

The following object is masked from ‘package:base’:
```
order
```
sna: Tools for Social Network Analysis Version 2.4 created on 2016-07-23. copyright (c) 2005, Carter T. Butts, University of California-Irvine For citation information, type citation("sna"). Type help(package="sna") to get started.

Loading required package: scales Error: Columns x, y, xend, yend must be 1d atomic vectors or lists Execution halted ```

ggalt

Version: 0.4.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘plotly’ All declared Imports should be used.

ggbio

Version: 1.24.1

checking examples ... ERROR ... > data(genesymbol, package = "biovizBase") > txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene > > > ################################################### > ### code chunk number 27: txdb-visual > ################################################### > p1 <- autoplot(txdb, which = genesymbol["ALDOA"], names.expr = "tx_name:::gene_id") Parsing transcripts... Parsing exons... Parsing cds... Parsing utrs... ------exons... ------cdss... ------introns... ------utr... aggregating... Done Constructing graphics... Error: Don't know how to add o to a plot Execution halted
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion' 'ggplot2:::rename_aes' 'ggplot2:::rescale01' 'ggplot2:::set_last_plot' See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... layout_karyogram,GRanges: no visible binding for global variable 'yend2' layout_karyogram,GRanges : <anonymous>: no visible binding for global variable 'name' layout_karyogram,GRanges : <anonymous>: no visible binding for global variable 'gieStain' plotFragLength,character-GRanges: no visible binding for global variable '.fragLength' plotSpliceSum,character-EnsDb: possible error in GRangesFilter(which, condition = "overlapping"): unused argument (condition = "overlapping") stat_mismatch,GRanges: no visible binding for global variable 'sts' stat_mismatch,GRanges: no visible binding for global variable 'eds' stat_mismatch,GRanges: no visible binding for global variable 'read' Undefined global functions or variables: .fragLength .layout_circle.stats .x breaks coefs cytobands data eds fe fl gieStain ideoCyto indexProbesProcessed midpoint mt name read se stepping sts value variable x xend y y.text y2 yend yend2 Consider adding importFrom("utils", "data") to your NAMESPACE file.

ggCompNet

Version: 0.1.0

checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Quitting from lines 79-98 (examples-from-paper.Rmd) Error: processing vignette 'examples-from-paper.Rmd' failed with diagnostics: Columns x, y, xend, yend must be 1d atomic vectors or lists Execution halted ```

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: doc 6.1Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dplyr’ ‘ggmap’ ‘gridExtra’ ‘scales’ ‘tnet’ All declared Imports should be used.

ggconf

Version: 0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tibble’ All declared Imports should be used.

ggcyto

Version: 1.4.1

checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: doc 5.8Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘scales’ All declared Imports should be used. Unexported objects imported by ':::' calls: ‘flowWorkspace:::.mergeGates’ ‘flowWorkspace:::compact’ ‘flowWorkspace:::fix_y_axis’ ‘ggplot2:::+.gg’ ‘ggplot2:::add_group’ ‘ggplot2:::check_aesthetics’ ‘ggplot2:::ggplot.data.frame’ ‘ggplot2:::is.waive’ ‘ggplot2:::is_calculated_aes’ ‘ggplot2:::make_scale’ ‘ggplot2:::plot_clone’ ‘ggplot2:::print.ggplot’ ‘ggplot2:::scales_add_defaults’ ‘ggplot2:::update_theme’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... fortify_fs.GatingSetList: no visible global function definition for ‘getS3method’ getFlowFrame.GatingSetList: no visible global function definition for ‘getS3method’ getFlowFrame.ncdfFlowList: no visible global function definition for ‘getS3method’ ggcyto.GatingSetList: no visible global function definition for ‘getS3method’ ggcyto.flowSet: no visible binding for global variable ‘name’ ggcyto.flowSet: no visible binding for global variable ‘axis’ ggcyto.ncdfFlowList: no visible global function definition for ‘getS3method’ ggcyto_arrange: no visible binding for global variable ‘name’ Undefined global functions or variables: approx axis density desc dist getS3method gray modifyList name Consider adding importFrom("grDevices", "gray") importFrom("graphics", "axis") importFrom("stats", "approx", "density", "dist") importFrom("utils", "getS3method", "modifyList") to your NAMESPACE file.

ggdmc

Version: 0.1.3.9

checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: libs 8.9Mb

GGEBiplots

Version: 0.1.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘GGEBiplotGUI’ ‘gge’ ‘utils’ All declared Imports should be used.

ggenealogy

Version: 0.3.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tibble’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 2356 marked UTF-8 strings

ggExtra

Version: 0.7

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘grDevices’ All declared Imports should be used.

ggfan

Version: 0.1.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 59-62 (geom_fan.Rmd) Error: processing vignette 'geom_fan.Rmd' failed with diagnostics: replacement has 0 rows, data has 1 Execution halted

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘colorspace’ ‘grid’ All declared Imports should be used.

ggforce

Version: 0.1.1

checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'geom_link': geom_link0 Code: function(mapping = NULL, data = NULL, stat = "identity", position = "identity", ..., arrow = NULL, lineend = "butt", linejoin = "round", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) Docs: function(mapping = NULL, data = NULL, stat = "identity", position = "identity", ..., arrow = NULL, lineend = "butt", na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) Argument names in code not in docs: linejoin Mismatches in argument names: Position: 8 Code: linejoin Docs: na.rm Position: 9 Code: na.rm Docs: show.legend Position: 10 Code: show.legend Docs: inherit.aes

ggformula

Version: 0.6

checking examples ... ERROR ``` Running examples in ‘ggformula-Ex.R’ failed The error most likely occurred in:

Name: gf_dist

Title: Plot distributions

Aliases: gf_dist

** Examples

gf_histogram( ..density.. ~ rnorm(100), bins = 20) %>% + gf_dist("norm", color = "red")

gf_dist(dist = "norm", color = "red") Error: Cannot add ggproto objects together. Did you forget to add this object to a ggplot object? Execution halted ```

ggfortify

Version: 0.4.1

checking examples ... ERROR ``` Running examples in ‘ggfortify-Ex.R’ failed The error most likely occurred in:

Name: gglagplot

Title: Plot time series against lagged versions of themselves

Aliases: gglagplot

** Examples

gglagplot(AirPassengers) Error: x must be a vector, not a ts object, do you want stats::lag()? Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:

^~

testthat results ================================================================ OK: 1616 SKIPPED: 0 FAILED: 6 1. Failure: autoplot.aareg works for lung (@test-surv.R#220) 2. Failure: autoplot.aareg works for lung (@test-surv.R#221) 3. Failure: autoplot.aareg works for lung (@test-surv.R#222) 4. Failure: autoplot.aareg works for lung (@test-surv.R#223) 5. Error: gglagplot (@test-tslib.R#103) 6. Failure: Code Lint (@test_lint.R#27)

Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: doc 5.0Mb

ggguitar

Version: 0.1.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘gridExtra’ ‘lazyeval’ ‘readr’ All declared Imports should be used.

ggimage

Version: 0.0.7

checking package dependencies ... ERROR ``` Package required but not available: ‘magick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

ggiraphExtra

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘XML’ ‘mapproj’ ‘moonBook’ All declared Imports should be used.

gglogo

Version: 0.1.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘knitr’ All declared Imports should be used.

ggmap

Version: 2.6.1

checking examples ... ERROR ``` ... Running examples in ‘ggmap-Ex.R’ failed The error most likely occurred in:

Name: theme_nothing

Title: Make a blank ggplot2 theme.

Aliases: theme_nothing

** Examples

no legend example

n <- 50 df <- expand.grid(x = 1:n,y = 1:n)[sample(n^2,.5*n^2),] p <- qplot(x, y, data = df, geom = 'tile') p p + theme_nothing() Warning: panel.margin is deprecated. Please use panel.spacing property instead Error in if (theme$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```

ggmosaic

Version: 0.1.2

checking examples ... ERROR ``` Running examples in ‘ggmosaic-Ex.R’ failed The error most likely occurred in:

Name: geom_mosaic

Title: Mosaic plots.

Aliases: geom_mosaic stat_mosaic

** Examples

data(Titanic) titanic <- as.data.frame(Titanic) titanic$Survived <- factor(titanic$Survived, levels=c("Yes", "No"))

ggplot(data=titanic) + + geom_mosaic(aes(weight=Freq, x=product(Class), fill=Survived)) Error in is.finite(x) : default method not implemented for type 'list' Calls: ... lapply -> FUN -> -> f -> lapply -> FUN -> f Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Attaching package: 'dplyr'

The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':
```
combine
```
Quitting from lines 171-175 (ggmosaic.Rmd) Error: processing vignette 'ggmosaic.Rmd' failed with diagnostics: default method not implemented for type 'list' Execution halted ```
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'scale_type.product': ‘scale_type.product’

S3 methods shown with full name in documentation object 'scale_type.productlist': ‘scale_type.productlist’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘NHANES’ ‘gridExtra’ All declared Imports should be used.

ggnetwork

Version: 0.5.1

checking examples ... ERROR ``` ... Skye Bender-deMoll, University of Washington For citation information, type citation("network"). Type help("network-package") to get started.

Loading required package: sna Loading required package: statnet.common

Attaching package: ‘statnet.common’

The following object is masked from ‘package:base’:
```
order
```
sna: Tools for Social Network Analysis Version 2.4 created on 2016-07-23. copyright (c) 2005, Carter T. Butts, University of California-Irvine For citation information, type citation("sna"). Type help(package="sna") to get started.

Error: Columns x, y, xend, yend must be 1d atomic vectors or lists Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... For citation information, type citation("network"). Type help("network-package") to get started.

Loading required package: statnet.common

Attaching package: 'statnet.common'

The following object is masked from 'package:base':
```
order
```
sna: Tools for Social Network Analysis Version 2.4 created on 2016-07-23. copyright (c) 2005, Carter T. Butts, University of California-Irvine For citation information, type citation("sna"). Type help(package="sna") to get started.

Quitting from lines 130-133 (ggnetwork.Rmd) Error: processing vignette 'ggnetwork.Rmd' failed with diagnostics: Columns x, y, xend, yend must be 1d atomic vectors or lists Execution halted ```

ggplotAssist

Version: 0.1.3

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’ All declared Imports should be used.

ggpubr

Version: 0.1.6

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘FactoMineR’

ggQC

Version: 0.0.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘plyr’ ‘reshape2’ All declared Imports should be used.

ggRandomForests

Version: 2.0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘randomForest’ All declared Imports should be used.

ggraph

Version: 1.0.0

checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'scale_type.geometry': ‘scale_type.geometry’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: doc 3.0Mb libs 2.8Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

ggraptR

Version: 1.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > > if (Sys.getenv("NOT_CRAN") == "true") { # like global skip_on_cran
- Sys.setenv("R_TESTS" = "") # accroding to https://github.com/hadley/testthat/issues/144
- test_check("ggraptR")
- }
Initial plotError in file(filename, "r", encoding = encoding) : cannot open the connection Calls: test_check ... source -> withVisible -> eval -> eval -> source -> file In addition: Warning message: In file(filename, "r", encoding = encoding) : cannot open file '../../inst/ggraptR/functions/helper.R': No such file or directory testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 0 Execution halted ```
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’ ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’ ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’ ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’ All declared Imports should be used.

ggrepel

Version: 0.7.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 332-362 (ggrepel.Rmd) Error: processing vignette 'ggrepel.Rmd' failed with diagnostics: there is no package called 'gridExtra' Execution halted

ggridges

Version: 0.4.1

checking data for non-ASCII characters ... NOTE Note: found 6242 marked UTF-8 strings

ggROC

Version: 1.0

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘ggplot2’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ggroc: no visible global function definition for ‘ggplot’ ggroc: no visible global function definition for ‘aes’ ggroc: no visible global function definition for ‘geom_point’ ggroc: no visible global function definition for ‘geom_line’ ggroc: no visible global function definition for ‘theme’ ggroc: no visible global function definition for ‘element_text’ ggroc: no visible global function definition for ‘labs’ ggroc: no visible global function definition for ‘ggsave’ Undefined global functions or variables: aes element_text geom_line geom_point ggplot ggsave labs theme

ggstance

Version: 0.3

checking tests ... ``` ...
1. Failure: facet_grid() with free scales flips (@test-geoms.R#95)
Error: testthat unit tests failed Execution halted Running the tests in ‘tests/vdiffr.[rR]’ failed. Last 13 lines of output: 15 20 25 30 mpg factor(cyl) stat_summaryh() with fun.x*()

```

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘lazyeval’ All declared Imports should be used.

ggtern

Version: 2.2.1

checking examples ... ERROR ``` ...

Name: annotate

Title: Create an annotation layer (ggtern version).

Aliases: annotate

** Examples

ggtern() + + annotate(geom = 'text', + x = c(0.5,1/3,0.0), + y = c(0.5,1/3,0.0), + z = c(0.0,1/3,1.0), + angle = c(0,30,60), + vjust = c(1.5,0.5,-0.5), + label = paste("Point",c("A","B","C")), + color = c("green","red",'blue')) + + theme_dark() + + theme_nomask() Error in f(..., self = self) : unused argument () Calls: -> print.ggplot -> ggplot_build -> Execution halted ```

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘sp’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘chemometrics’

ggthemes

Version: 3.4.0

checking examples ... ERROR ``` Running examples in ‘ggthemes-Ex.R’ failed The error most likely occurred in:

Name: scale_shape_stata

Title: Stata shape scale

Aliases: scale_shape_stata

** Examples

library("ggplot2") p <- ggplot(mtcars) + + geom_point(aes(x = wt, y = mpg, shape = factor(gear))) + + facet_wrap(~am) p + theme_stata() + scale_shape_stata() Error in if (theme$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 108-110 (./children/examples.Rmd) Quitting from lines 36-40 (./children/examples.Rmd) Error: processing vignette 'ggthemes.Rmd' failed with diagnostics: argument is of length zero Execution halted

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘latticeExtra’

GGtools

Version: 5.12.1

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘MatrixEQTL’ ‘foreach’ ‘doParallel’ ‘gwascat’
checking installed package size ... NOTE installed size is 73.2Mb sub-directories of 1Mb or more: data 27.0Mb doc 1.6Mb parts 2.0Mb pup 2.0Mb rdas 10.3Mb vcf 28.8Mb
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking dependencies in R code ... NOTE 'library' or 'require' call to 'Homo.sapiens' which was already attached by Depends. Please remove these calls from your code. Namespace in Imports field not imported from: 'stats' All declared Imports should be used. Packages in Depends field not imported from: 'Homo.sapiens' 'parallel' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... variable 'smoothScatter' plot,gwSnpScreenResult-character: no visible global function definition for 'axis' Undefined global functions or variables: %dopar% .N FDR Homo.sapiens Matrix_eQTL_engine SlicedData abline approx as.data.table as.formula assay assays axis bindcadd bindmaf binomial chi.squared coef colData curp detectCores dffits excl export.gff3 firstHalf firstThird foreach forestplot formula ftable gwastagger gwrngs hg19.si.df hist hmm878 i i1 i2 lastThird lm maf mafs mclapply midThird model.matrix modelLINEAR mtext npc overlapsAny par pl plogis points pos predict qqplot radiusUsed ranges<- relevel rowRanges runOneSplit runif segments select setkey setkeyv setnames smoothScatter snp snpcount snpsBySeqname target text tileGenome value vcov wald.test x Consider adding importFrom("graphics", "abline", "axis", "hist", "mtext", "par", "points", "segments", "smoothScatter", "text") importFrom("stats", "approx", "as.formula", "binomial", "coef", "dffits", "formula", "ftable", "lm", "model.matrix", "plogis", "predict", "qqplot", "relevel", "runif", "vcov") to your NAMESPACE file.
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘MatrixEQTL’, ‘gwascat’
checking re-building of vignette outputs ... NOTE ``` ... ... Loading required package: illuminaHumanv1.db

Attaching package: 'Biostrings'

The following object is masked from 'package:base':
```
strsplit
```
NOTE: some SNP in rsid were not found in location db SNPlocs.Hsapiens.dbSNP144.GRCh37 NOTE: expanding gene ranges by radius 75000 leads to negative start positions that are reset to 1. Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'GGtools.tex' failed. LaTeX errors: ! Package auto-pst-pdf Error: "shell escape" (or "write18") is not enabled: auto-pst-pdf will not work! . Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

ggtree

Version: 1.8.2

checking re-building of vignette outputs ... WARNING ``` ... collapse

The following object is masked from 'package:IRanges':
```
collapse
```
The following object is masked from 'package:S4Vectors':
```
expand
```
The following object is masked from 'package:ape':
```
rotate
```
Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale. Warning: The plyr::rename operation has created duplicates for the following name(s): (size) Quitting from lines 70-75 (advanceTreeAnnotation.Rmd) Error: processing vignette 'advanceTreeAnnotation.Rmd' failed with diagnostics: invalid line join Execution halted ```

checking installed package size ... NOTE installed size is 11.1Mb sub-directories of 1Mb or more: doc 6.8Mb examples 3.7Mb

ghibli

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

gitter

Version: 1.1.1

checking package dependencies ... ERROR ``` Package required but not available: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

GJRM

Version: 0.1-3

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘sp’

glmmTMB

Version: 0.1.4

checking re-building of vignette outputs ... WARNING ... Warning in f(x, order = 1) : value out of range in 'lgamma' Warning in f(x, order = 1) : value out of range in 'lgamma' Warning in f(x, order = 1) : value out of range in 'lgamma' Warning in f(x, order = 1) : value out of range in 'lgamma' Warning in f(x, order = 1) : value out of range in 'lgamma' Warning in f(x, order = 1) : value out of range in 'lgamma' Warning in f(x, order = 1) : value out of range in 'lgamma' Loading required package: stats4 Warning in qt((1 - level)/2, df) : NaNs produced Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'glmmTMB.tex' failed. BibTeX errors: The top-level auxiliary file: glmmTMB.aux I couldn't open style file chicago.bst ---line 19 of file glmmTMB.aux : \bibstyle{chicago : } I'm skipping whatever remains of this command I found no style file---while reading file glmmTMB.aux Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted
checking installed package size ... NOTE installed size is 44.4Mb sub-directories of 1Mb or more: libs 43.4Mb

gmum.r

Version: 0.2.1

checking installed package size ... NOTE installed size is 20.9Mb sub-directories of 1Mb or more: libs 19.9Mb

GOexpress

Version: 1.10.0

checking R code for possible problems ... NOTE GO_analyse: no visible binding for global variable ‘microarray2dataset’ GO_analyse: no visible binding for global variable ‘prefix2dataset’ mart_from_ensembl: no visible binding for global variable ‘prefix2dataset’ Undefined global functions or variables: microarray2dataset prefix2dataset
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘VennDiagram’

GoogleGenomics

Version: 1.8.1

checking examples ... ERROR ``` Running examples in ‘GoogleGenomics-Ex.R’ failed The error most likely occurred in:

Name: getReads

Title: Get reads from Google Genomics.

Aliases: getReads

** Examples

Authenticated on package load from the env variable GOOGLE_API_KEY.

reads <- getReads() Error in getSearchPage("reads", body, fields, pageToken) : You are not authenticated; see ?GoogleGenomics::authenticate. Calls: getReads -> getReadsPage -> getSearchPage Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'AnnotatingVariants.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

googlesheets

Version: 0.2.2

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(googlesheets) > > if (identical(tolower(Sys.getenv("NOT_CRAN")), "true")) {
- test_check("googlesheets")
- } Error: Cannot read token from alleged .rds file: googlesheets_token.rds testthat results ================================================================ OK: 2 SKIPPED: 0 FAILED: 0 Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 37-41 (basic-usage.Rmd) Error: processing vignette 'basic-usage.Rmd' failed with diagnostics: Cannot read token from alleged .rds file: ../tests/testthat/googlesheets_token.rds Execution halted

GOsummaries

Version: 2.10.0

checking R code for possible problems ... NOTE ... panel_boxplot: no visible binding for global variable ‘x’ panel_boxplot: no visible binding for global variable ‘y’ panel_boxplot: no visible binding for global variable ‘Class’ panel_dummy: no visible binding for global variable ‘y’ panel_dummy: no visible binding for global variable ‘x’ plotWordcloud: no visible global function definition for ‘colorRampPalette’ plotWordcloud: no visible global function definition for ‘runif’ plot_motor: no visible global function definition for ‘dev.off’ print.gosummaries: no visible global function definition for ‘head’ pspearman: no visible global function definition for ‘pt’ spearman_mds: no visible global function definition for ‘cor’ Undefined global functions or variables: Class bmp boxplot.stats colorRampPalette cor dev.off head jpeg packageVersion pdf png pt runif tiff x y Consider adding importFrom("grDevices", "bmp", "boxplot.stats", "colorRampPalette", "dev.off", "jpeg", "pdf", "png", "tiff") importFrom("stats", "cor", "pt", "runif") importFrom("utils", "head", "packageVersion") to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocStyle’
checking re-building of vignette outputs ... NOTE ``` Error in re-building vignettes: ...

Error: processing vignette 'GOsummaries-basics.Rnw' failed with diagnostics: chunk 1 (label = style-Sweave) Error in loadNamespace(name) : there is no package called ‘BiocStyle’ Execution halted ```

GOTHiC

Version: 1.12.0

checking dependencies in R code ... NOTE ':::' call which should be '::': ‘S4Vectors:::orderIntegerPairs’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... .getRestrictionSitesFromBSgenome: no visible global function definition for ‘seqlengths’ .importHicup: no visible global function definition for ‘read.table’ .onlyPairing: no visible global function definition for ‘read.table’ .onlyPairing: no visible global function definition for ‘ScanBamParam’ GOTHiC: no visible binding for global variable ‘BSgenome.Hsapiens.UCSC.hg19’ GOTHiC: no visible binding for global variable ‘filtered’ GOTHiC: no visible binding for global variable ‘interactingLoci’ mapReadsToRestrictionSites: no visible binding for global variable ‘resGR’ Undefined global functions or variables: BSgenome.Hsapiens.UCSC.hg19 IntervalTree ScanBamParam V1 binom.test biocLite chr1 chr2 dev.off filtered frequencies int1 int2 interactingLoci isCircular locus1 locus2 p.adjust pdf pvalue read.table resGR seqlengths x11 Consider adding importFrom("grDevices", "dev.off", "pdf", "x11") importFrom("stats", "binom.test", "p.adjust") importFrom("utils", "read.table") to your NAMESPACE file.

gpmap

Version: 0.1.1

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. Checking should be performed on sources prepared by ‘R CMD build’.
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘foreach’ ‘ggplot2’ ‘isotone’ ‘plyr’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... plot3_dec: no visible global function definition for ‘foreach’ plot3_dec: no visible global function definition for ‘ggplot’ plot3_dec: no visible global function definition for ‘aes_string’ plot3_dec: no visible global function definition for ‘geom_line’ plot3_dec: no visible global function definition for ‘facet_grid’ plot3_dec: no visible global function definition for ‘as.formula’ plot3_dec: no visible global function definition for ‘labs’ plot3_orig: no visible global function definition for ‘%do%’ plot3_orig: no visible global function definition for ‘foreach’ plot3_orig: no visible global function definition for ‘ggplot’ plot3_orig: no visible global function definition for ‘aes_string’ plot3_orig: no visible global function definition for ‘geom_line’ plot3_orig: no visible global function definition for ‘facet_wrap’ plot3_orig: no visible global function definition for ‘as.formula’ plot3_orig: no visible global function definition for ‘labs’ Undefined global functions or variables: %do% %dopar% aaply activeSet aes_string as.formula facet_grid facet_wrap foreach geom_line geom_point ggplot labs laply var Consider adding importFrom("stats", "as.formula", "var") to your NAMESPACE file.

gQTLstats

Version: 1.8.0

checking whether the package can be unloaded cleanly ... WARNING Error: package or namespace load failed for ‘gQTLstats’: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted
checking whether the namespace can be loaded with stated dependencies ... WARNING ``` Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking S3 generic/method consistency ... WARNING ... 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc Execution halted See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual.
checking replacement functions ... WARNING ... 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc Execution halted The argument of a replacement function which corresponds to the right hand side must be named ‘value’.
checking for code/documentation mismatches ... WARNING ... Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc Execution halted
checking installed package size ... NOTE installed size is 65.8Mb sub-directories of 1Mb or more: data 11.0Mb doc 1.1Mb registries 18.9Mb vcf 33.8Mb
checking dependencies in R code ... NOTE ... Call sequence: 6: stop(msg, call. = FALSE, domain = NA) 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc Execution halted
checking foreign function calls ... NOTE ... 5: value[[3L]](cond) 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc Execution halted See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘MultiAssayExperiment’
checking Rd \usage sections ... NOTE ... 3: tryCatchList(expr, classes, parentenv, handlers) 2: tryCatch({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps) }, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA) }) 1: library(package, lib.loc = lib.loc Execution halted The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking data for non-ASCII characters ... NOTE Note: found 8 marked Latin-1 strings Note: found 12 marked UTF-8 strings
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ‘org.Hs.eg.db’

grattan

Version: 1.5.2.5

checking package dependencies ... NOTE Package suggested but not available for checking: ‘taxstats’
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

Greg

Version: 1.2

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘rmeta’
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'printCrudeAndAdjustedModel': ‘rbind.printCrudeAndAdjusted’ ‘cbind.printCrudeAndAdjusted’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

GRENITS

Version: 1.28.1

checking installed package size ... NOTE installed size is 8.4Mb sub-directories of 1Mb or more: libs 8.0Mb
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... ‘scale_fill_gradient’ .plotDistribParents.LargeMat: no visible global function definition for ‘theme’ .plotDistribParents.LargeMat: no visible global function definition for ‘element_blank’ .plotDistribParents.LargeMat: no visible global function definition for ‘element_text’ .plotDistribParents.LargeMat: no visible global function definition for ‘ggtitle’ .plotDistribParents.LargeMat: no visible global function definition for ‘labs’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_x_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘scale_y_discrete’ .plotDistribParents.LargeMat: no visible global function definition for ‘facet_wrap’ Undefined global functions or variables: GeneNames Var1 Var2 aes element_blank element_text facet_wrap geom_tile ggplot ggtitle labs scale_fill_gradient scale_x_discrete scale_y_discrete theme value variable

greport

Version: 0.7-1

checking R code for possible problems ... NOTE accrualReport: multiple local function definitions for ‘gg’ with different formal arguments

gridsampler

Version: 0.6

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiasedUrn’ All declared Imports should be used.

GRmetrics

Version: 1.2.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'GRmetrics-vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

growcurves

Version: 0.2.4.1

checking installed package size ... NOTE installed size is 18.5Mb sub-directories of 1Mb or more: libs 18.0Mb

growfunctions

Version: 0.13

checking installed package size ... NOTE installed size is 13.2Mb sub-directories of 1Mb or more: libs 12.8Mb

GSCA

Version: 2.6.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘shiny’ ‘sp’ ‘gplots’ ‘ggplot2’ ‘reshape2’ ‘RColorBrewer’ ‘rhdf5’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘Affyhgu133A2Expr’ ‘Affyhgu133Plus2Expr’ ‘Affyhgu133aExpr’ ‘Affymoe4302Expr’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... GSCAplot: no visible global function definition for ‘title’ GSCAplot: no visible global function definition for ‘dev.off’ annotatePeaks: no visible binding for global variable ‘allreffile’ tabSearch: no visible global function definition for ‘data’ tabSearch: no visible binding for global variable ‘Affyhgu133aExprtab’ tabSearch: no visible binding for global variable ‘Affymoe4302Exprtab’ tabSearch: no visible binding for global variable ‘Affyhgu133A2Exprtab’ tabSearch: no visible binding for global variable ‘Affyhgu133Plus2Exprtab’ Undefined global functions or variables: Affyhgu133A2Exprtab Affyhgu133Plus2Exprtab Affyhgu133aExprtab Affymoe4302Exprtab P.value SampleType Var1 Var2 allreffile colorRampPalette data dev.off fisher.test geneid hist par pdf qnorm quantile sd str t.stat t.test title value variable write.csv write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf") importFrom("graphics", "hist", "par", "title") importFrom("stats", "fisher.test", "qnorm", "quantile", "sd", "t.test") importFrom("utils", "data", "str", "write.csv", "write.table") to your NAMESPACE file.

gsDesign

Version: 3.0-1

checking R code for possible problems ... NOTE plotgsCP: no visible global function definition for ‘opts’ plotgsPower: no visible global function definition for ‘opts’ qplotit: no visible global function definition for ‘opts’ Undefined global functions or variables: opts

GSE

Version: 4.1

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: libs 4.9Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rrcov’ All declared Imports should be used.

GUIgems

Version: 0.1

checking package dependencies ... ERROR ``` Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

Guitar

Version: 1.14.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘Rsamtools’ ‘GenomicFeatures’ ‘rtracklayer’ ‘GenomicAlignments’ ‘GenomicRanges’ ‘ggplot2’ ‘grid’ ‘IRanges’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: extdata 4.7Mb
checking R code for possible problems ... NOTE .makeFigure_fill: no visible global function definition for ‘pdf’ .makeFigure_fill: no visible global function definition for ‘dev.off’ .makeFigure_nofill: no visible global function definition for ‘pdf’ .makeFigure_nofill: no visible global function definition for ‘dev.off’ BED12toGRangesList: no visible global function definition for ‘read.table’ BED12toGRangesList: no visible global function definition for ‘head’ narrowPeaktoGRanges: no visible global function definition for ‘read.table’ Undefined global functions or variables: dev.off head pdf read.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("utils", "head", "read.table") to your NAMESPACE file.

gutenbergr

Version: 0.1.3

checking data for non-ASCII characters ... NOTE Note: found 13617 marked UTF-8 strings

gwascat

Version: 2.8.0

checking examples ... ERROR ``` ...

The following object is masked from 'package:DelayedArray':
```
type
```
The following object is masked from 'package:base':
```
strsplit
```
Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':
```
tabulate
```
expath = dir(system.file("vcf", package="GGtools"), patt=".exon.gz$", full=TRUE) tf = TabixFile(expath) Error: TabixFile: file(s) do not exist: '.tbi' Execution halted ```
checking whether the namespace can be loaded with stated dependencies ... WARNING ``` Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘SNPlocs.Hsapiens.dbSNP144.GRCh37’
checking installed package size ... NOTE installed size is 38.8Mb sub-directories of 1Mb or more: data 30.9Mb obo 3.1Mb olddata 2.2Mb tab 1.1Mb
checking R code for possible problems ... NOTE Error: .onLoad failed in loadNamespace() for 'Homo.sapiens', details: call: loadMethod(structure(function (object) error: could not find function "loadMethod" Execution halted
checking data for non-ASCII characters ... NOTE Note: found 6 marked Latin-1 strings Note: found 1 marked UTF-8 string
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘BiocStyle’
checking re-building of vignette outputs ... NOTE ``` ... gwascat loaded. Use data(ebicat38) for hg38 coordinates; data(ebicat37) for hg19 coordinates. Loading required package: ggplot2 Need specific help about ggbio? try mailing the maintainer or visit http://tengfei.github.com/ggbio/

Attaching package: 'ggbio'

The following objects are masked from 'package:ggplot2':
```
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity,
xlim
```
Loading required package: grid 'select()' returned 1:1 mapping between keys and columns Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Quitting from lines 18-22 (gwascatOnt.Rmd) Error: processing vignette 'gwascatOnt.Rmd' failed with diagnostics: there is no package called 'BiocStyle' Execution halted ```

h2o

Version: 3.14.0.3

checking installed package size ... NOTE installed size is 86.4Mb sub-directories of 1Mb or more: java 85.1Mb

h5vc

Version: 2.10.0

checking R code for possible problems ... NOTE ... callVariantsSingle : <anonymous> : <anonymous>: no visible binding for global variable ‘BlockID’ mergeTallyFiles : <anonymous>: no visible binding for global variable ‘group’ mergeTallyFiles: no visible binding for global variable ‘SourceFile’ mismatchPlot: no visible binding for global variable ‘Sample’ plotMutationSpectrum: no visible binding for global variable ‘altAllele’ plotMutationSpectrum: no visible binding for global variable ‘tmp’ rerunBatchTallies: no visible binding for global variable ‘regID’ resizeCohort: no visible binding for global variable ‘newSamples’ tallyRangesBatch : <anonymous>: no visible binding for global variable ‘bamFiles’ tallyRangesBatch: no visible binding for global variable ‘verbose’ Undefined global functions or variables: AF BlockID Sample SourceFile SupFwd SupRev Support altAllele bamFiles binom.test fisher.test group hist newSamples pValue regID tmp verbose Consider adding importFrom("graphics", "hist") importFrom("stats", "binom.test", "fisher.test") to your NAMESPACE file.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘deepSNV’

harrietr

Version: 0.2.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

hazus

Version: 0.1

checking R code for possible problems ... NOTE extract_hazus_functions: no visible global function definition for ‘data’ Undefined global functions or variables: data Consider adding importFrom("utils", "data") to your NAMESPACE file.

hBayesDM

Version: 0.4.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rstantools’ All declared Imports should be used.

hdr

Version: 0.1

checking examples ... ERROR ``` Running examples in ‘hdr-Ex.R’ failed The error most likely occurred in:

Name: get_data

Title: Fetch data from the UNDP Human Development Report

Aliases: get_data

** Examples

Get the Human Development Index for Germany in 2013

df <- get_data(indicator = 137506, country = "DEU", year = 2013) Error in curl::curl_fetch_memory(url, handle = handle) : Failed to connect to ec2-52-1-168-42.compute-1.amazonaws.com port 80: Connection refused Calls: get_data ... request_fetch -> request_fetch.write_memory -> -> .Call Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 31-33 (undp_hdr.Rmd) Error: processing vignette 'undp_hdr.Rmd' failed with diagnostics: Failed to connect to ec2-52-1-168-42.compute-1.amazonaws.com port 80: Connection refused Execution halted

heatmaply

Version: 0.13.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘d3heatmap’

hexSticker

Version: 0.4.1

checking package dependencies ... ERROR ``` Package required but not available: ‘ggimage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

hiAnnotator

Version: 1.11.1

checking R code for possible problems ... NOTE ... makeChunks: no visible global function definition for ‘breakInChunks’ makeChunks: no visible global function definition for ‘detectCores’ makeChunks : <anonymous>: no visible global function definition for ‘keepSeqlevels’ makeChunks : <anonymous>: no visible global function definition for ‘seqlevelsInUse’ makeGRanges: no visible global function definition for ‘IRanges’ makeGRanges: no visible global function definition for ‘seqlengths’ makeGRanges: no visible global function definition for ‘seqlevels<-’ makeGRanges: no visible global function definition for ‘sortSeqlevels’ makeGRanges: no visible global function definition for ‘seqlevelsInUse’ makeGRanges: no visible global function definition for ‘seqlengths<-’ makeGRanges: no visible global function definition for ‘seqlevels’ Undefined global functions or variables: IRanges breakInChunks countQueryHits detectCores dist featureName keepSeqlevels mid n overlapsAny qStrand queryHits seqlengths seqlengths<- seqlevels seqlevels<- seqlevelsInUse sortSeqlevels subjectHits Consider adding importFrom("stats", "dist") to your NAMESPACE file.
checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.

hierarchicalDS

Version: 2.9

checking R code for possible problems ... NOTE ... rrw: no visible global function definition for ‘rnorm’ simulate_data: no visible global function definition for ‘pnorm’ simulate_data: no visible global function definition for ‘rpois’ switch_pdf: no visible global function definition for ‘dpois’ switch_pdf: no visible global function definition for ‘dnorm’ switch_sample: no visible global function definition for ‘rpois’ switch_sample: no visible global function definition for ‘rnorm’ switch_sample: no visible global function definition for ‘runif’ switch_sample_prior: no visible global function definition for ‘rgamma’ switch_sample_prior: no visible global function definition for ‘rnorm’ table.mcmc: no visible global function definition for ‘write.csv’ Undefined global functions or variables: abline dnorm dpois legend median model.matrix optimize par plot pnorm points rgamma rnorm rpois runif var write.csv Consider adding importFrom("graphics", "abline", "legend", "par", "plot", "points") importFrom("stats", "dnorm", "dpois", "median", "model.matrix", "optimize", "pnorm", "rgamma", "rnorm", "rpois", "runif", "var") importFrom("utils", "write.csv") to your NAMESPACE file.

hierarchicalSets

Version: 1.0.2

checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘ggplot2:::build_guides’ ‘ggplot2:::guide_axis’ ‘ggplot2:::scales_list’ See the note in ?`:::` about the use of this operator.

highcharter

Version: 0.5.0

checking installed package size ... NOTE installed size is 16.5Mb sub-directories of 1Mb or more: doc 13.7Mb htmlwidgets 1.9Mb

HighDimOut

Version: 1.0.0

checking R code for possible problems ... NOTE Func.ABOD: no visible global function definition for ‘combn’ Func.ABOD: no visible global function definition for ‘var’ Func.SOD: no visible global function definition for ‘var’ Func.trans : erf: no visible global function definition for ‘pnorm’ Func.trans: no visible global function definition for ‘sd’ Undefined global functions or variables: combn pnorm sd var Consider adding importFrom("stats", "pnorm", "sd", "var") importFrom("utils", "combn") to your NAMESPACE file.

HistData

Version: 0.8-2

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘psych’, ‘Guerry’, ‘alr3’, ‘agridat’, ‘coin’

HMP

Version: 1.5

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘genalg’

horserule

Version: 0.1.0

checking whether package ‘horserule’ can be installed ... WARNING Found the following significant warnings: Warning: No Rd macros in package 'Rdpack'. See ‘/home/muelleki/git/R/ggplot2/revdep/checks/horserule/new/horserule.Rcheck/00install.out’ for details.
checking Rd files ... WARNING Warning: No Rd macros in package 'Rdpack'. prepare_Rd: HorseRuleFit.Rd:75: unknown macro '\insertRef' prepare_Rd: hs.Rd:33: unknown macro '\insertRef'
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘MASS’ All declared Imports should be used.

HRM

Version: 0.7.4

checking whether package ‘HRM’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/HRM/new/HRM.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE ```

(R:95155): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() ```

HTSSIP

Version: 1.3.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Sparsity threshold: 0 Density window: 1.72-1.75 Sparsity threshold: 0.2 Density window: 1.72-1.75 Sparsity threshold with the most rejected hypotheses: 0 testthat results ================================================================ OK: 189 SKIPPED: 0 FAILED: 5
1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2)
2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9)
3. Error: Make a data.frame for ordination plotting (parallel) (@test-BD_ordinations.R#20)
4. Error: Plots created from phyloseq object (@test-BD_ordinations.R#46)
5. Error: Plot comparing all (@test-BD_ordinations.R#70)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ... converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode converting counts to integer mode Quitting from lines 68-72 (beta_diversity_ordinations.Rmd) Error: processing vignette 'beta_diversity_ordinations.Rmd' failed with diagnostics: Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength' Execution halted
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘igraph’ All declared Imports should be used.

httk

Version: 1.7

checking installed package size ... NOTE installed size is 13.8Mb sub-directories of 1Mb or more: data 12.3Mb doc 1.0Mb

hurricaneexposure

Version: 0.0.1

checking examples ... ERROR ``` Running examples in ‘hurricaneexposure-Ex.R’ failed The error most likely occurred in:

Name: default_map

Title: Create a default map with eastern US states

Aliases: default_map

** Examples

default_map() Warning: panel.margin is deprecated. Please use panel.spacing property instead Theme element panel.border missing Error in if (theme$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```

checking package dependencies ... NOTE Package suggested but not available for checking: ‘hurricaneexposuredata’

huxtable

Version: 1.1.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message) 5: withVisible(code) 6: rmarkdown::render("table-tester-2.Rmd", quiet = TRUE, output_format = "pdf_document") 7: convert(output_file, run_citeproc) 8: pandoc_convert(utf8_input, pandoc_to, output_format$pandoc$from, output, citeproc, output_format$pandoc$args, !quiet) 9: stop("pandoc document conversion failed with error ", result, call. = FALSE)

testthat results ================================================================ OK: 289 SKIPPED: 48 FAILED: 2 1. Error: Row heights do not screw up LaTeX multicol (@test-with-pandoc.R#20) 2. Error: table-tester-2.Rmd renders without errors in LaTeX (@test-with-pandoc.R#27)

Error: testthat unit tests failed Execution halted ```
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘xtable’

hyperSpec

Version: 0.99-20171005

checking R code for possible problems ... NOTE Warning: local assignments to syntactic functions: ~
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘caTools’

IAPWS95

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘ggplot2’ ‘pander’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 3 marked UTF-8 strings

iBMQ

Version: 1.16.0

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Biobase’ ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE eqtlMcmc: no visible global function definition for ‘is’ eqtlMcmc: no visible global function definition for ‘exprs’ Undefined global functions or variables: exprs is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script.

icd9

Version: 1.3.1

checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: libs 4.6Mb
checking data for non-ASCII characters ... NOTE Note: found 14 marked Latin-1 strings Note: found 39 marked UTF-8 strings

ICtest

Version: 0.3

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘fICA’

ideal

Version: 1.0.0

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ideal: no visible binding for '<<-' assignment to ‘ideal_env’ ideal : <anonymous>: no visible binding for global variable ‘airway’ ideal : <anonymous>: no visible binding for global variable ‘ideal_env’ Undefined global functions or variables: airway ideal_env

IGM.MEA

Version: 0.3.5

checking whether package ‘IGM.MEA’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/IGM.MEA/new/IGM.MEA.Rcheck/00install.out’ for details.

IGP

Version: 0.1.0

checking package dependencies ... ERROR ``` Package required but not available: ‘PythonInR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

IHW

Version: 1.4.0

checking re-building of vignette outputs ... WARNING ``` ...
```
intersect, setdiff, setequal, union
```
estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing

Attaching package: 'ggplot2'

The following object is masked from 'package:IHW':
```
alpha
```
Warning: Removed 30633 rows containing missing values (geom_point). Warning: Removed 12861 rows containing missing values (geom_point). Error: processing vignette 'introduction_to_ihw.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE ... ihw.default: no visible global function definition for ‘p.adjust’ ihw_convex: no visible global function definition for ‘gurobi’ ihw_internal: no visible global function definition for ‘p.adjust’ ihw_milp: no visible global function definition for ‘str’ ihw_milp: no visible global function definition for ‘gurobi’ plot_decisionboundary: no visible binding for global variable ‘stratum’ plot_decisionboundary: no visible binding for global variable ‘covariate’ plot_decisionboundary: no visible binding for global variable ‘pvalue’ plot_decisionboundary: no visible binding for global variable ‘fold’ thresholds_ihwResult: no visible global function definition for ‘na.exclude’ thresholds,ihwResult: no visible global function definition for ‘na.exclude’ Undefined global functions or variables: covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude p.adjust pvalue runif str stratum Consider adding importFrom("stats", "na.exclude", "p.adjust", "runif") importFrom("utils", "str") to your NAMESPACE file.

IHWpaper

Version: 1.4.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'BH-explanation.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking installed package size ... NOTE installed size is 14.9Mb sub-directories of 1Mb or more: doc 3.4Mb extdata 9.8Mb
checking R code for possible problems ... NOTE scott_fdrreg: no visible global function definition for ‘FDRreg’ scott_fdrreg: no visible global function definition for ‘getFDR’ sim_fun_eval: no visible binding for global variable ‘fdr_method’ sim_fun_eval: no visible binding for global variable ‘fdr_pars’ sim_fun_eval: no visible binding for global variable ‘FDP’ sim_fun_eval: no visible binding for global variable ‘rj_ratio’ sim_fun_eval: no visible binding for global variable ‘FPR’ sim_fun_eval: no visible binding for global variable ‘FWER’ Undefined global functions or variables: FDP FDRreg FPR FWER fdr_method fdr_pars getFDR rj_ratio

imager

Version: 0.40.2

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘spatstat’
checking installed package size ... NOTE installed size is 43.7Mb sub-directories of 1Mb or more: data 1.4Mb doc 4.9Mb extdata 1.0Mb include 2.8Mb libs 33.0Mb

Imetagene

Version: 1.6.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'imetagene.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

ImmuneSpaceR

Version: 1.4.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... A .netrc file is required to connect to ImmuneSpace. For more information on how to create one, refer to the Configuration section of the introduction vignette. Quitting from lines 71-74 (Using_RImmuneSpace.Rmd) Error: processing vignette 'Using_RImmuneSpace.Rmd' failed with diagnostics: HTTP request was unsuccessful. Status code = 401, Error message = NA 401 Execution halted
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ``` File ‘ImmuneSpaceR/R/zzz.R’: .onLoad calls: packageStartupMessage("A .netrc file is required to connect to ImmuneSpace. For more information on how to create one, refer to the Configuration section of the introduction vignette.")

See section ‘Good practice’ in '?.onAttach'.

CreateConnection: no visible global function definition for ‘packageVersion’ Undefined global functions or variables: packageVersion Consider adding importFrom("utils", "packageVersion") to your NAMESPACE file. ```

ImpulseDE2

Version: 1.0.0

checking R code for possible problems ... NOTE plotGenes: no visible global function definition for ‘error’ plotGenes: no visible binding for global variable ‘normCounts’ plotGenes: no visible binding for global variable ‘Condition’ plotGenes: no visible binding for global variable ‘Batch’ plotGenes: no visible binding for global variable ‘value’ plotGenes: no visible binding for global variable ‘BatchFit’ Undefined global functions or variables: Batch BatchFit Condition error normCounts value

imputeTestbench

Version: 3.0.1

checking whether package ‘imputeTestbench’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘forecast::autolayer’ by ‘ggplot2::autolayer’ when loading ‘imputeTestbench’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/imputeTestbench/new/imputeTestbench.Rcheck/00install.out’ for details.

incidence

Version: 1.2.1

checking examples ... ERROR ``` ...
- plot data and model (recommended)
- plot(i.7, fit=f)
- plot(i.7[1:25], fit=f)
- EXAMPLE WITH 2 PHASES
- specifying the peak manually
- f2 <- fit(i.7, split=as.Date("2014-10-15"))
- f2
- plot(i.7, fit=f2)
- finding the best 'peak' date
- f3 <- fit_optim_split(i.7)
- f3
- plot(i.7, fit=f3$fit)
- } Loading required package: outbreaks Error in as.Date.default(x.major_source, origin = "1970-01-01") : do not know how to convert 'x.major_source' to class “Date” Calls: plot -> plot.incidence -> as.Date -> as.Date.default Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1: plot(i.isoweek) at testthat/test-plot.R:32 2: plot.incidence(i.isoweek) 3: as.Date(x.major_source, origin = "1970-01-01") 4: as.Date.default(x.major_source, origin = "1970-01-01") 5: stop(gettextf("do not know how to convert '%s' to class %s", deparse(substitute(x)), dQuote("Date")), domain = NA)

testthat results ================================================================ OK: 213 SKIPPED: 0 FAILED: 3 1. Failure: fit_optim_split (@test-fit.R#34) 2. Failure: fit_optim_split (@test-fit.R#35) 3. Error: plot for incidence object (@test-plot.R#32)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 80-86 (conversions.Rmd) Error: processing vignette 'conversions.Rmd' failed with diagnostics: do not know how to convert 'x.major_source' to class "Date" Execution halted

InformationValue

Version: 1.2.3

checking DESCRIPTION meta-information ... NOTE BugReports field should be the URL of a single webpage

inlabru

Version: 2.1.2

checking examples ... ERROR ``` Running examples in ‘inlabru-Ex.R’ failed The error most likely occurred in:

Name: cprod

Title: Cross product of integration points

Aliases: cprod

** Examples

Create integration points in dimension 'myDim' and 'myDiscreteDim'

ips1 = ipoints(c(0,8), name = "myDim") Error in loadNamespace(name) : there is no package called ‘INLA’ Calls: ipoints ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘INLA’

INLAutils

Version: 0.0.4

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘INLA’

IntClust

Version: 0.0.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘prodlim’ All declared Imports should be used.

interactiveDisplay

Version: 1.14.0

checking dependencies in R code ... WARNING '::' or ':::' import not declared from: ‘.interactiveDisplayBase’
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘rstudio’
checking R code for possible problems ... NOTE ... for global variable ‘Var1’ display,RangedSummarizedExperiment : <anonymous>: no visible binding for global variable ‘Var2’ display,RangedSummarizedExperiment : <anonymous>: no visible binding for global variable ‘value’ Undefined global functions or variables: AnnotationTrack GO.db GRanges GRangesList GenomeAxisTrack IRanges IdeogramTrack MRcounts Var1 Var2 as.dendrogram assays cim colorRampPalette coord_flip cutree dendrapply dev.off dist elementMetadata experimentData exprs fData hclust installed.packages is.leaf layout_circle legend libSize mcols pData plot plotFeature plotOrd plotTracks png rainbow ranges rowRanges seqlengths seqlengths<- seqlevels<- seqnames ucscGenomes value Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "png", "rainbow") importFrom("graphics", "legend", "plot") importFrom("stats", "as.dendrogram", "cutree", "dendrapply", "dist", "hclust", "is.leaf") importFrom("utils", "installed.packages") to your NAMESPACE file.

IONiseR

Version: 2.0.0

checking re-building of vignette outputs ... WARNING ``` ... The following object is masked from 'package:base':
```
apply
```
Attaching package: 'GenomicAlignments'

The following object is masked from 'package:dplyr':
```
last
```
Attaching package: 'ShortRead'

The following object is masked from 'package:dplyr':
```
id
```
Error: processing vignette 'IONiseR.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: doc 3.6Mb extdata 1.5Mb
checking R code for possible problems ... NOTE ... ‘start_time’ readFast5Summary.mc: no visible binding for global variable ‘duration’ readFast5Summary.mc: no visible binding for global variable ‘num_events’ [,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable ‘baseCalledTemplate’ [,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable ‘baseCalledComplement’ [,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable ‘component’ [,Fast5Summary-ANY-ANY-ANY: no visible binding for global variable ‘idx’ show,Fast5Summary: no visible binding for global variable ‘full_2D’ show,Fast5Summary: no visible binding for global variable ‘pass’ Undefined global functions or variables: := AAAAA TTTTT accumulation baseCalledComplement baseCalledTemplate bases_called category channel circleFun component duration error freq full_2D group hour idx matrixCol matrixRow meanZValue mean_value median_signal minute mux name nbases new_reads num_events oddEven pass pentamer rbindlist readIDs seq_length start_time time_bin time_group x y zvalue

ipft

Version: 0.7.1

checking examples ... ERROR ``` Running examples in ‘ipft-Ex.R’ failed The error most likely occurred in:
Name: ipfPlotLoc

Title: Plots the spatial location of the observations

Aliases: ipfPlotLoc

** Examples
```
ipfPlotLoc(ipftrain[, 169:170])

ipfPlotLoc(ipftrain[, 169:170], plabel = TRUE, reverseAxis = TRUE,
```
- title = 'Position of training set observations') Error: Columns x, y must be 1d atomic vectors or lists Execution halted ```

iprior

Version: 0.7.0

checking installed package size ... NOTE installed size is 10.1Mb sub-directories of 1Mb or more: doc 1.1Mb libs 8.7Mb

iqspr

Version: 2.3

checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: data 6.8Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ggplot2’ ‘gridExtra’ ‘rBayesianOptimization’ All declared Imports should be used.

isobar

Version: 1.22.0

checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.as.matrix’ ‘.as.vect’ ‘.convertPeptideModif’ ‘.proteinGroupAsConciseDataFrame’ ‘.read.idfile’ ‘.sum.bool’
checking R code for possible problems ... NOTE ... coerce,IBSpectra-MSnSet: no visible binding for global variable ‘o’ coerce,MSnSet-IBSpectra: no visible global function definition for ‘qual’ df,Tlsd: no visible global function definition for ‘param’ estimateRatio,IBSpectra-ANY-missing-missing-character-missing: no visible binding for global variable ‘i’ estimateRatio,IBSpectra-ANY-missing-missing-missing-character: no visible binding for global variable ‘i’ estimateRatioNumeric,numeric-numeric-NoiseModel: no visible binding for global variable ‘center.var’ location,Tlsd: no visible global function definition for ‘param’ plotRatio,IBSpectra-character-character-character: no visible binding for global variable ‘pch’ plotRatio,IBSpectra-character-character-character: no visible binding for global variable ‘noise.model.col’ plotRatio,IBSpectra-character-character-character: no visible binding for global variable ‘pch.p’ scale,Tlsd: no visible global function definition for ‘param’ Undefined global functions or variables: center.var d g i mz name noise.model.col o param pch pch.p peptide qual ratio type

isomiRs

Version: 1.4.0

checking tests ... ``` ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: 1 Test Suite : isomiRs RUnit Tests - 3 test functions, 0 errors, 1 failure FAILURE in test_plotFunctions: Error in checkTrue(class(isoPlot(mirData, type = "iso5", column = "group"))[1] == : Test not TRUE

Test files with failing tests
```
 test_singleFunctions.R 
   test_plotFunctions
```
Error in BiocGenerics:::testPackage("isomiRs") : unit tests failed for package isomiRs Execution halted ```

checking R code for possible problems ... NOTE ... isoSelect.IsomirDataSeq: no visible binding for global variable ‘freq’ isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global variable ‘mir’ isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global variable ‘mism’ isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global variable ‘add’ isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global variable ‘t5’ isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global variable ‘t3’ isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global variable ‘id’ isoSelect,IsomirDataSeq : <anonymous>: no visible binding for global variable ‘freq’ isoSelect,IsomirDataSeq: no visible binding for global variable ‘freq’ Undefined global functions or variables: Count DB X1 X2 add af ambiguity average change condition current enrich enrichGO error freq gene go group id mir mir_f mir_n mism mism_f mism_n ngene pct_abundance reference rowMax rowMin sel_genes t3 t5 term term_short type value y

ITGM

Version: 0.6

checking whether package ‘ITGM’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/ITGM/new/ITGM.Rcheck/00install.out’ for details.

jcolors

Version: 0.0.1

checking examples ... ERROR ``` Running examples in ‘jcolors-Ex.R’ failed The error most likely occurred in:

Name: theme_dark_bg

Title: minimal theme for dark backgrounds

Aliases: theme_dark_bg theme_light_bg

** Examples

library(ggplot2)

p <- ggplot(mtcars) + geom_point(aes(x = wt, y = mpg, + colour = factor(gear))) + facet_grid(vs~am) p + theme_dark_bg() Error in if (theme$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```

jmv

Version: 0.8

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘PMCMR’ ‘R6’ ‘afex’ ‘car’ ‘ggridges’ ‘lavaan’ ‘lsmeans’ ‘multcomp’ ‘mvnormtest’ ‘psych’ ‘vcd’ ‘vcdExtra’ All declared Imports should be used.

jmvcore

Version: 0.8.1.6

checking package dependencies ... NOTE Package suggested but not available for checking: ‘RProtoBuf’

joineRML

Version: 0.4.0

checking re-building of vignette outputs ... WARNING `` Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'technical.tex' failed. LaTeX errors: ! LaTeX Error: Filebiblatex.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.17 ^^M

! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```
checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: data 1.3Mb libs 4.9Mb

jpndistrict

Version: 0.2.0

checking data for non-ASCII characters ... NOTE Note: found 188 marked UTF-8 strings

jtools

Version: 0.9.0

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘effects’, ‘ReporteRs’, ‘arm’, ‘rockchalk’, ‘pequod’, ‘MuMIn’

kdetrees

Version: 0.1.5

checking R code for possible problems ... NOTE ... as.matrix.multiPhylo : tip2tip: no visible global function definition for ‘cophenetic’ bw.nn : <anonymous>: no visible global function definition for ‘quantile’ dist.diss: no visible binding for global variable ‘median’ dist.diss: no visible global function definition for ‘dist’ hist.kdetrees: no visible binding for global variable ‘density’ kdetrees : cutoff: no visible global function definition for ‘quantile’ kdetrees.complete: no visible global function definition for ‘plot’ kdetrees.complete: no visible global function definition for ‘hist’ kdetrees.complete: no visible global function definition for ‘write.csv’ plot.kdetrees: no visible binding for global variable ‘density’ Undefined global functions or variables: cophenetic density dist hist median plot quantile write.csv Consider adding importFrom("graphics", "hist", "plot") importFrom("stats", "cophenetic", "density", "dist", "median", "quantile") importFrom("utils", "write.csv") to your NAMESPACE file.

Kmisc

Version: 0.5.0

checking R code for possible problems ... NOTE ... pp_plot : <anonymous>: no visible global function definition for ‘rgb’ rcpp_apply_generator: no visible global function definition for ‘packageVersion’ rcpp_tapply_generator: no visible global function definition for ‘packageVersion’ read.cb: no visible global function definition for ‘read.table’ remove_na: no visible global function definition for ‘complete.cases’ size: no visible global function definition for ‘object.size’ write.cb: no visible global function definition for ‘write.table’ Undefined global functions or variables: anova capture.output coef colorRampPalette complete.cases dev.off kmeans object.size packageVersion par qbeta read.table rgb svg write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "rgb", "svg") importFrom("graphics", "par") importFrom("stats", "anova", "coef", "complete.cases", "kmeans", "qbeta") importFrom("utils", "capture.output", "object.size", "packageVersion", "read.table", "write.table") to your NAMESPACE file.

kobe

Version: 1.3.2

checking R code for possible problems ... NOTE ... actual arguments theme_ms: possible error in colour = "grey50")): formal argument "strip.background" matched by multiple actual arguments theme_ms: no visible global function definition for ‘modifyList’ kobe2sm,data.frame: no visible global function definition for ‘colorRampPalette’ kobe2sm,data.frame: no visible global function definition for ‘par’ kobe2sm,data.frame: no visible global function definition for ‘kobe2smFn’ kobe2sm,data.frame: no visible global function definition for ‘mtext’ kobe,data.frame-missing : <anonymous>: no visible global function definition for ‘kobeFn’ Undefined global functions or variables: colorRampPalette grey kobe2smFn kobeFn median modifyList mtext par quantile read.csv read.table Consider adding importFrom("grDevices", "colorRampPalette", "grey") importFrom("graphics", "mtext", "par") importFrom("stats", "median", "quantile") importFrom("utils", "modifyList", "read.csv", "read.table") to your NAMESPACE file.

KraljicMatrix

Version: 0.2.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dplyr’ ‘tibble’ All declared Imports should be used.

Lahman

Version: 6.0-0

checking installed package size ... NOTE installed size is 7.5Mb sub-directories of 1Mb or more: data 7.2Mb

LANDD

Version: 1.1.0

checking R code for possible problems ... NOTE getGO: no visible global function definition for ‘new’ getGO: no visible global function definition for ‘getGeneric’ graph.kd: no visible global function definition for ‘as’ Undefined global functions or variables: as getGeneric new Consider adding importFrom("methods", "as", "getGeneric", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

largeVis

Version: 0.2.1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: with expansion: 88 == 90

=============================================================================== test cases: 2 | 1 passed | 1 failed assertions: 32 | 12 passed | 20 failed

testthat results ================================================================ OK: 147 SKIPPED: 1 FAILED: 1 1. Failure: Catch unit tests pass (@test-cpp.R#6)

Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE installed size is 19.7Mb sub-directories of 1Mb or more: libs 14.7Mb testdata 1.8Mb vignettedata 2.0Mb

learningCurve

Version: 1.1.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘gridExtra’ ‘scales’ ‘tidyverse’ All declared Imports should be used.

learnstats

Version: 0.1.1

checking whether package ‘learnstats’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/learnstats/new/learnstats.Rcheck/00install.out’ for details.
checking R code for possible problems ... NOTE ... qqsim: no visible global function definition for ‘mtext’ qqsim: no visible global function definition for ‘jpeg’ qqsim: no visible global function definition for ‘dev.off’ timeseressim: no visible global function definition for ‘rnorm’ timeseressim: no visible global function definition for ‘par’ timeseressim: no visible global function definition for ‘plot’ timeseressim: no visible global function definition for ‘mtext’ timeseressim: no visible global function definition for ‘jpeg’ timeseressim: no visible global function definition for ‘dev.off’ Undefined global functions or variables: axis dchisq dev.off dnorm dt hist jpeg legend mtext par pchisq pf plot pnorm polygon pt qchisq qf qqline qqnorm qt rchisq rnorm rt runif segments title Consider adding importFrom("grDevices", "dev.off", "jpeg") importFrom("graphics", "axis", "hist", "legend", "mtext", "par", "plot", "polygon", "segments", "title") importFrom("stats", "dchisq", "dnorm", "dt", "pchisq", "pf", "pnorm", "pt", "qchisq", "qf", "qqline", "qqnorm", "qt", "rchisq", "rnorm", "rt", "runif") to your NAMESPACE file.

LedPred

Version: 1.10.0

checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT
checking R code for possible problems ... NOTE .plotCostGamma: no visible global function definition for ‘title’ .plotCostGamma: no visible global function definition for ‘points’ mapFeaturesToCRMs: no visible global function definition for ‘write.table’ mapFeaturesToCRMs: no visible global function definition for ‘read.table’ mapFeaturesToCRMs: no visible global function definition for ‘download.file’ scoreData: no visible global function definition for ‘write.table’ Undefined global functions or variables: download.file points read.table title write.table Consider adding importFrom("graphics", "points", "title") importFrom("utils", "download.file", "read.table", "write.table") to your NAMESPACE file.

lfa

Version: 1.6.1

checking R code for possible problems ... NOTE compute.nulls: no visible global function definition for ‘rbinom’ lfa: no visible binding for global variable ‘sd’ lreg: no visible global function definition for ‘glm’ read.bed: no visible global function definition for ‘read.table’ trunc.svd: no visible global function definition for ‘rnorm’ Undefined global functions or variables: glm rbinom read.table rnorm sd Consider adding importFrom("stats", "glm", "rbinom", "rnorm", "sd") importFrom("utils", "read.table") to your NAMESPACE file.

likeLTD

Version: 6.2.1

checking whether package ‘likeLTD’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/likeLTD/new/likeLTD.Rcheck/00install.out’ for details.

likert

Version: 1.3.5

checking data for non-ASCII characters ... NOTE Note: found 7 marked UTF-8 strings

LINC

Version: 1.4.0

checking installed package size ... NOTE installed size is 7.2Mb sub-directories of 1Mb or more: doc 3.6Mb libs 1.4Mb
checking R/sysdata.rda ... NOTE ```

Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress sysdata.rda 449Kb 313Kb xz ```

Linnorm

Version: 2.0.8

checking tests ... ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Linnorm) > > test_check("Linnorm") Error in library(matrixStats) : there is no package called 'matrixStats' Calls: test_check ... with_reporter -> force -> source_file -> eval -> eval -> library testthat results ================================================================ OK: 4 SKIPPED: 0 FAILED: 0 Execution halted
checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: data 2.3Mb doc 1.9Mb
checking R code for possible problems ... NOTE Linnorm.HClust: no visible binding for global variable ‘x’ Linnorm.HClust: no visible binding for global variable ‘y’ Linnorm.HClust: no visible binding for global variable ‘xend’ Linnorm.HClust: no visible binding for global variable ‘yend’ Linnorm.HClust: no visible binding for global variable ‘cluster’ Linnorm.HClust: no visible binding for global variable ‘X1’ Linnorm.HClust: no visible binding for global variable ‘X2’ Linnorm.HVar: no visible binding for global variable ‘SD’ Linnorm.HVar: no visible binding for global variable ‘group’ Undefined global functions or variables: SD X1 X2 cluster group x xend y yend

lme4

Version: 1.1-14

checking installed package size ... NOTE installed size is 26.8Mb sub-directories of 1Mb or more: doc 1.5Mb libs 21.7Mb testdata 1.5Mb

LocFDRPois

Version: 1.0.0

checking R code for possible problems ... NOTE AnalyticalOptim: no visible global function definition for ‘optim’ LLConstructor : LL: no visible global function definition for ‘dpois’ MixtureDensity: no visible global function definition for ‘glm’ MixtureDensity : f_hat: no visible global function definition for ‘predict’ NullDensity : f0: no visible global function definition for ‘dpois’ Undefined global functions or variables: dpois glm optim predict Consider adding importFrom("stats", "dpois", "glm", "optim", "predict") to your NAMESPACE file.

lslx

Version: 0.6.0

checking installed package size ... NOTE installed size is 44.1Mb sub-directories of 1Mb or more: doc 1.5Mb libs 42.4Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘ggplot2’ ‘lavaan’ All declared Imports should be used.

LymphoSeq

Version: 1.4.1

checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: doc 2.6Mb extdata 5.5Mb

m2b

Version: 1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘e1071’ ‘utils’ All declared Imports should be used.

MAc

Version: 1.1

checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘R2wd’

Packages which this enhances but not available for checking: ‘compute.es’ ‘irr’ ```
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘R2wd’ ‘ggplot2’ ‘metafor’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... wd.mareg: no visible global function definition for ‘wdGet’ wd.mareg: no visible global function definition for ‘wdNewDoc’ wd.mareg: no visible global function definition for ‘wdHeading’ wd.mareg: no visible global function definition for ‘wdTable’ wd.omni: no visible global function definition for ‘wdGet’ wd.omni: no visible global function definition for ‘wdNewDoc’ wd.omni: no visible global function definition for ‘wdHeading’ wd.omni: no visible global function definition for ‘wdTable’ Undefined global functions or variables: TukeyHSD aes aggregate anova aov contrasts facet_wrap g geom_boxplot geom_errorbarh geom_jitter geom_point geom_smooth geom_vline ggplot id l.ci95 lm model.extract model.matrix model.response na.omit opts pchisq pf pnorm printCoefmat qf qt r rma scale_y_continuous se.z se.z.tau stat_abline stat_summary u.ci95 var var.g wdGet wdHeading wdNewDoc wdTable wi wi.tau xlab xlim ylab ylim z Consider adding importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "contrasts", "lm", "model.extract", "model.matrix", "model.response", "na.omit", "pchisq", "pf", "pnorm", "printCoefmat", "qf", "qt", "var") to your NAMESPACE file.

macleish

Version: 0.3.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘DBI’ All declared Imports should be used.

MAd

Version: 0.8-2

checking package dependencies ... NOTE ``` Package suggested but not available for checking: ‘R2wd’

Packages which this enhances but not available for checking: ‘compute.es’ ‘irr’ ```
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘R2wd’ ‘ggplot2’ ‘metafor’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... omni: no visible global function definition for ‘pnorm’ omni: no visible global function definition for ‘pchisq’ p.ancova_to_d1: no visible global function definition for ‘qt’ p.ancova_to_d2: no visible global function definition for ‘qt’ p_to_d1: no visible global function definition for ‘qt’ p_to_d2: no visible global function definition for ‘qt’ print.summary.mareg: no visible global function definition for ‘printCoefmat’ robustSE: no visible global function definition for ‘residuals’ robustSE: no visible global function definition for ‘pt’ robustSE: no visible global function definition for ‘qt’ Undefined global functions or variables: TukeyHSD aggregate anova aov contrasts model.extract model.matrix model.response na.omit pchisq pf pnorm printCoefmat pt qf qt residuals var Consider adding importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "contrasts", "model.extract", "model.matrix", "model.response", "na.omit", "pchisq", "pf", "pnorm", "printCoefmat", "pt", "qf", "qt", "residuals", "var") to your NAMESPACE file.

mafs

Version: 0.0.3

checking whether package ‘mafs’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘forecast::autolayer’ by ‘ggplot2::autolayer’ when loading ‘mafs’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/mafs/new/mafs.Rcheck/00install.out’ for details.

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’ ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’ All declared Imports should be used.

maftools

Version: 1.2.30

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'maftools.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ Execution halted
checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: doc 1.8Mb extdata 4.2Mb
checking R code for possible problems ... NOTE ... SubstitutionMotif SubstitutionTypeMotif T>A T>C T>G TCA TCGA TCT TGA T[C>A]A T[C>A]T T[C>G]A T[C>G]T T[C>T]A T[C>T]T T[G>A]A T[G>C]A T[G>T]A TiTv Time TumorSampleBarcode Tumor_Sample_Barcode Tumor_Seq_Allele2 Unique_Name V1 V2 Var1 Var2 Variant_Classification Variant_Type Wide_Peak_Limits aa.length amp assembly_version bg chromosome chromosome_end chromosome_start ci.low ci.up clusters cohort con con.class consequence_type conv count count2 cytoband dat distance downstream endDist ens_id fdr fisher_pvalue flow fract fract_muts_in_clusters fraction fraction_APOBEC_mutations fs gene gene_affected hgnc_symbol i.End_Position i.Start_Position icgc_sample_id id idx lab labThis label loc log10OR mutated_from_allele mutated_to_allele mutations muts_in_clusters nGenes nMut nMuts nSamples nVars n_A n_C n_C>G_and_C>T n_G n_T n_mutations nonApobec non_APOBEC_mutations or peakID pfam poissonFdr pos pos2 posRounded protein.ID pval qvalues reference_genome_allele refseq.ID sequencing_strategy significant site sort_by_anno startDist statFontSize survLower survProb survUp tCw tCw_to_A tCw_to_G tCw_to_G+tCw_to_T tCw_to_T tFdr t_alt_count t_ref_count t_vaf tcw th total trinucleotide uid updown upstream value variable variantId verification_platform verification_status wGa wGa_to_A wGa_to_C wGa_to_T wga x y ymax ymin ystart
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘corrplot’ 'library' or 'require' call not declared from: ‘corrplot’

magick

Version: 1.5

checking package dependencies ... NOTE Package suggested but not available for checking: ‘tesseract’
checking installed package size ... NOTE installed size is 12.8Mb sub-directories of 1Mb or more: doc 6.8Mb libs 5.8Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘tesseract’

manhattanly

Version: 0.2.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘qqman’

mapr

Version: 0.3.4

checking tests ... ``` ERROR Running the tests in ‘tests/test-that.R’ failed. Last 13 lines of output: 9: request_build("POST", hu$url, body_config(body, match.arg(encode)), as.request(config), ...) 10: as.request(config) 11: gist_auth() 12: stop("In non-interactive environments, please set GITHUB_PAT env to a GitHub", " access token (https://help.github.com/articles/creating-an-access-token-for-command-line-use)", call. = FALSE)

testthat results ================================================================ OK: 7 SKIPPED: 0 FAILED: 1 1. Error: map_gist works as expected (@test-map_gist.R#13)

Error: testthat unit tests failed In addition: Warning message: closing unused connection 3 (/home/muelleki/tmp/RtmpwlKRRD/filee483fcb058d.geojson) Execution halted ```
checking data for non-ASCII characters ... NOTE Note: found 164 marked UTF-8 strings

marmap

Version: 0.9.6

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘maptools’

MAST

Version: 1.2.1

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: data 3.7Mb doc 1.9Mb

matrixStats

Version: 0.52.2

checking installed package size ... NOTE installed size is 8.3Mb sub-directories of 1Mb or more: libs 7.6Mb

mcaGUI

Version: 1.24.0

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

Packages which this enhances but not available for checking: ‘iplots’ ‘reshape’

Depends: includes the non-default packages: ‘lattice’ ‘MASS’ ‘proto’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘OTUbase’ ‘vegan’ ‘bpca’ Adding so many packages to the search path is excessive and importing selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

MCbiclust

Version: 1.0.1

checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: data 3.2Mb doc 4.9Mb

mcMST

Version: 1.0.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘parallelMap’ ‘reshape2’ All declared Imports should be used.

mdpeer

Version: 1.0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘glmnet’ All declared Imports should be used.

mdsr

Version: 0.1.4

checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: data 5.4Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tidyverse’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 2698 marked UTF-8 strings

MEAL

Version: 1.6.0

checking re-building of vignette outputs ... WARNING ... Fitting chr22... Fitting chr3... Fitting chr4... Fitting chr5... Fitting chr6... Fitting chr7... Fitting chr8... Fitting chr9... Fitting chrX... Fitting chrY... Demarcating regions... Done! Warning in rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 100 steps Warning: In BioC 3.5, the 'force' argument was replaced by the more flexible 'pruning.mode' argument, and is deprecated. See ?seqinfo for the supported pruning modes. Note that 'force=TRUE' is equivalent to 'pruning.mode="coarse"'. Error: processing vignette 'MEAL.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking R code for possible problems ... NOTE correlationMethSNPs: no visible binding for global variable 'num_cores' prepareMethylationSet: no visible global function definition for 'colData' Undefined global functions or variables: colData num_cores

meaRtools

Version: 1.0.1

checking whether package ‘meaRtools’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/meaRtools/new/meaRtools.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 6.3Mb sub-directories of 1Mb or more: extdata 3.9Mb libs 1.4Mb

medmod

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R6’ ‘ggplot2’ ‘lavaan’ All declared Imports should be used.

memapp

Version: 2.6

checking package dependencies ... NOTE Package suggested but not available for checking: ‘magick’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘formattable’ ‘ggplot2’ ‘ggthemes’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ All declared Imports should be used.

meme

Version: 0.0.7

checking package dependencies ... ERROR ``` Package required but not available: ‘magick’

Package suggested but not available for checking: ‘ggimage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

MergeGUI

Version: 0.2-1

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

messina

Version: 1.12.0

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMC’
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘Biobase’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... ‘quantile’ messinaSurvKMplot : <anonymous>: no visible binding for global variable ‘sd’ messinaSurvKMplotSingleGroup: no visible binding for global variable ‘median’ messinaSurvKMplotSingleGroup: no visible binding for global variable ‘quantile’ messinaSurvKMplotSingleGroup: no visible binding for global variable ‘sd’ messinaSurvObjPlot: no visible global function definition for ‘quantile’ messinaSurvObjectiveFunc: no visible global function definition for ‘coef’ messinaSurvPlot: no visible global function definition for ‘str’ Undefined global functions or variables: approx coef median quantile reorder sd str Consider adding importFrom("stats", "approx", "coef", "median", "quantile", "reorder", "sd") importFrom("utils", "str") to your NAMESPACE file.

metagen

Version: 1.0

checking R code for possible problems ... NOTE ... pivotalStream: no visible global function definition for ‘rchisq’ pivotalStream : <anonymous>: no visible global function definition for ‘rchisq’ pivotalStream: no visible global function definition for ‘rnorm’ rBinomGauss: no visible global function definition for ‘rnorm’ rBinomGauss: no visible global function definition for ‘rbinom’ rD: no visible global function definition for ‘rchisq’ rY: no visible global function definition for ‘rnorm’ render: no visible global function definition for ‘pdf’ render: no visible global function definition for ‘dev.off’ renderSVG: no visible global function definition for ‘svg’ renderSVG: no visible global function definition for ‘dev.off’ Undefined global functions or variables: data dev.off pdf qchisq qnorm qt quantile rbinom rchisq rnorm svg uniroot var Consider adding importFrom("grDevices", "dev.off", "pdf", "svg") importFrom("stats", "qchisq", "qnorm", "qt", "quantile", "rbinom", "rchisq", "rnorm", "uniroot", "var") importFrom("utils", "data") to your NAMESPACE file.

metagene

Version: 2.8.0

checking re-building of vignette outputs ... WARNING ``` ... as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':
```
expand.grid
```
Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: BiocParallel Error: processing vignette 'metagene.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE get_demo_design: no visible global function definition for ‘read.table’ get_promoters_txdb: no visible global function definition for ‘is’ plot_metagene: no visible binding for global variable ‘position’ plot_metagene: no visible binding for global variable ‘value’ plot_metagene: no visible binding for global variable ‘qinf’ plot_metagene: no visible binding for global variable ‘qsup’ plot_metagene: no visible binding for global variable ‘group’ Undefined global functions or variables: group is position qinf qsup read.table value Consider adding importFrom("methods", "is") importFrom("utils", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

MetaIntegrator

Version: 1.0.3

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

metaMix

Version: 0.2

checking R code for possible problems ... NOTE ... visible global function definition for ‘runif’ parallel.temper.nucl : parallel.temper.nucl.wrapped : singleChain: no visible global function definition for ‘quantile’ parallel.temper.nucl.explicit : singleChain : moveRemove: no visible global function definition for ‘quantile’ parallel.temper.nucl.explicit : singleChain: no visible global function definition for ‘runif’ parallel.temper.nucl.explicit : singleChain: no visible global function definition for ‘quantile’ reduce.space : reduce.space.wrapped: no visible global function definition for ‘quantile’ reduce.space.explicit: no visible global function definition for ‘quantile’ Undefined global functions or variables: dev.off pdf plot ppois quantile runif write.table Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "plot") importFrom("stats", "ppois", "quantile", "runif") importFrom("utils", "write.table") to your NAMESPACE file.

meteogRam

Version: 1.0

checking R code for possible problems ... NOTE crosssection: no visible global function definition for ‘colorRampPalette’ crosssection: no visible global function definition for ‘filled.contour’ crosssection: no visible global function definition for ‘axis’ crosssection: no visible global function definition for ‘par’ crosssection: no visible global function definition for ‘contour’ temperatures: no visible binding for global variable ‘time’ Undefined global functions or variables: axis colorRampPalette contour filled.contour par time Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "axis", "contour", "filled.contour", "par") importFrom("stats", "time") to your NAMESPACE file.

Methplot

Version: 1.0

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE getdata: no visible global function definition for ‘read.csv’ plotdata: no visible global function definition for ‘head’ Undefined global functions or variables: head read.csv Consider adding importFrom("utils", "head", "read.csv") to your NAMESPACE file.

MethylAid

Version: 1.10.0

checking package dependencies ... NOTE Package suggested but not available for checking: ‘MethylAidData’

methylInheritance

Version: 1.0.0

checking re-building of vignette outputs ... WARNING ``` ... duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':
```
expand.grid
```
Loading required package: IRanges Loading required package: GenomeInfoDb Warning message: In max(i) : no non-missing arguments to max; returning -Inf Error: processing vignette 'methylInheritance.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

MethylMix

Version: 2.4.0

checking examples ... ERROR ``` ... FOXD1 : 2 components are best. ME1 : 2 components are best. MGMT : 2 components are best. OAS1 : 2 components are best. SOX10 : 2 components are best. TRAF6 : 2 components are best. ZNF217 : 2 components are best. > > # Plot the most famous methylated gene for glioblastoma > MethylMix_PlotModel("MGMT", MethylMixResults, METcancer) $MixtureModelPlot

$CorrelationPlot NULL

Plot MGMT also with its normal methylation variation

MethylMix_PlotModel("MGMT", MethylMixResults, METcancer, METnormal = METnormal) $MixtureModelPlot Error: Aesthetics must be either length 1 or the same as the data (251): x, y, xend, yend Execution halted ```

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘digest’ All declared Imports should be used.

methylumi

Version: 2.22.0

checking for missing documentation entries ... WARNING Undocumented code objects: ‘IDATsToMatrices’ ‘IDATtoMatrix’ ‘tcgaPipeline’ Undocumented S4 methods: generic '[' and siglist 'MethyLumiM,ANY,ANY,ANY' generic '[' and siglist 'MethyLumiSet,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual.
checking contents of ‘data’ directory ... WARNING Files not of a type allowed in a ‘data’ directory: ‘5318317007_A_Grn.idat’ ‘5318317007_A_Red.idat’ ‘5318317007_B_Grn.idat’ ‘5318317007_B_Red.idat’ ‘5318317007_C_Grn.idat’ ‘5318317007_C_Red.idat’ Please use e.g. ‘inst/extdata’ for non-R data files
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘Biobase’ ‘scales’ ‘reshape2’ ‘ggplot2’ ‘matrixStats’ ‘FDb.InfiniumMethylation.hg19’ ‘minfi’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 9.8Mb sub-directories of 1Mb or more: data 6.8Mb extdata 1.7Mb
checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’ ‘reshape2’ ‘scales’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘graphics’ All declared Imports should be used. Packages in Depends field not imported from: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’ ‘reshape2’ ‘scales’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... IlluminaHumanMethylation450kCOLORCHANNEL MethylSet RGChannelSet abline addColorChannelInfo aes allele as.dist axis box capture.output channel.probes colMedians colQuantiles colSds colorRampPalette coord_flip data dnorm dropouts drops ecdf facet_grid features gamma.integral gamma.mle gamma.mode geom_histogram ggplot hclust hm27.controls hm27.ordering hm450.controls hm450.ordering huber index intensity lines log_trans mclapply melt mu offset opts p.adjust packageDescription packageVersion par plot.density pnorm points position_identity read.csv read.delim read.table rect rowMins scale_colour_manual scale_fill_manual scale_shape_manual scale_x_continuous scale_y_continuous scale_y_discrete subsetCommonProbes text theme_bw title value variable weighted.mean Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "abline", "axis", "box", "lines", "par", "points", "rect", "text", "title") importFrom("stats", "as.dist", "dnorm", "ecdf", "hclust", "offset", "p.adjust", "pnorm", "weighted.mean") importFrom("utils", "capture.output", "data", "packageDescription", "packageVersion", "read.csv", "read.delim", "read.table") to your NAMESPACE file.
checking Rd files ... NOTE prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

microbenchmark

Version: 1.4-2.1

checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

micromap

Version: 1.9.2

checking R code for possible problems ... NOTE ... dot_cl_build: no visible global function definition for ‘median’ lmplot: no visible global function definition for ‘gray’ map_att: no visible global function definition for ‘gray’ mmgroupedplot: no visible global function definition for ‘median’ mmplot: no visible global function definition for ‘gray’ mmplot: no visible global function definition for ‘median’ print.mm: no visible global function definition for ‘dev.new’ print.mm: no visible global function definition for ‘pdf’ print.mm: no visible global function definition for ‘tiff’ print.mm: no visible global function definition for ‘jpeg’ print.mm: no visible global function definition for ‘png’ print.mm: no visible global function definition for ‘postscript’ print.mm: no visible global function definition for ‘dev.off’ Undefined global functions or variables: aggregate dev.new dev.off gray jpeg median pdf png poly postscript tiff Consider adding importFrom("grDevices", "dev.new", "dev.off", "gray", "jpeg", "pdf", "png", "postscript", "tiff") importFrom("stats", "aggregate", "median", "poly") to your NAMESPACE file.

MIGSA

Version: 1.0.1

checking tests ... ``` ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output:

  Filter, Find, Map, Position, Reduce, anyDuplicated, append,
  as.data.frame, cbind, colMeans, colSums, colnames, do.call,
  duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
  lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
  pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
  setdiff, sort, table, tapply, union, unique, unsplit, which,
  which.max, which.min

Error in library("RUnit", quietly = TRUE) : there is no package called 'RUnit' Calls: -> library Execution halted ```

checking re-building of vignette outputs ... NOTE ``` ... df' not found.

See the pdftex.def package documentation for explanation. Type H for immediate help. ! Package pdftex.def Error: File `ClassDiagrams/SEAparams-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation. Type H for immediate help. ! Package pdftex.def Error: File `ClassDiagrams/GSEAparams-eps-converted-to.pdf ' not found.

See the pdftex.def package documentation for explanation. Type H for immediate help. ! Package pdftex.def Error: File `ClassDiagrams/FitOptions-eps-converted-to.pdf ' not found.

See the pdftex.def package documentation for explanation. Type H texi2pdf -> texi2dvi Execution halted ```

MIMOSA

Version: 1.14.0

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... Undefined global functions or variables: AnnotatedDataFrame ExpressionSet PTID Proportion Proportion_REF RefTreat aes as.formula callNextMethod contour coord_trans dbeta dexp ecdf facet_grid facet_wrap fisher.test geom_boxplot geom_jitter geom_line ggtitle gray.colors huber image is.formula ldply legend lines mclapply model.frame na.omit optim p.adjust pData<- par pbeta plot points position_jitter qbeta quantile rbeta rbinom read.table rmultinom rnorm runif scale_color_brewer scale_fill_brewer show terms title var Consider adding importFrom("grDevices", "gray.colors") importFrom("graphics", "contour", "image", "legend", "lines", "par", "plot", "points", "title") importFrom("methods", "callNextMethod", "show") importFrom("stats", "as.formula", "dbeta", "dexp", "ecdf", "fisher.test", "model.frame", "na.omit", "optim", "p.adjust", "pbeta", "qbeta", "quantile", "rbeta", "rbinom", "rmultinom", "rnorm", "runif", "terms", "var") importFrom("utils", "read.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

MineICA

Version: 1.16.0

checking package dependencies ... NOTE ``` Package which this enhances but not available for checking: ‘doMC’

Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘plyr’ ‘ggplot2’ ‘scales’ ‘foreach’ ‘xtable’ ‘biomaRt’ ‘gtools’ ‘GOstats’ ‘cluster’ ‘marray’ ‘mclust’ ‘RColorBrewer’ ‘colorspace’ ‘igraph’ ‘Rgraphviz’ ‘graph’ ‘annotate’ ‘Hmisc’ ‘fastICA’ ‘JADE’ Adding so many packages to the search path is excessive and importing selectively is preferable. ```
checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘biomaRt’ ‘GOstats’ ‘cluster’ ‘mclust’ ‘igraph’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘GOstats’ which was already attached by Depends. Please remove these calls from your code. Namespace in Imports field not imported from: ‘lumiHumanAll.db’ All declared Imports should be used. Packages in Depends field not imported from: ‘GOstats’ ‘Hmisc’ ‘JADE’ ‘RColorBrewer’ ‘Rgraphviz’ ‘annotate’ ‘biomaRt’ ‘cluster’ ‘colorspace’ ‘fastICA’ ‘foreach’ ‘ggplot2’ ‘graph’ ‘gtools’ ‘igraph’ ‘marray’ ‘mclust’ ‘methods’ ‘plyr’ ‘scales’ ‘xtable’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' calls which should be '::': ‘Biobase:::annotation’ ‘Biobase:::validMsg’ ‘fpc:::pamk’ ‘lumi:::getChipInfo’ ‘mclust:::adjustedRandIndex’ See the note in ?`:::` about the use of this operator. Unexported object imported by a ':::' call: ‘Biobase:::isValidVersion’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... reorder scale_colour_gradientn scale_colour_manual scale_fill_manual scale_linetype_manual scale_shape_manual scale_x_continuous scale_x_discrete scale_y_continuous shapiro.test sigCategories terrain_hcl theme theme_bw title tkplot.fit.to.screen unit useMart validObject vcount viewport wilcox.test write.table xlab xtable Consider adding importFrom("grDevices", "cm.colors", "dev.off", "graphics.off", "heat.colors", "pdf") importFrom("graphics", "abline", "axis", "frame", "hist", "layout", "legend", "mtext", "par", "plot", "plot.new", "points", "title") importFrom("methods", "callNextMethod", "new", "validObject") importFrom("stats", "aggregate", "as.dendrogram", "as.dist", "as.hclust", "chisq.test", "cor", "cor.test", "cutree", "dist", "hclust", "kmeans", "kruskal.test", "lm", "median", "na.omit", "order.dendrogram", "p.adjust", "quantile", "reorder", "shapiro.test", "wilcox.test") importFrom("utils", "capture.output", "combn", "read.table", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

MiRAnorm

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’ All declared Imports should be used.

mirIntegrator

Version: 1.6.0

checking R code for possible problems ... NOTE integrate_mir : isGraphNEL: no visible global function definition for ‘is’ pathways2pdf: no visible global function definition for ‘pdf’ pathways2pdf: no visible global function definition for ‘par’ pathways2pdf: no visible global function definition for ‘graphics.off’ plotLines: no visible binding for global variable ‘x’ plotLines: no visible binding for global variable ‘y’ plotLines: no visible binding for global variable ‘pathways_set’ plotPathway2Colors: no visible global function definition for ‘legend’ plot_change: no visible global function definition for ‘complete.cases’ Undefined global functions or variables: complete.cases graphics.off is legend par pathways_set pdf x y Consider adding importFrom("grDevices", "graphics.off", "pdf") importFrom("graphics", "legend", "par") importFrom("methods", "is") importFrom("stats", "complete.cases") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

MissingDataGUI

Version: 0.2-5

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

MixSIAR

Version: 3.1.7

checking examples ... ERROR ``` ... Running examples in ‘MixSIAR-Ex.R’ failed The error most likely occurred in:

Name: mixsiar_gui

Title: Run the GUI version of MixSIAR

Aliases: mixsiar_gui

** Examples

mixsiar_gui() Error in mixsiar_gui() : gWidgetsRGtk2 package not able to be loaded. If 'library('gWidgetsRGtk2')' does not work, MixSIAR GUI will not run. On Windows/Linux, try 'install.packages('gWidgetsRGtk2')'. On Mac, close R, download and install GTK+ from: http://r.research.att.com/#other. Then install latest X11 application (xQuartz) from http://xquartz.macosforge.org/landing/.
```
    If installing GTK+ continues to be problematic, consider using the
    script version of MixSIAR. See manual for help and examples.
```
Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘gWidgetsRGtk2’
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rjags’ All declared Imports should be used.

mizer

Version: 0.2

checking R code for possible problems ... NOTE ... ‘Species’ plotM2,MizerSim: no visible binding for global variable ‘w’ plotM2,MizerSim: no visible binding for global variable ‘value’ plotM2,MizerSim: no visible binding for global variable ‘Species’ plotSpectra,MizerSim: no visible binding for global variable ‘w’ plotSpectra,MizerSim: no visible binding for global variable ‘value’ plotSpectra,MizerSim: no visible binding for global variable ‘Species’ plotYield,MizerSim: no visible binding for global variable ‘time’ plotYield,MizerSim: no visible binding for global variable ‘value’ plotYield,MizerSim: no visible binding for global variable ‘Species’ plotYieldGear,MizerSim: no visible binding for global variable ‘time’ plotYieldGear,MizerSim: no visible binding for global variable ‘value’ plotYieldGear,MizerSim: no visible binding for global variable ‘Species’ plotYieldGear,MizerSim: no visible binding for global variable ‘gear’ Undefined global functions or variables: Species combn gear lm time value w Consider adding importFrom("stats", "lm", "time") importFrom("utils", "combn") to your NAMESPACE file.

mlmm

Version: 1.0

checking examples ... ERROR ``` ...
- for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
- if (censor[i]==1) var1[i]=0.05}
- pdata=data.frame(var1,var2,miss,censor,geneid,sid)
- pathdir=getwd()
- if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
- if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
- mcfit=readRDS(fp)
- model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
- formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
- respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
- iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
- }
  
  system.time(testfun()) Error in prep_call_sampler(object) : the compiled object from C++ code for this model is invalid, possible reasons:
- compiled with save_dso=FALSE;
- compiled on a different platform;
- does not exist (created from reading csv files). Calls: system.time ... sampling -> .local -> -> prep_call_sampler Timing stopped at: 0.224 0.008 0.234 Execution halted ```
checking installed package size ... NOTE installed size is 43.9Mb sub-directories of 1Mb or more: chunks 3.4Mb libs 40.3Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rstantools’ All declared Imports should be used.

mlr

Version: 2.11

checking whether package ‘mlr’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘BBmisc::isFALSE’ by ‘backports::isFALSE’ when loading ‘mlr’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/mlr/new/mlr.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Package suggested but not available for checking: ‘mlrMBO’
checking dependencies in R code ... NOTE Missing or unexported objects: ‘batchtools::getAlgorithmIds’ ‘batchtools::getProblemIds’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘mlrMBO’

mlrMBO

Version: 1.1.0

checking whether package ‘mlrMBO’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘BBmisc::isFALSE’ by ‘backports::isFALSE’ when loading ‘mlrMBO’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/mlrMBO/new/mlrMBO.Rcheck/00install.out’ for details.

mlxR

Version: 3.2.0

checking whether package ‘mlxR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/mlxR/new/mlxR.Rcheck/00install.out’ for details.

MMDiff2

Version: 1.4.0

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used.
checking R code for possible problems ... NOTE DBAmmd: no visible global function definition for ‘new’ Undefined global functions or variables: new Consider adding importFrom("methods", "new") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

mmnet

Version: 1.13.0

checking package dependencies ... ERROR ``` Package required but not available: ‘biom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

Mobilize

Version: 2.16-4

checking R code for possible problems ... NOTE ... ‘theme_text’ mapmobility: no visible global function definition for ‘lines’ responseplot: no visible global function definition for ‘na.omit’ scatterplot: no visible global function definition for ‘na.omit’ scatterplot: no visible global function definition for ‘opts’ scatterplot: no visible global function definition for ‘theme_text’ sharedtimeplot: no visible global function definition for ‘na.omit’ timeplot: no visible global function definition for ‘na.omit’ timeplot: no visible global function definition for ‘opts’ timeplot.character: no visible global function definition for ‘runif’ timeplot.character: no visible global function definition for ‘rnorm’ timeplot.character: no visible binding for global variable ‘text’ userplot: no visible global function definition for ‘na.omit’ Undefined global functions or variables: head lines na.omit opts quantile rnorm runif text theme_blank theme_text Consider adding importFrom("graphics", "lines", "text") importFrom("stats", "na.omit", "quantile", "rnorm", "runif") importFrom("utils", "head") to your NAMESPACE file.

modelr

Version: 0.1.1

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘lme4’, ‘rstanarm’

modeval

Version: 0.1.3

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Warning: Deprecated Quitting from lines 112-115 (modeval.Rmd) Error: processing vignette 'modeval.Rmd' failed with diagnostics: the argument has already been evaluated Execution halted

momentuHMM

Version: 1.2.0

checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: data 2.0Mb doc 1.8Mb libs 3.4Mb

Momocs

Version: 1.2.2

checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: data 1.5Mb doc 2.3Mb

monocle

Version: 2.4.0

checking re-building of vignette outputs ... WARNING ... the condition has length > 1 and only the first element will be used Warning in if (method == "num_genes") { : the condition has length > 1 and only the first element will be used Warning in if (method == "num_genes") { : the condition has length > 1 and only the first element will be used Warning in if (method == "num_genes") { : the condition has length > 1 and only the first element will be used Warning in if (method == "num_genes") { : the condition has length > 1 and only the first element will be used Warning in if (method == "num_genes") { : the condition has length > 1 and only the first element will be used Warning: Deprecated, use tibble::rownames_to_column() instead. Warning: Removed 3576038 rows containing non-finite values (stat_density). Warning: Deprecated, use tibble::rownames_to_column() instead. Warning: Deprecated, use tibble::rownames_to_column() instead. Warning: Transformation introduced infinite values in continuous y-axis Warning: Transformation introduced infinite values in continuous y-axis Quitting from lines 327-334 (monocle-vignette.Rnw) Error: processing vignette 'monocle-vignette.Rnw' failed with diagnostics: BLAS/LAPACK routine 'DLASCL' gave error code -4 Execution halted
checking R code for possible problems ... NOTE assign_cell_lineage: no visible global function definition for ‘nei’ buildBranchCellDataSet: no visible global function definition for ‘nei’ clusterCells: no visible binding for global variable ‘rho’ clusterCells: no visible binding for global variable ‘delta’ count_leaf_descendents: no visible global function definition for ‘nei’ cth_classifier_cds: no visible global function definition for ‘nei’ cth_classifier_cell: no visible global function definition for ‘nei’ diff_test_helper: no visible binding for global variable ‘Size_Factor’ extract_good_ordering: no visible global function definition for ‘nei’ fit_model_helper: no visible binding for global variable ‘Size_Factor’ get_next_node_id: no visible binding for '<<-' assignment to ‘next_node’ get_next_node_id: no visible binding for global variable ‘next_node’ make_canonical: no visible global function definition for ‘nei’ measure_diameter_path: no visible global function definition for ‘nei’ orderCells: no visible binding for '<<-' assignment to ‘next_node’ project2MST: no visible global function definition for ‘nei’ Undefined global functions or variables: Size_Factor delta nei next_node rho

moonBook

Version: 0.1.3

checking R code for possible problems ... NOTE ... num_summary: no visible binding for global variable ‘sd’ num_summary: no visible binding for global variable ‘median’ num_summary: no visible binding for global variable ‘mad’ num_summary: no visible binding for global variable ‘IQR’ num_summary: no visible binding for global variable ‘fivenum’ Undefined global functions or variables: IQR abline anova as.formula chisq.test coef confint density fisher.test fivenum kruskal.test legend lines lm mad median na.omit par plot points rainbow rect resid sd segments shapiro.test t.test terms text var.test write.csv write.table xtabs Consider adding importFrom("grDevices", "rainbow") importFrom("graphics", "abline", "legend", "lines", "par", "plot", "points", "rect", "segments", "text") importFrom("stats", "IQR", "anova", "as.formula", "chisq.test", "coef", "confint", "density", "fisher.test", "fivenum", "kruskal.test", "lm", "mad", "median", "na.omit", "resid", "sd", "shapiro.test", "t.test", "terms", "var.test", "xtabs") importFrom("utils", "write.csv", "write.table") to your NAMESPACE file.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'cbind.mytable': ‘cbind.mytable’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```
checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.

mosaic

Version: 1.1.0

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘manipulate’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘cubature’

mosaicData

Version: 0.14.0

checking data for non-ASCII characters ... NOTE Note: found 7 marked UTF-8 strings

mosaicModel

Version: 0.3.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’ All declared Imports should be used.

mousetrap

Version: 3.1.0

checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: data 2.0Mb libs 4.5Mb

mrfDepth

Version: 1.0.5

checking examples ... ERROR ``` ... Running examples in ‘mrfDepth-Ex.R’ failed The error most likely occurred in:

Name: fom

Title: Draws the Functional Outlier Map (FOM)

Aliases: fom

Keywords: Graphical

** Examples

data(octane)

To construct the FOM, one first need to calculate

the functional outlyingness.

Note that the option diagnostic in fOutl must be

set to TRUE. If not calling fom will result in an

error

Result <- fOutl(octane, alpha = 0, type = "fAO", diagnostic = TRUE); fom(Result) Error: Columns x, y must be 1d atomic vectors or lists Execution halted ```

checking installed package size ... NOTE installed size is 15.9Mb sub-directories of 1Mb or more: libs 15.1Mb

mrMLM

Version: 2.1

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

MSCMT

Version: 1.3.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rdpack’ All declared Imports should be used.

msgbsR

Version: 1.0.0

checking data for ASCII and uncompressed saves ... WARNING ```

Note: significantly better compression could be obtained by using R CMD build --resave-data old_size new_size compress ratdata.rda 318Kb 128Kb xz ratdata2.rda 287Kb 116Kb xz ```
checking installed package size ... NOTE installed size is 16.1Mb sub-directories of 1Mb or more: extdata 15.2Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'utils' All declared Imports should be used.

MSnbase

Version: 2.2.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in has_utility("convert", "ImageMagick") : ImageMagick not installed or not in PATH Quitting from lines 1022-1029 (MSnbase-demo.Rnw) Error: processing vignette 'MSnbase-demo.Rnw' failed with diagnostics: package or namespace load failed for 'Rdisop' in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/muelleki/git/R/ggplot2/revdep/library/MSnbase/Rdisop/libs/Rdisop.so': libRcppClassic.so: cannot open shared object file: No such file or directory Execution halted
checking installed package size ... NOTE installed size is 9.0Mb sub-directories of 1Mb or more: data 1.9Mb doc 4.3Mb
checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Laurent Gatto <lg390@cam.ac.uk> [aut, cre] Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘Biobase:::.showAnnotatedDataFrame’ ‘MALDIquant:::.estimateNoise’ ‘MALDIquant:::.localMaxima’ ‘MALDIquant:::.movingAverage’ ‘MALDIquant:::.savitzkyGolay’ See the note in ?`:::` about the use of this operator.

MSnID

Version: 1.10.0

checking R code for possible problems ... NOTE ... .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘modification’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘DatabaseAccess’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘DatabaseDescription’ .read_mzIDs.mzR.engine.single.file: no visible binding for global variable ‘DBseqLength’ infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for global variable ‘accession’ infer_parsimonious_accessions,MSnID : infer_acc: no visible binding for global variable ‘pepSeq’ recalibrate,MSnID: no visible global function definition for ‘median’ recalibrate,MSnID: no visible global function definition for ‘density’ Undefined global functions or variables: DBseqLength DatabaseAccess DatabaseDescription accession density i location mass median modification name optim pepSeq quantile rnorm spectrumID Consider adding importFrom("stats", "density", "median", "optim", "quantile", "rnorm") to your NAMESPACE file.

msPurity

Version: 1.2.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'msPurity-vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘Rcpp’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. package 'methods' is used but not declared
checking R code for possible problems ... NOTE ... removeIsotopes: no visible global function definition for ‘write.csv’ rsde: no visible global function definition for ‘sd’ snrFilter: no visible global function definition for ‘median’ stde: no visible global function definition for ‘sd’ stderror: no visible global function definition for ‘sd’ averageSpectra,purityD: no visible binding for global variable ‘i’ subtract,purityD: no visible binding for global variable ‘i’ validate,purityA: no visible global function definition for ‘head’ writeOut,purityD: no visible global function definition for ‘write.csv’ Undefined global functions or variables: abline alli approxfun as.dist dev.off dist dnorm fix head i idx legend lines median mtch mtchi na.omit parallel plot png points purity read.csv scanid sd text variable write.csv Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "abline", "legend", "lines", "plot", "points", "text") importFrom("stats", "approxfun", "as.dist", "dist", "dnorm", "median", "na.omit", "sd") importFrom("utils", "fix", "head", "read.csv", "write.csv") to your NAMESPACE file.

MSstats

Version: 3.8.6

checking whether package ‘MSstats’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘MSnbase::image’ by ‘graphics::image’ when loading ‘MSstats’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/MSstats/new/MSstats.Rcheck/00install.out’ for details.
checking R code for possible problems ... NOTE ... dataProcessPlots: no visible binding for global variable ‘Name’ dataProcessPlots: no visible binding for global variable ‘analysis’ dataProcessPlots: no visible binding for global variable ‘Mean’ dataProcessPlots: no visible binding for global variable ‘ciw’ groupComparisonPlots: no visible binding for global variable ‘Protein’ groupComparisonPlots: no visible binding for global variable ‘logFC’ groupComparisonPlots: no visible binding for global variable ‘ciw’ linear_quantlim: no visible binding for global variable ‘label’ modelBasedQCPlots: no visible binding for global variable ‘residual’ nonlinear_quantlim: no visible binding for global variable ‘label’ plot_quantlim: no visible binding for global variable ‘x’ plot_quantlim: no visible binding for global variable ‘y’ plot_quantlim: no visible binding for global variable ‘ymin’ plot_quantlim: no visible binding for global variable ‘ymax’ plot_quantlim: no visible binding for global variable ‘shape’ transformMSnSetToMSstats: no visible global function definition for ‘pData’ Undefined global functions or variables: ABUNDANCE LABEL Mean Name Protein RUN analysis ciw datafeature grid.layout grid.newpage label logFC missing.col pData pushViewport residual shape weight x y ymax ymin

mudata2

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘hms’ ‘methods’ All declared Imports should be used.

MultiBD

Version: 0.2.0

checking installed package size ... NOTE installed size is 9.5Mb sub-directories of 1Mb or more: libs 7.9Mb

multilevelPSA

Version: 1.2.4

checking R code for possible problems ... NOTE missing.plot: possible error in theme(axis.text.x = element_text(size = 6, angle = -90, hjust = 0.5, vjust = 0.5), axis.text.x = element_blank(), axis.ticks = element_blank()): formal argument "axis.text.x" matched by multiple actual arguments

MultiMeta

Version: 0.1

checking R code for possible problems ... NOTE ... multi_meta: no visible global function definition for ‘write.table’ multi_meta: no visible global function definition for ‘read.table’ multi_meta: no visible global function definition for ‘pchisq’ qqplotter: no visible global function definition for ‘read.table’ qqplotter: no visible global function definition for ‘qchisq’ qqplotter: no visible global function definition for ‘ppoints’ qqplotter: no visible global function definition for ‘median’ qqplotter: no visible global function definition for ‘pchisq’ qqplotter: no visible global function definition for ‘pdf’ qqplotter: no visible global function definition for ‘plot’ qqplotter: no visible global function definition for ‘abline’ qqplotter: no visible global function definition for ‘dev.off’ Undefined global functions or variables: abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot points ppoints qchisq read.table write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf") importFrom("graphics", "abline", "axis", "plot", "points") importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq") importFrom("utils", "read.table", "write.table") to your NAMESPACE file.

munsell

Version: 0.4.3

checking examples ... ERROR ``` Running examples in ‘munsell-Ex.R’ failed The error most likely occurred in:

Name: complement_slice

Title: A vertical slice through the Munsell space

Aliases: complement_slice

** Examples

complement_slice("5PB") Warning: Removed 41 rows containing missing values (geom_text). Error: Free scales are only supported with coord_cartesian() and coord_flip() Execution halted ```

MutationalPatterns

Version: 1.2.1

checking re-building of vignette outputs ... NOTE `` ... Warning: Transformation introduced infinite values in continuous y-axis Warning: Removed 8 rows containing missing values (geom_point). Using by, region as id variables Warning: Ignoring unknown aesthetics: ymax Warning: Using alpha for a discrete variable is not advised. Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'Introduction_to_MutationalPatterns.tex' failed. LaTeX errors: ! LaTeX Error: Fileapacite.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.5 \bibliographystyle {apacite}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

mvdalab

Version: 1.4

checking examples ... ERROR ``` Running examples in ‘mvdalab-Ex.R’ failed The error most likely occurred in:

Name: plot.plusminus

Title: 2D Graph of the PCA scores associated with a plusminusFit

Aliases: plot.plusminus

** Examples

PLUS-Minus CLASSIFIER WITH validation = 'none', i.e. no CV

data(plusMinusDat) mod1 <- plusminusFit(Y ~., data = plusMinusDat, validation = "none", n_cores = 2) plot(mod1, ncomp = 2, comps = c(1, 2)) Error: Columns colour, shape must be 1d atomic vectors or lists Execution halted ```

MWASTools

Version: 1.0.0

checking re-building of vignette outputs ... WARNING ``` ... % metabolite features with CV < 0.3 : 99

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Error: processing vignette 'MWASTools.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE MWAS_scatterplotMS: no visible binding for global variable ‘logpval’ QC_CV_scatterplot: no visible binding for global variable ‘abs.CV’ Undefined global functions or variables: abs.CV logpval

myTAI

Version: 0.6.0

checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: data 2.0Mb doc 2.7Mb

nandb

Version: 0.2.1

checking package dependencies ... ERROR ``` Packages required but not available: ‘autothresholdr’ ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

natserv

Version: 0.1.4

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: 3: cli$get(query = query) 4: private$make_url(self$url, self$handle, path, query) 5: add_query(query, url) 6: check_key(key) 7: getOption("NatureServeKey", stop("You need an API key for NatureServe")) 8: stop("You need an API key for NatureServe")

testthat results ================================================================ OK: 14 SKIPPED: 0 FAILED: 3 1. Error: ns_data works as expected (@test-ns_data.R#6) 2. Error: ns_images works as expected (@test-ns_images.R#6) 3. Error: ns_search works as expected (@test-ns_search.R#6)

Error: testthat unit tests failed Execution halted ```

NeatMap

Version: 0.3.6.2

checking R code for possible problems ... NOTE data.reduction: no visible global function definition for ‘prcomp’ data.reduction: no visible global function definition for ‘hclust’ data.reduction: no visible global function definition for ‘as.dist’ data.reduction: no visible global function definition for ‘cor’ data.reduction: no visible global function definition for ‘dist’ heatmap1: no visible global function definition for ‘sd’ lineplot: no visible global function definition for ‘sd’ normalize: no visible global function definition for ‘sd’ profileplot3d : ColorFunction: no visible global function definition for ‘rgb’ profileplot3d : ColorFunction: no visible global function definition for ‘colorRamp’ profileplot3d: no visible global function definition for ‘sd’ profileplot3d: no visible global function definition for ‘gray’ Undefined global functions or variables: as.dist colorRamp cor dist gray hclust prcomp rgb sd Consider adding importFrom("grDevices", "colorRamp", "gray", "rgb") importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd") to your NAMESPACE file.
checking compiled code ... NOTE ``` File ‘NeatMap/libs/NeatMap.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘nMDS_R.o’ Found ‘srand’, possibly from ‘srand’ (C) Object: ‘nMDS_R.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

nethet

Version: 1.8.0

checking R code for possible problems ... NOTE ... t2cov.lr: no visible global function definition for ‘var’ t2cov.lr: no visible global function definition for ‘pchisq’ t2diagcov.lr: no visible global function definition for ‘var’ t2diagcov.lr: no visible global function definition for ‘pchisq’ test.sd: no visible global function definition for ‘var’ test.sd: no visible global function definition for ‘pnorm’ twosample_single_regr: no visible global function definition for ‘coef’ twosample_single_regr: no visible global function definition for ‘lm’ Undefined global functions or variables: abline boxplot coef cor cov.wt dev.off dnorm grey hist kmeans legend lines lm median optimize p.adjust par pchisq pdf pnorm quantile rbeta rnorm segments shapiro.test var write.csv Consider adding importFrom("grDevices", "dev.off", "grey", "pdf") importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines", "par", "segments") importFrom("stats", "coef", "cor", "cov.wt", "dnorm", "kmeans", "lm", "median", "optimize", "p.adjust", "pchisq", "pnorm", "quantile", "rbeta", "rnorm", "shapiro.test", "var") importFrom("utils", "write.csv") to your NAMESPACE file.

netprioR

Version: 1.2.0

checking re-building of vignette outputs ... WARNING ``` ...

Warning: executing %dopar% sequentially: no parallel backend registered Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Error: processing vignette 'netprioR.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

netresponse

Version: 1.36.0

checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘NetResponse.Rmd’, ‘NetResponse.md’, ‘TODO/TODO.Rmd’, ‘fig/NetResponse2-1.png’, ‘fig/NetResponse2b-1.png’, ‘fig/NetResponse3-1.png’, ‘fig/NetResponse4-1.png’, ‘fig/NetResponse5-1.png’, ‘fig/NetResponse7-1.png’, ‘fig/vdp-1.png’, ‘main.R’, ‘netresponse.bib’, ‘netresponse.pdf’ Package has no Sweave vignette sources and no VignetteBuilder field.
checking compiled code ... NOTE ``` File ‘netresponse/libs/netresponse.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘netresponse.o’ Found ‘srand’, possibly from ‘srand’ (C) Object: ‘netresponse.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

NetworkChange

Version: 0.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘abind’ All declared Imports should be used.

networkreporting

Version: 0.1.1

checking re-building of vignette outputs ... WARNING ``` ... Attaching package: 'dplyr'

The following objects are masked from 'package:plyr':
```
arrange, count, desc, failwith, id, mutate, rename, summarise,
summarize
```
The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Loading required package: functional Loading required package: stringr Quitting from lines 221-222 (network_scaleup.Rmd) Error: processing vignette 'network_scaleup.Rmd' failed with diagnostics: Column x must be a 1d atomic vector or a list Execution halted ```

networktools

Version: 1.1.0

checking examples ... ERROR ``` Running examples in ‘networktools-Ex.R’ failed The error most likely occurred in:

Name: plot.expectedInf

Title: Plot "expectedInf" objects

Aliases: plot.expectedInf

** Examples

Don't show:

myNetwork <- cor(depression[,1:5])

End(Don't show)

out1 <- expectedInf(myNetwork) plot(out1$step1) Error: Column x must be a 1d atomic vector or a list Execution halted ```

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘devtools’ All declared Imports should be used.

neuropsychology

Version: 0.5.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘htmlTable’ ‘lme4’ ‘stringi’ All declared Imports should be used.

NFP

Version: 0.99.2

checking package dependencies ... NOTE Package suggested but not available for checking: ‘NFPdata’
checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: data 7.5Mb

nima

Version: 0.4.5

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘survival’ All declared Imports should be used.

nimble

Version: 0.6-7

checking installed package size ... NOTE installed size is 14.5Mb sub-directories of 1Mb or more: CppCode 1.0Mb R 3.4Mb classic-bugs 1.6Mb include 5.8Mb tests 1.2Mb

nlmixr

Version: 0.9.0-1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 195 SKIPPED: 0 FAILED: 11
1. Failure: ODE (@test-model68.R#64)
2. Failure: ODE (@test-model68.R#65)
3. Failure: ODE (@test-model68.R#66)
4. Failure: ODE (@test-model68.R#68)
5. Failure: ODE (@test-model68.R#69)
6. Failure: ODE (@test-model68.R#71)
7. Failure: ODE (@test-model68.R#72)
8. Failure: ODE (@test-model68.R#73)
9. Failure: ODE (@test-model68.R#76)
10. ...
Error: testthat unit tests failed Execution halted ```
checking compiled code ... WARNING ``` File ‘nlmixr/libs/nlmixr.so’: Found ‘__assert_fail’, possibly from ‘assert’ (C) Objects: ‘RcppExportMod.o’, ‘RcppExports.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```
checking installed package size ... NOTE installed size is 13.7Mb sub-directories of 1Mb or more: libs 12.5Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dparser’ ‘inline’ ‘n1qn1’ All declared Imports should be used.

NlsyLinks

Version: 2.0.6

checking installed package size ... NOTE installed size is 8.6Mb sub-directories of 1Mb or more: data 4.3Mb reports 2.3Mb

NMF

Version: 0.20.6

checking Rd cross-references ... WARNING Unknown package ‘RcppOctave’ in Rd xrefs
checking re-building of vignette outputs ... WARNING `` ... ... Error in citation(x) : package 'doMC' not found Converted 9 of 10 package citations to BibTeX Writing 11 Bibtex entries ... OK Results written to file 'Rpackages.bib' Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'NMF-vignette.tex' failed. LaTeX errors: ! LaTeX Error: Filebiblatex.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.131 \AtEveryCitekey {\clearfield{url}}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘RcppOctave’
checking R code for possible problems ... NOTE algorithm,NMFStrategyOctave: no visible global function definition for ‘fstop’ evar,ANY: no visible binding for global variable ‘Biobase’ nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global variable ‘n’ nmf,matrix-numeric-NMFStrategy : run.all: no visible binding for global variable ‘RNGobj’ rss,matrix: no visible binding for global variable ‘Biobase’ Undefined global functions or variables: Biobase RNGobj fstop n

noaastormevents

Version: 0.1.0

checking package dependencies ... NOTE Package suggested but not available for checking: ‘hurricaneexposuredata’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’ ‘hurricaneexposure’ ‘plyr’ All declared Imports should be used.

NormalizeMets

Version: 0.22

checking installed package size ... NOTE installed size is 9.2Mb sub-directories of 1Mb or more: doc 8.6Mb

NORRRM

Version: 1.0.0

checking R code for possible problems ... NOTE CIPW: no visible global function definition for ‘data’ CIPW: no visible binding for global variable ‘AtomWeight’ CIPW: no visible binding for global variable ‘MinWeight’ CIPW: no visible binding for global variable ‘OxiWeight’ CIPW.trace: no visible global function definition for ‘data’ CIPW.trace: no visible binding for global variable ‘AtomWeight’ CIPW.trace: no visible binding for global variable ‘MinWeight’ CIPW.trace: no visible binding for global variable ‘OxiWeight’ Undefined global functions or variables: AtomWeight MinWeight OxiWeight data Consider adding importFrom("utils", "data") to your NAMESPACE file.

NPflow

Version: 0.13.1

checking installed package size ... NOTE installed size is 10.8Mb sub-directories of 1Mb or more: libs 10.4Mb

nullabor

Version: 0.3.1

checking R code for possible problems ... NOTE ... reg_dist: no visible global function definition for ‘lm’ resid_boot: no visible global function definition for ‘resid’ resid_pboot: no visible global function definition for ‘rnorm’ resid_rotate: no visible global function definition for ‘rnorm’ resid_rotate: no visible global function definition for ‘update’ resid_rotate: no visible global function definition for ‘resid’ resid_sigma: no visible global function definition for ‘rnorm’ rorschach: no visible global function definition for ‘rbinom’ rss: no visible global function definition for ‘resid’ sep_dist: no visible global function definition for ‘dist’ sep_dist: no visible global function definition for ‘cutree’ sep_dist: no visible global function definition for ‘hclust’ uni_dist: no visible global function definition for ‘sd’ Undefined global functions or variables: coef cutree dist filter hclust lm predict quantile rbinom resid rnorm sd update Consider adding importFrom("stats", "coef", "cutree", "dist", "filter", "hclust", "lm", "predict", "quantile", "rbinom", "resid", "rnorm", "sd", "update") to your NAMESPACE file.

nzelect

Version: 0.4.0

checking data for non-ASCII characters ... NOTE Note: found 6409 marked UTF-8 strings

oapackage

Version: 2.0.23

checking installed package size ... NOTE installed size is 27.4Mb sub-directories of 1Mb or more: libs 27.3Mb

observer

Version: 0.1.2

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘ensurer’, ‘validate’

oddsratio

Version: 1.0.0

checking examples ... ERROR ``` ...
- pred = "x2", values = c(0.099, 0.198))
  
  insert first odds ratios to plot
  
  plot_object <- insert_or(plot_object, or_object1, or_yloc = 3,
- values_xloc = 0.04, line_size = 0.5,
- line_type = "dotdash", text_size = 6,
- values_yloc = 0.5, arrow_col = "red")
  
  calculate second odds ratio
  
  or_object2 <- or_gam(data = data_gam, model = fit_gam, pred = "x2",
- values = c(0.4, 0.6))
  
  add or_object2 into plot
  
  insert_or(plot_object, or_object2, or_yloc = 2.1, values_yloc = 2,
- line_col = "green4", text_col = "black",
- rect_col = "green4", rect_alpha = 0.2,
- line_alpha = 1, line_type = "dashed",
- arrow_xloc_r = 0.01, arrow_xloc_l = -0.01,
- arrow_length = 0.01, rect = TRUE) Error: Aesthetics must be either length 1 or the same as the data (1): xmin, xmax, ymin, ymax, fill, alpha Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:

Loading required package: nlme This is mgcv 1.8-22. For overview type 'help("mgcv-package")'. Warning: No confident interval calculation possible for 'glmmPQL' models

testthat results ================================================================ OK: 5 SKIPPED: 0 FAILED: 3 1. Failure: check bevhaviour of ggplot_build (changed in ggplot2 v2.2) (@test-insert-or.R#19) 2. Failure: check bevhaviour of ggplot_build (changed in ggplot2 v2.2) (@test-insert-or.R#20) 3. Failure: check bevhaviour of ggplot_build (changed in ggplot2 v2.2) (@test-insert-or.R#21)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 124-133 (function_tutorial.Rmd) Error: processing vignette 'function_tutorial.Rmd' failed with diagnostics: Aesthetics must be either length 1 or the same as the data (1): xmin, xmax, ymin, ymax, fill, alpha Execution halted

officer

Version: 0.1.8

checking examples ... ERROR ``` Running examples in ‘officer-Ex.R’ failed The error most likely occurred in:

Name: slip_in_img

Title: append an image

Aliases: slip_in_img

** Examples

library(magrittr) img.file <- file.path( Sys.getenv("R_HOME"), "doc", "html", "logo.jpg" ) x <- read_docx() %>% + body_add_par("R logo: ", style = "Normal") %>% + slip_in_img(src = img.file, style = "strong", width = .3, height = .3) Error: file.exists(src) is not TRUE Execution halted ```
checking tests ... `` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 6: freduce(value,_function_list`) 7: withVisible(function_list[k]) 8: function_list[k] 9: ph_with_img(., type = "body", src = img.file, height = 1.06, width = 1.39) 10: external_img(src, width = width/914400, height = height/914400) 11: stopifnot(file.exists(src)) 12: stop(msg, call. = FALSE, domain = NA)

testthat results ================================================================ OK: 341 SKIPPED: 1 FAILED: 2 1. Error: image add (@test-docx-add.R#68) 2. Error: add img into placeholder (@test-pptx-add.R#67)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Quitting from lines 180-190 (powerpoint.Rmd) Error: processing vignette 'powerpoint.Rmd' failed with diagnostics: file.exists(src) is not TRUE Execution halted ```

OncoSimulR

Version: 2.6.0

checking installed package size ... NOTE installed size is 11.0Mb sub-directories of 1Mb or more: doc 5.4Mb libs 4.9Mb

onemap

Version: 2.1.1

checking whether package ‘onemap’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available Warning: loading Rplot failed See ‘/home/muelleki/git/R/ggplot2/revdep/checks/onemap/new/onemap.Rcheck/00install.out’ for details.
checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: libs 3.9Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘maps’ All declared Imports should be used.

openwindfarm

Version: 0.1.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Quitting from lines 22-24 (openwindfarm-vignette.Rmd) Error: processing vignette 'openwindfarm-vignette.Rmd' failed with diagnostics: there is no package called 'webshot' Execution halted

OperaMate

Version: 1.8.0

checking R code for possible problems ... NOTE ... generateReport: no visible global function definition for ‘write.table’ operaMate : configParser: no visible global function definition for ‘read.csv’ parseFullTab: no visible global function definition for ‘read.delim’ parseMatrix: no visible global function definition for ‘read.delim’ parseTab: no visible global function definition for ‘read.delim’ wellQC : <anonymous>: no visible global function definition for ‘boxplot’ wellQC: no visible global function definition for ‘boxplot’ cellNorm,cellData: no visible global function definition for ‘capture.output’ show,cellData: no visible global function definition for ‘str’ show,expData: no visible global function definition for ‘str’ Undefined global functions or variables: abline boxplot capture.output combn read.csv read.delim str strheight strwidth write.table Consider adding importFrom("graphics", "abline", "boxplot", "strheight", "strwidth") importFrom("utils", "capture.output", "combn", "read.csv", "read.delim", "str", "write.table") to your NAMESPACE file.

optiRum

Version: 0.37.3

checking tests ... `` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:check1inherits fromggplot_builtnotlist`.
1. Failure: giniChart correctly produce a chart, factor outcome (@test-giniChart.R#14) check1 inherits from ggplot_built not list.
testthat results ================================================================ OK: 201 SKIPPED: 0 FAILED: 3 1. Error: generatePDF - correct behaviour, DATED=FALSE,CLEANUP=TRUE, compiler=xelatex (@test-generatePDF.R#75) 2. Failure: giniChart correctly produce a chart, numeric outcome (@test-giniChart.R#7) 3. Failure: giniChart correctly produce a chart, factor outcome (@test-giniChart.R#14)

Error: testthat unit tests failed Execution halted ```

optiSel

Version: 1.0.0

checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: extdata 1.8Mb libs 5.5Mb

orderedLasso

Version: 1.7

checking R code for possible problems ... NOTE ... plot.orderedLasso.cv: no visible global function definition for ‘abline’ plot.timeLagLasso.cv: no visible global function definition for ‘par’ plot.timeLagLasso.cv: no visible global function definition for ‘plot’ plot.timeLagLasso.cv: no visible global function definition for ‘axis’ plot.timeLagLasso.cv: no visible global function definition for ‘mtext’ plot.timeLagLasso.cv: no visible global function definition for ‘points’ plot.timeLagLasso.cv: no visible global function definition for ‘abline’ timeLagLasso: no visible binding for global variable ‘sd’ timeLagLasso.cv: no visible binding for global variable ‘sd’ timeLagLasso.cv: no visible binding for global variable ‘var’ timeLagLasso.path: no visible binding for global variable ‘sd’ Undefined global functions or variables: abline approx axis mtext par plot points sd segments var Consider adding importFrom("graphics", "abline", "axis", "mtext", "par", "plot", "points", "segments") importFrom("stats", "approx", "sd", "var") to your NAMESPACE file.

ordinalForest

Version: 2.1

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: libs 5.9Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

Organism.dplyr

Version: 1.2.2

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'Organism.dplyr.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘AnnotationDbi:::smartKeys’ ‘GenomicFeatures:::.exons_with_3utr’ ‘GenomicFeatures:::.exons_with_5utr’ ‘GenomicFeatures:::get_TxDb_seqinfo0’ ‘S4Vectors:::extract_data_frame_rows’ See the note in ?`:::` about the use of this operator.

osmplotr

Version: 0.3.0

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: doc 5.9Mb

otvPlots

Version: 0.2.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘quantreg’ All declared Imports should be used.

P2C2M

Version: 0.7.6

checking package dependencies ... ERROR ``` Package required but not available: ‘rPython’

Packages suggested but not available for checking: ‘genealogicalSorting’ ‘phybase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

pa

Version: 1.2-1

checking dependencies in R code ... NOTE Package in Depends field not imported from: ‘grid’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE .formula.make: no visible global function definition for ‘formula’ regress: no visible global function definition for ‘lm’ regress: no visible global function definition for ‘model.matrix’ Undefined global functions or variables: formula lm model.matrix Consider adding importFrom("stats", "formula", "lm", "model.matrix") to your NAMESPACE file.

pacotest

Version: 0.2.2

checking installed package size ... NOTE installed size is 7.1Mb sub-directories of 1Mb or more: libs 6.9Mb

PairedData

Version: 1.0.1

checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘MASS’ ‘gld’ ‘mvtnorm’ Please remove these calls from your code.
checking R code for possible problems ... NOTE ... winvar.Z: no visible global function definition for ‘qnorm’ yuen.t.test.formula: no visible global function definition for ‘terms’ yuen1.test: no visible global function definition for ‘qt’ yuen1.test: no visible global function definition for ‘pt’ yuen2.test: no visible global function definition for ‘complete.cases’ yuen2.test: no visible global function definition for ‘qt’ yuen2.test: no visible global function definition for ‘pt’ yuenp.test: no visible global function definition for ‘complete.cases’ yuenp.test: no visible global function definition for ‘qt’ yuenp.test: no visible global function definition for ‘pt’ summary,paired: no visible global function definition for ‘cor’ Undefined global functions or variables: IQR complete.cases cor cor.test dnorm integrate mad median pchisq pf pnorm pt qchisq qf qnorm qt rbinom reorder sd t.test terms var wilcox.test Consider adding importFrom("stats", "IQR", "complete.cases", "cor", "cor.test", "dnorm", "integrate", "mad", "median", "pchisq", "pf", "pnorm", "pt", "qchisq", "qf", "qnorm", "qt", "rbinom", "reorder", "sd", "t.test", "terms", "var", "wilcox.test") to your NAMESPACE file.

paleofire

Version: 1.2.0

checking whether package ‘paleofire’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘paleofire’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/paleofire/new/paleofire.Rcheck/00install.out’ for details.

checking re-building of vignette outputs ... NOTE ``` ... trying URL 'http://blarquez.com/public/data/data_cageo.zip' Content type 'application/zip' length 14857 bytes (14 KB) ================================================== downloaded 14 KB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'paleofire-paper.tex' failed. LaTeX errors: ! LaTeX Error: File `elsarticle.cls' not found.

Type X to quit or to proceed, or enter new name. (Default extension: cls)

! Emergency stop.

l.4 ^^M

! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

pandaR

Version: 1.8.0

checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: data 9.0Mb
checking R code for possible problems ... NOTE dFunction: no visible global function definition for ‘cor’ importPandaMatlab: no visible global function definition for ‘read.delim’ panda: no visible global function definition for ‘cor’ panda: no visible global function definition for ‘aggregate’ plot.panda: no visible global function definition for ‘hist’ plotCommunityDetection: no visible global function definition for ‘title’ plotZbyTF: no visible global function definition for ‘aggregate’ prepResult: no visible global function definition for ‘pnorm’ Undefined global functions or variables: aggregate cor hist pnorm read.delim title Consider adding importFrom("graphics", "hist", "title") importFrom("stats", "aggregate", "cor", "pnorm") importFrom("utils", "read.delim") to your NAMESPACE file.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'plot.panda': ‘plot.panda’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

parallelDist

Version: 0.2.0

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: libs 4.8Mb

parlitools

Version: 0.2.1

checking data for non-ASCII characters ... NOTE Note: found 13 marked UTF-8 strings

parsemsf

Version: 0.1.0

checking examples ... ERROR ``` Running examples in ‘parsemsf-Ex.R’ failed The error most likely occurred in:

Name: make_area_table

Title: Make a table of peptide areas

Aliases: make_area_table

** Examples

make_area_table(parsemsf_example("test_db.msf")) Error: Condition message must be a string Execution halted ```
checking tests ... `` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 13: glubort(NULL, "The {name} package is required to {reason}.", if (install) "\nPlease install it withinstall.packages(\"{name}\")`") 14: .abort(text) 15: cnd_error(type, .msg = msg, .call = sys.call(-1)) 16: new_cnd(c(.type, "error"), ..., .msg = .msg) 17: stop("Condition message must be a string", call. = FALSE)

Error: Condition message must be a string testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 3 1. Error: make_area_table creates a data frame with the correct column names (@test_make_area_table.R#16) 2. Error: make_pep_table creates a data frame with the correct column names (@test_make_pep_table.R#13) 3. Error: map_peptides creates a data frame with the correct column names (@test_map_peptides.R#16)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 20-25 (introduction.Rmd) Error: processing vignette 'introduction.Rmd' failed with diagnostics: Condition message must be a string Execution halted
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘RSQLite’ All declared Imports should be used.

passport

Version: 0.1.1

checking examples ... ERROR ``` Running examples in ‘passport-Ex.R’ failed The error most likely occurred in:

Name: parse_country

Title: Parse country names to standardized form

Aliases: parse_country

** Examples

parse_country(c("United States", "USA", "U.S.", "us", "United States of America")) [1] "US" "US" "US" "US" "US"

Unicode support for parsing accented or non-Latin scripts

parse_country(c("\u65e5\u672c", "Japon", "\u0698\u0627\u067e\u0646"), how = "dstk") Error in open.connection(con, "rb") : Timeout was reached: Connection timed out after 10001 milliseconds Calls: parse_country ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 7: fromJSON(url) 8: jsonlite::fromJSON(...) 9: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, simplifyMatrix = simplifyMatrix, flatten = flatten, ...) 10: parseJSON(txt, bigint_as_char) 11: parse_con(txt, bigint_as_char) 12: open(con, "rb") 13: open.connection(con, "rb")

testthat results ================================================================ OK: 34 SKIPPED: 0 FAILED: 1 1. Error: parsing country names with live geocoding APIs works (@test_parse_country.R#61)

Error: testthat unit tests failed Execution halted ```

PathoStat

Version: 1.2.1

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning: Transformation introduced infinite values in discrete y-axis Error: processing vignette 'PathoStatAdvanced.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

pathVar

Version: 1.6.0

checking R code for possible problems ... NOTE ... plotOneSample: no visible binding for global variable ‘Number_of_genes’ plotTwoSamplesCont: no visible binding for global variable ‘PwayName’ plotTwoSamplesCont: no visible binding for global variable ‘NumOfGenesFromDataSetInPathway’ plotTwoSamplesCont: no visible binding for global variable ‘value’ plotTwoSamplesCont: no visible binding for global variable ‘..density..’ plotTwoSamplesCont: no visible binding for global variable ‘group’ plotTwoSamplesDisc: no visible binding for global variable ‘Cluster’ plotTwoSamplesDisc: no visible binding for global variable ‘Number_of_genes’ sigOneSample: no visible binding for global variable ‘APval’ sigOneSample: no visible binding for global variable ‘PwayName’ sigTwoSamplesCont: no visible binding for global variable ‘APval’ sigTwoSamplesCont: no visible binding for global variable ‘PwayName’ sigTwoSamplesDisc: no visible binding for global variable ‘APval’ sigTwoSamplesDisc: no visible binding for global variable ‘PwayName’ Undefined global functions or variables: ..density.. APval Cluster NumOfGenesFromDataSetInPathway Number_of_genes PercOfGenesInPway PwayName avg cv group medAbsDev standDev value

patPRO

Version: 1.1.0

checking DESCRIPTION meta-information ... NOTE Checking should be performed on sources prepared by ‘R CMD build’.

patternplot

Version: 0.2

checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

pauwels2014

Version: 1.0

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking R code for possible problems ... NOTE add_noise: no visible global function definition for ‘rnorm’ estimate_risk_dream6 : <anonymous>: no visible global function definition for ‘var’ generate_sample: no visible global function definition for ‘rnorm’ generate_sample: no visible global function definition for ‘runif’ sample_function: no visible global function definition for ‘runif’ sample_function : <anonymous>: no visible global function definition for ‘var’ sample_function_multi_mod_weight: no visible global function definition for ‘runif’ sample_function_multi_mod_weight : <anonymous>: no visible global function definition for ‘var’ sample_function_single_mod: no visible global function definition for ‘runif’ Undefined global functions or variables: rnorm runif var Consider adding importFrom("stats", "rnorm", "runif", "var") to your NAMESPACE file.

PAWL

Version: 0.5

checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘PAWL’ for: ‘show’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘foreach’ ‘ggplot2’ ‘reshape’ Please remove these calls from your code. Packages in Depends field not imported from: ‘foreach’ ‘ggplot2’ ‘methods’ ‘mvtnorm’ ‘reshape’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... smcparameters.constructor: no visible global function definition for ‘new’ systematic_resampling: no visible global function definition for ‘runif’ target.constructor: no visible global function definition for ‘new’ tuningparameters.constructor: no visible global function definition for ‘new’ show,smcparameters: no visible global function definition for ‘tail’ Undefined global functions or variables: %do% abline aes aes_string cov element_text facet_wrap foreach geom_density2d geom_line geom_point geom_step geom_vline ggplot hist labs mahalanobis melt new quantile rgamma rmultinom rmvnorm rnorm runif stat_bin2d tail theme xlab ylab ylim Consider adding importFrom("graphics", "abline", "hist") importFrom("methods", "new") importFrom("stats", "cov", "mahalanobis", "quantile", "rgamma", "rmultinom", "rnorm", "runif") importFrom("utils", "tail") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

Pbase

Version: 0.16.0

checking examples ... ERROR ``` ...

Attaching package: 'AnnotationFilter'

The following object is masked from 'package:Gviz':
```
feature
```
library(EnsDb.Hsapiens.v86) edb <- EnsDb.Hsapiens.v86

Define a filter to retrieve all genes from chromosome Y

sqnf <- SeqNameFilter("Y")

Retrieve the proteins without protein domains but specify to retrieve in

addition the transcript biotype for the encoding transcripts and the gene

names

prts <- Proteins(edb, filter = sqnf, loadProteinDomains = FALSE, + columns = c("tx_biotype", "gene_name")) Error in validObject(.Object) : invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class Calls: Proteins ... .AnnotationFilterList -> new -> initialize -> initialize -> validObject Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 9: validObject(.Object) 10: stop(msg, ": ", errors, domain = NA)

testthat results ================================================================ OK: 84 SKIPPED: 0 FAILED: 7 1. Error: Proteins,EnsDb,missing constructor (@test_Proteins-ensembldb.R#9) 2. Error: Proteins,EnsDb,missing protein_id n:1 uniprot_id mapping (@test_Proteins-ensembldb.R#91) 3. Error: pfeatures (@test_Proteins-methods.R#185) 4. Error: .mapToGenome2 internal function (@test_mapToGenome-ensembldb.R#9) 5. Error: mapToGenome,Proteins,EnsDb (@test_mapToGenome-ensembldb.R#140) 6. Error: mapToGenome,Proteins,EnsDb with Uniprot IDs (@test_mapToGenome-ensembldb.R#183) 7. Error: .checkPcol (@test_utils.R#87)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Loading required package: Rcpp Loading required package: Gviz Loading required package: S4Vectors Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':
```
expand.grid
```
Loading required package: IRanges Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: grid

This is Pbase version 0.16.0

Error: processing vignette 'Pbase-data.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Laurent Gatto <lg390@cam.ac.uk> [aut, cre] Johannes Rainer <Johannes.Rainer@eurac.edu> [aut, cre] Sebastian Gibb <mail@sebastiangibb.de> [aut, cre]

pbcmc

Version: 1.4.0

checking tests ... ``` ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Welcome to Bioconductor
```
  Vignettes contain introductory material; view with
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")', and for packages 'citation("pkgname")'.
```
No methods found in "BiocGenerics" for requests: unlist Error in library("RUnit", quietly = TRUE) : there is no package called 'RUnit' Calls: -> library Execution halted ```

pcadapt

Version: 3.0.4

checking installed package size ... NOTE installed size is 5.1Mb sub-directories of 1Mb or more: doc 1.9Mb extdata 1.6Mb libs 1.5Mb

PCADSC

Version: 0.8.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Matrix’ ‘pander’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘data.table’

pcaExplorer

Version: 2.2.1

checking re-building of vignette outputs ... WARNING ``` ... colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':
```
apply
```
Loading required package: AnnotationDbi

'select()' returned 1:many mapping between keys and columns Warning in cor.test.default(x[, j], coldata[, i], method = "spearman") : Cannot compute exact p-value with ties Warning in cor.test.default(x[, j], coldata[, i], method = "spearman") : Cannot compute exact p-value with ties Warning in cor.test.default(x[, j], coldata[, i], method = "spearman") : Cannot compute exact p-value with ties Warning in cor.test.default(x[, j], coldata[, i], method = "spearman") : Cannot compute exact p-value with ties Warning: Removed 8 rows containing missing values (geom_text). Error: processing vignette 'pcaExplorer.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: doc 4.8Mb
checking R code for possible problems ... NOTE pcaExplorer: no visible binding for '<<-' assignment to ‘pcaexplorer_env’ pcaExplorer : <anonymous>: no visible binding for global variable ‘airway’ pcaExplorer : <anonymous>: no visible binding for global variable ‘pcaexplorer_env’ Undefined global functions or variables: airway pcaexplorer_env

pcaMethods

Version: 1.68.0

checking R code for possible problems ... NOTE ... svdImpute: no visible global function definition for ‘prcomp’ svdPca: no visible global function definition for ‘prcomp’ plot,pcaRes: no visible global function definition for ‘gray’ plot,pcaRes: no visible global function definition for ‘barplot’ plot,pcaRes: no visible global function definition for ‘legend’ slplot,pcaRes: no visible global function definition for ‘par’ slplot,pcaRes: no visible global function definition for ‘layout’ slplot,pcaRes: no visible global function definition for ‘abline’ slplot,pcaRes: no visible global function definition for ‘lines’ Undefined global functions or variables: abline barplot cor cov gray layout legend lines median na.omit pairs par points prcomp qf rnorm runif setTxtProgressBar text txtProgressBar Consider adding importFrom("grDevices", "gray") importFrom("graphics", "abline", "barplot", "layout", "legend", "lines", "pairs", "par", "points", "text") importFrom("stats", "cor", "cov", "median", "na.omit", "prcomp", "qf", "rnorm", "runif") importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ade4’

PDN

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘glmnet’ All declared Imports should be used.

pdp

Version: 0.6.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ICEbox’

PedCNV

Version: 0.1

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... Inde: no visible global function definition for ‘var’ STE: no visible global function definition for ‘pchisq’ STIM: no visible global function definition for ‘cor’ STIM: no visible global function definition for ‘pchisq’ plot.clust: no visible global function definition for ‘princomp’ plot.clust: no visible global function definition for ‘loadings’ plot.clust: no visible global function definition for ‘qplot’ plot.clust: no visible global function definition for ‘geom_histogram’ plot.clust: no visible global function definition for ‘aes_string’ plot.clust: no visible global function definition for ‘barplot’ plot.clust: no visible global function definition for ‘title’ plot.clust: no visible global function definition for ‘mtext’ plot.clust: no visible global function definition for ‘text’ Undefined global functions or variables: aes_string barplot cor cov geom_histogram kmeans lm loadings mtext pchisq prcomp princomp qplot rbinom text title var Consider adding importFrom("graphics", "barplot", "mtext", "text", "title") importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq", "prcomp", "princomp", "rbinom", "var") to your NAMESPACE file.

pepStat

Version: 1.10.0

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘pepStat’ for: ‘end’, ‘start’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking R code for possible problems ... NOTE ... coerce,peptideSet-ExpressionSet: no visible global function definition for ‘annotation’ end,peptideSet: no visible global function definition for ‘end’ position,peptideSet: no visible global function definition for ‘start’ position,peptideSet: no visible global function definition for ‘end’ start,peptideSet: no visible global function definition for ‘start’ write.pSet,peptideSet: no visible global function definition for ‘start’ write.pSet,peptideSet: no visible global function definition for ‘end’ write.pSet,peptideSet: no visible global function definition for ‘write.csv’ Undefined global functions or variables: annotation dev.flush dev.hold dev.interactive devAskNewPage end lm.fit lm.wfit mcols mcols<- median read.csv sd start write.csv Consider adding importFrom("grDevices", "dev.flush", "dev.hold", "dev.interactive", "devAskNewPage") importFrom("stats", "end", "lm.fit", "lm.wfit", "median", "sd", "start") importFrom("utils", "read.csv", "write.csv") to your NAMESPACE file.

perccalc

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MASS’ ‘devtools’ ‘ggplot2’ ‘haven’ ‘tidyverse’ All declared Imports should be used.

perry

Version: 0.2.0

checking R code for possible problems ... NOTE hasMethod: no visible global function definition for ‘getS3method’ Undefined global functions or variables: getS3method Consider adding importFrom("utils", "getS3method") to your NAMESPACE file.

petro.One

Version: 0.1.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rgraphviz’ ‘cluster’ ‘graph’ All declared Imports should be used.

PGA

Version: 1.6.0

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: extdata 1.8Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘biomaRt:::martBM’ ‘biomaRt:::martDataset’ ‘biomaRt:::martHost’ ‘customProDB:::makeTranscriptDbFromBiomart_archive’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... reportSNV: no visible binding for global variable ‘isUnique’ reportSNV: no visible binding for global variable ‘Index’ reportSNV: no visible binding for global variable ‘aaref’ reportSNV: no visible binding for global variable ‘aavar’ reportSNV: no visible binding for global variable ‘genename’ reportSNV: no visible binding for global variable ‘proname’ reportSNV: no visible binding for global variable ‘.SD’ reportSNV: no visible binding for global variable ‘ID’ reportSNV: no visible binding for global variable ‘Change’ reportSNV: no visible binding for global variable ‘aapos’ reportSNV: no visible binding for global variable ‘abc’ reportSNV: no visible binding for global variable ‘xyz’ Undefined global functions or variables: . .I .N .SD CUFF_ID Change Class Evalue Frame Freq ID Index Mass MutNum Query Qvalue Strand Substring Type aapos aaref aavar abc alleleCount alleles charge chr chrom cumlen delta_da delta_ppm evalue gene_name genename genome<- id isSAP isUnique junType jun_type label miss mods mrnaAcc mz name output pep peptide pincoding position pro_name proname prot protAcc protein rbindlist readAAStringSet readDNAStringSet refbase rsid seqlengths seqlevels seqlevels<- subseq transcript tx_name txid txname varbase writeXStringSet x xyz y

PGPC

Version: 1.4.0

checking package dependencies ... ERROR ``` Packages required but not available: ‘EBImage’ ‘imageHTS’

Depends: includes the non-default packages: ‘EBImage’ ‘imageHTS’ ‘SearchTrees’ ‘limma’ ‘RColorBrewer’ ‘gplots’ ‘splots’ ‘ggplot2’ ‘geneplotter’ ‘ChemmineR’ ‘reshape2’ ‘plyr’ Adding so many packages to the search path is excessive and importing selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

PGRdup

Version: 0.2.3.2

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘RecordLinkage’

PhaseType

Version: 0.1.3

checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘ggplot2’ ‘reshape’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE plot.phtMCMC: no visible global function definition for ‘ggplot’ plot.phtMCMC: no visible global function definition for ‘melt’ plot.phtMCMC: no visible global function definition for ‘geom_line’ plot.phtMCMC: no visible global function definition for ‘aes_string’ plot.phtMCMC: no visible global function definition for ‘geom_smooth’ plot.phtMCMC: no visible global function definition for ‘facet_wrap’ plot.phtMCMC: no visible global function definition for ‘ggtitle’ plot.phtMCMC: no visible global function definition for ‘xlab’ plot.phtMCMC: no visible global function definition for ‘ylab’ plot.phtMCMC: no visible global function definition for ‘geom_density’ Undefined global functions or variables: aes_string facet_wrap geom_density geom_line geom_smooth ggplot ggtitle melt xlab ylab
checking compiled code ... NOTE ``` File ‘PhaseType/libs/PhaseType.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘LJMA_arms.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

phenoTest

Version: 1.24.0

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘org.Ce.eg.db’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘org.Dm.eg.db’
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘annotate’ ‘GSEABase’ A package should be listed in only one of these fields.
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘phenoTest’ for: ‘show’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘ggplot2’ which was already attached by Depends. Please remove these calls from your code. Namespace in Imports field not imported from: ‘annotate’ All declared Imports should be used. Packages in Depends field not imported from: ‘BMA’ ‘Heatplus’ ‘annotate’ ‘ggplot2’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘sortDragHtmlTable’
checking R code for possible problems ... NOTE ... gray hclust heatmap_plus image integrate kruskal.test layout legend lines lm median model.matrix new p.adjust pData par pc1 pc2 pchisq pdf png pnorm polygon prcomp predict qplot quantile rect rgb sd text theme wilcox.test write.csv y Consider adding importFrom("grDevices", "densCols", "dev.off", "gray", "pdf", "png", "rgb") importFrom("graphics", "abline", "axTicks", "axis", "barplot", "boxplot", "dotchart", "image", "layout", "legend", "lines", "par", "polygon", "rect", "text") importFrom("methods", "new") importFrom("stats", "BIC", "anova", "approx", "approxfun", "as.dendrogram", "as.dist", "binom.test", "chisq.test", "coef", "coefficients", "complete.cases", "confint", "cor", "cov", "cutree", "density", "dist", "hclust", "integrate", "kruskal.test", "lm", "median", "model.matrix", "p.adjust", "pchisq", "pnorm", "prcomp", "predict", "quantile", "sd", "wilcox.test") importFrom("utils", "write.csv") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'plot.gseaData': ‘plot.gseaData’

S3 methods shown with full name in documentation object 'plot.gseaSignatures': ‘plot.gseaSignaturesSign’

S3 methods shown with full name in documentation object 'summary.gseaData': ‘summary.gseaData’

S3 methods shown with full name in documentation object 'summary.gseaSignificance': ‘summary.gseaSignificanceSign’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

philr

Version: 1.2.0

checking re-building of vignette outputs ... WARNING ``` ...
```
intersect, setdiff, setequal, union
```
Found more than one class "phylo" in cache; using the first, from namespace 'treeio' Also defined by 'phyloseq' Found more than one class "phylo" in cache; using the first, from namespace 'treeio' Also defined by 'phyloseq'

Attaching package: 'tidyr'

The following object is masked from 'package:ggtree':
```
expand
```
The following object is masked from 'package:Matrix':
```
expand
```
Error: processing vignette 'philr-intro.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE name.balance: no visible global function definition for ‘as’ vote.annotation: no visible global function definition for ‘is’ Undefined global functions or variables: as is Consider adding importFrom("methods", "as", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘compositions’

PhyInformR

Version: 1.0

checking whether package ‘PhyInformR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/PhyInformR/new/PhyInformR.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘gplots’ ‘phytools’ All declared Imports should be used.

phyloseq

Version: 1.20.0

checking examples ... ERROR ``` Running examples in ‘phyloseq-Ex.R’ failed The error most likely occurred in:

Name: UniFrac

Title: Calculate weighted or unweighted (Fast) UniFrac distance for all

sample pairs.

Aliases: UniFrac UniFrac,phyloseq-method

** Examples

Perform UniFrac on esophagus data

data("esophagus") (y <- UniFrac(esophagus, TRUE)) Error in .C(ape:::node_depth_edgelength, PACKAGE = "ape", as.integer(Ntip), : Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength' Calls: UniFrac ... UniFrac -> fastUniFrac -> ape_node_depth_edge_length -> .C Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat-phyloseq.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 541 SKIPPED: 0 FAILED: 62
1. Failure: The specialized read_tree_greengenes function works: (@test-IO.R#323)
2. Error: UniFrac produces correct values on an example subset from Global Patterns. 'Correct' values are results from pyCogent (@test-distance.R#33)
3. Error: Check that regular-expression matching for unifrac method flag is working (@test-distance.R#53)
4. Failure: all 4 plot_ordination type options result in valid ggplot2 object (@test-plot.R#51)
5. Failure: all 4 plot_ordination type options result in valid ggplot2 object (@test-plot.R#52)
6. Failure: all 4 plot_ordination type options result in valid ggplot2 object (@test-plot.R#53)
7. Failure: all 4 plot_ordination type options result in valid ggplot2 object (@test-plot.R#54)
8. Failure: plot_ordination: When variables are present or not, color SampleType (@test-plot.R#83)
9. Failure: plot_ordination: When variables are present or not, color SampleType (@test-plot.R#84)
10. ...
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 181-183 (phyloseq-FAQ.Rmd) Error: processing vignette 'phyloseq-FAQ.Rmd' failed with diagnostics: Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength' Execution halted
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doParallel’
checking dependencies in R code ... NOTE ':::' calls which should be '::': ‘ape:::node_depth_edgelength’ ‘ape:::node_height’ See the note in ?`:::` about the use of this operator.
checking foreign function calls ... NOTE Foreign function calls to a different package: .C(ape:::node_depth_edgelength, ..., PACKAGE = "ape") .C(ape:::node_height, ..., PACKAGE = "ape") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... merge_phyloseq_pair,sample_data-sample_data : <anonymous>: no visible binding for global variable ‘X0’ merge_samples,sample_data: no visible global function definition for ‘aggregate’ plot_phyloseq,phyloseq: no visible binding for global variable ‘esophagus’ Undefined global functions or variables: #OTU ID .SD := Abundance Classification Consensus Lineage J OTU OTULabel SE.sim Sample V1 V2 X0 aggregate as.dist as.formula as.hclust axis capture.output combn complete.cases count cutree dcast.data.table download.file eigenvalue esophagus gap h.adj.index head i k label queryID queryString read read.table relevel se tail untar unzip value vmax vmin write.table x xdodge xend xfartiplab xleft xright y yend Consider adding importFrom("graphics", "axis") importFrom("stats", "aggregate", "as.dist", "as.formula", "as.hclust", "complete.cases", "cutree", "relevel") importFrom("utils", "capture.output", "combn", "download.file", "head", "read.table", "tail", "untar", "unzip", "write.table") to your NAMESPACE file.

Pi

Version: 1.4.0

checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: doc 5.2Mb

pifpaf

Version: 1.0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gridExtra’ All declared Imports should be used.

pitchRx

Version: 1.8.2

checking package dependencies ... NOTE Package suggested but not available for checking: ‘ggsubplot’

pkggraph

Version: 0.2.2

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 34-58 (vignette_pkggraph.Rmd) Error: processing vignette 'vignette_pkggraph.Rmd' failed with diagnostics: Columns `xend`, `yend`, `x`, `y` must be 1d atomic vectors or lists Execution halted

PKgraph

Version: 1.7

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

Depends: includes the non-default packages: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’ ‘proto’ Adding so many packages to the search path is excessive and importing selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

PKPDmisc

Version: 2.0.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘purrr’ All declared Imports should be used.

PKreport

Version: 1.5

checking R code for possible problems ... NOTE ... generate.plot: no visible global function definition for ‘dev.off’ writeHTML: no visible global function definition for ‘packageDescription’ writeLst: no visible global function definition for ‘packageDescription’ writeLst.tab: no visible global function definition for ‘packageDescription’ writeTable: no visible global function definition for ‘packageDescription’ writeTable: no visible global function definition for ‘quantile’ initialize,nonmem: no visible global function definition for ‘read.table’ Undefined global functions or variables: bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg packageDescription png quantile read.table tiff Consider adding importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg", "png", "tiff") importFrom("stats", "formula", "heatmap", "quantile") importFrom("utils", "browseURL", "packageDescription", "read.table") to your NAMESPACE file.

planar

Version: 1.6

checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: libs 5.4Mb

platetools

Version: 0.0.2

checking examples ... ERROR ``` ... > > ### ** Examples > > df01 <- data.frame(well = num_to_well(1:96),
- vals = rnorm(96),
- plate = 1)
  
  df02 <- data.frame(well = num_to_well(1:96),
- vals = rnorm(96),
- plate = 2)
  
  df <- rbind(df01, df02)
  
  b_grid(data = df$vals,
- well = df$well,
- plate_id = df$plate,
- plate = 96) Warning: panel.margin.x is deprecated. Please use panel.spacing.x property instead Warning: panel.margin is deprecated. Please use panel.spacing property instead Error: Free scales are only supported with coord_cartesian() and coord_flip() Execution halted ```

playwith

Version: 0.9-54

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

Package suggested but not available for checking: ‘latticist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

plethy

Version: 1.14.0

checking examples ... ERROR ... > count = c(NA,900, NA,150, 150, 110) > measure_break = c(FALSE, FALSE, TRUE, FALSE, FALSE,FALSE) > table_break = c(TRUE, rep(FALSE, length(samples)-1)) > phase = rep("D1", length(samples)) > > err.dta <- data.frame(samples=samples, count=count, measure_break=measure_break, table_break=table_break, phase=phase, stringsAsFactors=FALSE) > > sim.bux.lines <- plethy:::generate.sample.buxco(err.dta) > > temp.file <- tempfile() > temp.db.file <- tempfile() > write(sim.bux.lines, file=temp.file) > test.bux.db <- parse.buxco(file.name=temp.file, db.name=temp.db.file, chunk.size=10000) Processing /home/muelleki/tmp/RtmpbAgMTr/fileec16587710f9 in chunks of 10000 Starting chunk 1 Reached breakpoint change Processing breakpoint 1 Starting sample sample_1 Error in if (sum(which.gt) > 0) { : missing value where TRUE/FALSE needed Calls: parse.buxco ... write.sample.breaks -> write.sample.db -> sanity.check.time Execution halted
checking tests ... ``` ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: Test files with failing tests
```
 test_check_helpers.R 
   test.add.labels.by.sample 
   test.dbImport 
   test.get.err.breaks 
   test.summaryMeasures
```
Error in BiocGenerics:::testPackage("plethy") : unit tests failed for package plethy In addition: Warning message: In .Internal(gc(verbose, reset)) : closing unused connection 3 (/home/muelleki/tmp/RtmpX9oekr/filef53251cebac7) Execution halted ```
checking dependencies in R code ... NOTE There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’
checking R code for possible problems ... NOTE ... mvtsplot.data.frame: no visible global function definition for ‘bxp’ mvtsplot.data.frame : <anonymous>: no visible binding for global variable ‘median’ mvtsplot.data.frame: no visible global function definition for ‘lines’ mvtsplot.data.frame: no visible global function definition for ‘Axis’ mvtsplot.data.frame: no visible global function definition for ‘legend’ retrieveMatrix,BuxcoDB: no visible global function definition for ‘terms’ tsplot,BuxcoDB: no visible binding for global variable ‘Days’ tsplot,BuxcoDB: no visible binding for global variable ‘Value’ tsplot,BuxcoDB: no visible binding for global variable ‘Sample_Name’ Undefined global functions or variables: Axis Days Sample_Name Value abline bxp colors layout legend lines median mtext packageDescription par plot rnorm strwidth terms Consider adding importFrom("grDevices", "colors") importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend", "lines", "mtext", "par", "plot", "strwidth") importFrom("stats", "median", "rnorm", "terms") importFrom("utils", "packageDescription") to your NAMESPACE file.

plotluck

Version: 1.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘hexbin’ ‘quantreg’ All declared Imports should be used.

plotly

Version: 4.7.1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 1252 SKIPPED: 2 FAILED: 18
1. Error: api() returns endpoints (@test-api.R#7)
2. Error: Can search with white-space (@test-api.R#16)
3. Error: Changing a filename works (@test-api.R#25)
4. Error: Downloading plots works (@test-api.R#35)
5. Error: Downloading grids works (@test-api.R#53)
6. Error: Creating produces a new file by default (@test-api.R#79)
7. Error: Can overwrite a grid (@test-api.R#95)
8. Error: Can overwrite a plot (@test-api.R#107)
9. Error: Can create plots with non-trivial src attributes (@test-api.R#123)
10. ...
Error: testthat unit tests failed Execution halted ```

politeness

Version: 0.1.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ROCR’ All declared Imports should be used.

popEpi

Version: 0.4.4

R CMD check timed out

PopGenReport

Version: 3.0.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ecodist’

popReconstruct

Version: 1.0-4

checking R code for possible problems ... NOTE estMod.rinvGamma.mar29: no visible global function definition for ‘rgamma’ life.expectancy.stationary: no visible global function definition for ‘head’ life.expectancy.stationary: no visible global function definition for ‘tail’ log.lhood.mar29: no visible global function definition for ‘dnorm’ log.post.mar29: no visible global function definition for ‘dnorm’ popRecon.sampler: no visible global function definition for ‘rnorm’ popRecon.sampler: no visible global function definition for ‘runif’ Undefined global functions or variables: dnorm head rgamma rnorm runif tail Consider adding importFrom("stats", "dnorm", "rgamma", "rnorm", "runif") importFrom("utils", "head", "tail") to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE ``` ...

The following object is masked from ‘package:base’:
```
startsWith
```
Calculating life expectancy at birth ... ... done Calculating net number of migrants ... ... done Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'burkina-faso-females.tex' failed. BibTeX errors: The top-level auxiliary file: burkina-faso-females.aux I couldn't open style file apa.bst ---line 19 of file burkina-faso-females.aux : \bibstyle{apa : } I'm skipping whatever remains of this command I found no style file---while reading file burkina-faso-females.aux Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

PortfolioEffectHFT

Version: 1.8

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: java 5.1Mb

POUMM

Version: 1.3.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘utils’ All declared Imports should be used.

powerlmm

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘testthat’ All declared Imports should be used.

PPInfer

Version: 1.2.4

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘biomaRt’ ‘fgsea’ ‘kernlab’ ‘ggplot2’ ‘igraph’ ‘STRINGdb’ ‘yeastExpData’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking R code for possible problems ... NOTE ... ORA: no visible global function definition for ‘setTxtProgressBar’ ORA: no visible global function definition for ‘p.adjust’ ORA.dotplot: no visible global function definition for ‘p.adjust’ enrich.net: no visible global function definition for ‘stack’ enrich.net: no visible global function definition for ‘adjustcolor’ enrich.net : <anonymous>: no visible global function definition for ‘adjustcolor’ enrich.net: no visible binding for global variable ‘legend’ net.infer: no visible global function definition for ‘na.omit’ net.infer.ST: no visible global function definition for ‘na.omit’ ppi.infer.human: no visible global function definition for ‘na.omit’ ppi.infer.mouse: no visible global function definition for ‘na.omit’ Undefined global functions or variables: adjustcolor fisher.test legend na.omit p.adjust setTxtProgressBar stack txtProgressBar Consider adding importFrom("grDevices", "adjustcolor") importFrom("graphics", "legend") importFrom("stats", "fisher.test", "na.omit", "p.adjust") importFrom("utils", "setTxtProgressBar", "stack", "txtProgressBar") to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘httr’
checking re-building of vignette outputs ... NOTE ``` ... as.data.frame, cbind, colMeans, colSums, colnames, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min

Attaching package: ‘graph’

The following objects are masked from ‘package:igraph’:
```
degree, edges, intersection
```
Error in net.infer(names(V(sg))[1:50], K, top = 20) : size of list is too large

Error: processing vignette 'PPInfer.Rnw' failed with diagnostics: chunk 14 Error in library(httr) : there is no package called ‘httr’ Execution halted ```

PPtreeViz

Version: 2.0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

pqsfinder

Version: 1.4.9

checking re-building of vignette outputs ... WARNING ``` ...

The following object is masked from 'package:base':
```
expand.grid
```
Loading required package: IRanges Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':
```
strsplit
```
Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: grid Loading required package: BSgenome Error: processing vignette 'pqsfinder.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking if this is a source package ... NOTE Found the following apparent object files/libraries: src/boost_regex/c_regex_traits.o src/boost_regex/cpp_regex_traits.o src/boost_regex/cregex.o src/boost_regex/fileiter.o src/boost_regex/icu.o src/boost_regex/instances.o src/boost_regex/posix_api.o src/boost_regex/regex.o src/boost_regex/regex_debug.o src/boost_regex/regex_raw_buffer.o src/boost_regex/regex_traits_defaults.o src/boost_regex/static_mutex.o src/boost_regex/usinstances.o src/boost_regex/w32_regex_traits.o src/boost_regex/wc_regex_traits.o src/boost_regex/wide_posix_api.o src/boost_regex/winstances.o Object files/libraries should not be included in a source package.
checking installed package size ... NOTE installed size is 24.9Mb sub-directories of 1Mb or more: lib 20.3Mb libs 4.0Mb
checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for ‘BH’ is only usable in R >= 3.0.2
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

precrec

Version: 0.9.1

checking installed package size ... NOTE installed size is 9.4Mb sub-directories of 1Mb or more: doc 1.2Mb libs 7.4Mb

predictmeans

Version: 0.99

checking examples ... ERROR ``` Running examples in ‘predictmeans-Ex.R’ failed The error most likely occurred in:

Name: covariatemeans

Title: Predicted Means of a Linear Model with Covariate Variable(s)

Aliases: covariatemeans

** Examples

library(predictmeans) data(Oats, package="nlme") fm <- lme(yield ~ nitro*Variety, random=~1|Block/Variety, data=Oats)

library(lme4)

fm <- lmer(yield ~ nitro*Variety+(1|Block/Variety), data=Oats)

covariatemeans(fm, "Variety", covariate="nitro") dev.new(): using pdf(file="Rplots2.pdf") Error: Column y must be a 1d atomic vector or a list Execution halted ```

checking R code for possible problems ... NOTE ... terms.gls: no visible global function definition for ‘model.frame’ Undefined global functions or variables: abline anova as.formula axis box coef delete.response dev.new edit family fitted formula ftable identify image legend lines lm.influence loess.smooth model.frame model.matrix na.omit na.pass p.adjust par plot points ppoints predict pt ptukey qnorm qqline qqnorm qt resid residuals slot terms text title update vcov xtabs Consider adding importFrom("grDevices", "dev.new") importFrom("graphics", "abline", "axis", "box", "identify", "image", "legend", "lines", "par", "plot", "points", "text", "title") importFrom("methods", "slot") importFrom("stats", "anova", "as.formula", "coef", "delete.response", "family", "fitted", "formula", "ftable", "lm.influence", "loess.smooth", "model.frame", "model.matrix", "na.omit", "na.pass", "p.adjust", "ppoints", "predict", "pt", "ptukey", "qnorm", "qqline", "qqnorm", "qt", "resid", "residuals", "terms", "update", "vcov", "xtabs") importFrom("utils", "edit") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

PredictTestbench

Version: 1.1.3

checking whether package ‘PredictTestbench’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘forecast::autolayer’ by ‘ggplot2::autolayer’ when loading ‘PredictTestbench’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/PredictTestbench/new/PredictTestbench.Rcheck/00install.out’ for details.

checking R code for possible problems ... NOTE prediction_errors: possible error in psf(data = dataIn1, n.ahead = nextVal): unused argument (n.ahead = nextVal)

PReMiuM

Version: 3.1.6

checking installed package size ... NOTE installed size is 13.3Mb sub-directories of 1Mb or more: libs 13.1Mb

preprosim

Version: 0.2.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘e1071’ All declared Imports should be used.

prevR

Version: 3.3

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘sparr’

primerTree

Version: 1.0.3

checking data for non-ASCII characters ... NOTE Error in .requirePackage(package) : unable to find required package 'RCurl' Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage Execution halted

prism

Version: 0.0.7

checking whether package ‘prism’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘prism’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/prism/new/prism.Rcheck/00install.out’ for details.

profr

Version: 0.3.1

checking dependencies in R code ... NOTE 'library' or 'require' call to ‘ggplot2’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... ggplot.profr: no visible binding for global variable ‘start’ ggplot.profr: no visible binding for global variable ‘end’ ggplot.profr: no visible global function definition for ‘geom_text’ ggplot.profr: no visible binding for global variable ‘time’ ggplot.profr: no visible global function definition for ‘scale_y_continuous’ ggplot.profr: no visible global function definition for ‘scale_x_continuous’ plot.profr: no visible global function definition for ‘plot’ plot.profr: no visible global function definition for ‘rect’ plot.profr: no visible binding for global variable ‘time’ plot.profr: no visible global function definition for ‘text’ profr: no visible global function definition for ‘Rprof’ Undefined global functions or variables: Rprof aes end geom_rect geom_text ggplot hist plot rect scale_x_continuous scale_y_continuous start text time Consider adding importFrom("graphics", "hist", "plot", "rect", "text") importFrom("stats", "end", "start", "time") importFrom("utils", "Rprof") to your NAMESPACE file.

ProgGUIinR

Version: 0.0-4

checking package dependencies ... NOTE Packages suggested but not available for checking: ‘qtbase’ ‘gWidgetsRGtk2’
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... definition for ‘apropos’ showGtkWidgetInfo : getMethodForObject: no visible global function definition for ‘help’ showGtkWidgetInfo: no visible global function definition for ‘gSignalConnect’ Undefined global functions or variables: PangoStyle addSpring apropos gSignalConnect gbutton gframe ggroup gnotebook gpanedgroup gstatusbar gtable gtext gtkAction gtkCellRendererText gtkEntry gtkEntryCompletionNew gtkFrame gtkHBox gtkHBoxNew gtkHPaned gtkLabel gtkListStore gtkNotebook gtkScrolledWindow gtkSeparatorToolItem gtkStatusbar gtkTextBuffer gtkTextView gtkToolButton gtkToolbar gtkTreeView gtkTreeViewColumn gtkTypeGetSignals gtkVBox gtkVBoxNew gtkWindow gwindow help rGtkDataFrame svalue svalue<- tcl tclvalue tkbind tkconfigure tkdelete tkget tkgrid tkgrid.columnconfigure tkgrid.rowconfigure tkinsert tkmenu tkpack tksee tkset tktag.add tktag.configure tktag.remove tktext tktoplevel tkwm.title tkxview ttkbutton ttkframe ttklabel ttkpanedwindow ttkscrollbar ttktreeview visible<- Consider adding importFrom("utils", "apropos", "help") to your NAMESPACE file.

projmanr

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R6’ All declared Imports should be used.

pRoloc

Version: 1.16.1

checking re-building of vignette outputs ... WARNING ``` ...
```
nChrom
```
Loading required package: cluster Warning: replacing previous import 'BiocGenerics::var' by 'stats::var' when loading 'MLInterfaces'

This is pRoloc version 1.16.1 Read '?pRoloc' and references therein for information about the package and how to get started.

This is pRolocdata version 1.14.0. Use 'pRolocdata()' to list available data sets. Loading required namespace: GO.db

Loading required package: GO.db Retaining 84 out of 524 in GOAnnotations Retaining 79 out of 84 in GOAnnotations Error: processing vignette 'pRoloc-goannotations.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: doc 3.3Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘MLInterfaces:::.macroF1’ ‘MLInterfaces:::.precision’ ‘MLInterfaces:::.recall’ ‘MLInterfaces:::es2df’ ‘caret:::predict.plsda’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘checkSortedFeatureNames’ ‘opt’
checking R code for possible problems ... NOTE Found the following possibly unsafe calls: File ‘pRoloc/R/annotation.R’: unlockBinding("params", .pRolocEnv)
checking files in ‘vignettes’ ... NOTE The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.

pRolocGUI

Version: 1.10.0

checking whether package ‘pRolocGUI’ can be installed ... WARNING Found the following significant warnings: Warning: namespace ‘lme4’ is not available and has been replaced Warning: namespace ‘MatrixModels’ is not available and has been replaced See ‘/home/muelleki/git/R/ggplot2/revdep/checks/pRolocGUI/new/pRolocGUI.Rcheck/00install.out’ for details.
checking DESCRIPTION meta-information ... NOTE Authors@R field gives more than one person with maintainer role: Lisa Breckels <lms79@cam.ac.uk> [aut, cre] Laurent Gatto <lg390@cam.ac.uk> [aut, cre]
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘pRoloc:::remap’ See the note in ?`:::` about the use of this operator.

prophet

Version: 0.2.1

checking installed package size ... NOTE installed size is 22.9Mb sub-directories of 1Mb or more: libs 21.7Mb

proportion

Version: 2.0.0

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘binom’, ‘PropCIs’, ‘BlakerCI’, ‘prevalence’

propr

Version: 3.1.1

checking installed package size ... NOTE installed size is 5.5Mb sub-directories of 1Mb or more: data 1.5Mb libs 2.8Mb

proteomics

Version: 0.2

checking R code for possible problems ... NOTE addIonSatistics: no visible binding for global variable ‘median’ adjustOne: no visible binding for global variable ‘median’ attachModifications: no visible global function definition for ‘na.omit’ avrgLoadingCalculation: no visible binding for global variable ‘median’ channelResponses : estimate: no visible binding for global variable ‘var’ responseStatisics : func: no visible global function definition for ‘aggregate’ testing: no visible global function definition for ‘aov’ testingOneshot: no visible global function definition for ‘anova’ testingTukey: no visible global function definition for ‘TukeyHSD’ Undefined global functions or variables: TukeyHSD aggregate anova aov median na.omit var Consider adding importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median", "na.omit", "var") to your NAMESPACE file.

proteoQC

Version: 1.12.3

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'proteoQC.Rmd' failed with diagnostics: there is no package called ‘prettydoc’ Execution halted
checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: doc 3.2Mb extdata 4.0Mb
checking R code for possible problems ... NOTE ... plotMS2boxplot: no visible binding for global variable ‘techRep’ plotMS2boxplot: no visible binding for global variable ‘fraction’ plotMS2boxplot: no visible binding for global variable ‘MS2QC’ plotSampleIDResultErrorBar: no visible binding for global variable ‘fraction’ plotSampleIDResultErrorBar: no visible binding for global variable ‘val’ plotSampleIDResultErrorBar: no visible binding for global variable ‘se’ plotSampleVenn: no visible global function definition for ‘grid.draw’ plotTechRepVenn : <anonymous>: no visible global function definition for ‘grid.draw’ qcHist: no visible binding for global variable ‘error’ qcHist: no visible binding for global variable ‘techRep’ qcHist: no visible binding for global variable ‘bioRep’ qcHist2: no visible binding for global variable ‘error’ qcHist2: no visible binding for global variable ‘fractile’ Undefined global functions or variables: ..count.. Intensity MS1QC MS2QC TMT10 TMT6 Tag V1 V2 V3 V4 V5 bioRep curenv delta error exprs fractile fraction grid.draw iTRAQ4 iTRAQ8 label peplength peptide_summary precursorCharge quantify ratio readMgfData se techRep val x y

PSAboot

Version: 1.1.4

checking data for non-ASCII characters ... NOTE Note: found 4 marked UTF-8 strings

pscore

Version: 0.1-2

checking R code for possible problems ... NOTE mahalanobisComposite: no visible global function definition for ‘princomp’ prepareComposite: no visible global function definition for ‘cov’ winsorizor : f: no visible global function definition for ‘quantile’ Undefined global functions or variables: cov princomp quantile Consider adding importFrom("stats", "cov", "princomp", "quantile") to your NAMESPACE file.

psd

Version: 1.0-1

checking package dependencies ... NOTE Package suggested but not available for checking: ‘fftw’
checking R code for possible problems ... NOTE ... psdcore.default: no visible global function definition for ‘ts’ pspectrum.ts: no visible global function definition for ‘frequency’ spec_confint.default: no visible global function definition for ‘pchisq’ spec_confint.default: no visible global function definition for ‘qchisq’ splineGrad.default: no visible global function definition for ‘par’ splineGrad.default: no visible global function definition for ‘plot’ splineGrad.default: no visible global function definition for ‘lines’ Undefined global functions or variables: abline acf as.ts frequency head is.ts layout legend lines lm loess.control mtext par pchisq plot qchisq residuals spec.pgram start tail title ts var Consider adding importFrom("graphics", "abline", "layout", "legend", "lines", "mtext", "par", "plot", "title") importFrom("stats", "acf", "as.ts", "frequency", "is.ts", "lm", "loess.control", "pchisq", "qchisq", "residuals", "spec.pgram", "start", "ts", "var") importFrom("utils", "head", "tail") to your NAMESPACE file.

psda

Version: 1.0.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘raster’ All declared Imports should be used.

psychmeta

Version: 0.1.2

checking data for non-ASCII characters ... NOTE Note: found 5 marked UTF-8 strings

psycho

Version: 0.0.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘rtf’ ‘tidyverse’ All declared Imports should be used.

psygenet2r

Version: 1.9.1

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Quitting from lines 2-32 (case_study.Rmd) Error: processing vignette 'case_study.Rmd' failed with diagnostics: could not find function "doc_date" Execution halted
checking installed package size ... NOTE installed size is 5.8Mb sub-directories of 1Mb or more: doc 5.4Mb
checking dependencies in R code ... NOTE package 'methods' is used but not declared
checking R code for possible problems ... NOTE ... ‘Disease1’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘Disease2’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘JaccardIndex’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘value’ plot,JaccardIndexPsy-ANY: no visible binding for global variable ‘variable’ Undefined global functions or variables: Category Disease1 Disease2 JaccardIndex Var1 c0.Number_of_Abstracts c0.Score c1.Gene_Symbol c2.DiseaseName c2.Disease_code c2.PsychiatricDisorder category combn database diseases gene new perc phyper pie read.csv read.delim value variable Consider adding importFrom("graphics", "pie") importFrom("methods", "new") importFrom("stats", "phyper") importFrom("utils", "combn", "read.csv", "read.delim") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

PTXQC

Version: 0.92.0

checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: doc 3.8Mb examples 2.3Mb

PureCN

Version: 1.6.3

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 1.6Mb extdata 2.7Mb

pxweb

Version: 0.6.3

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
1. Failure: baseURL 1 (@test-get_pxweb_metadata.R#23) -------------------------- dim(test_file) not equivalent to test$test_dims. 1/2 mismatches [1] 17 - 16 == 1
testthat results ================================================================ OK: 120 SKIPPED: 10 FAILED: 2 1. Failure: baseURL 1 (@test-get_pxweb_metadata.R#23) 2. Failure: baseURL 1 (@test-get_pxweb_metadata.R#23)

Error: testthat unit tests failed Execution halted ```

qcmetrics

Version: 1.14.0

checking R code for possible problems ... NOTE ... n15qc : <anonymous>: no visible global function definition for ‘median’ n15qc : <anonymous>: no visible global function definition for ‘legend’ n15qc : <anonymous>: no visible global function definition for ‘par’ n15qc : <anonymous>: no visible global function definition for ‘layout’ n15qc : <anonymous>: no visible global function definition for ‘barplot’ n15qc: no visible global function definition for ‘fileNames’ n15qc: no visible global function definition for ‘experimentData’ rnadeg : <anonymous>: no visible global function definition for ‘legend’ rnadeg : <anonymous>: no visible global function definition for ‘par’ Undefined global functions or variables: abline aes barplot combineFeatures density dev.off experimentData exprs fData fData<- fileNames fvarLabels geom_boxplot geom_hline geom_jitter ggplot labs layout legend lines median par pdf png rect Consider adding importFrom("grDevices", "dev.off", "pdf", "png") importFrom("graphics", "abline", "barplot", "layout", "legend", "lines", "par", "rect") importFrom("stats", "density", "median") to your NAMESPACE file.

qdap

Version: 2.2.9

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘gplots’

qrqc

Version: 1.30.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’ ‘brew’ ‘xtable’ ‘Rsamtools’ ‘testthat’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘reshape’ ‘ggplot2’ ‘Biostrings’ ‘biovizBase’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE Packages in Depends field not imported from: 'Rsamtools' 'brew' 'testthat' 'xtable' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... kmerKLPlot,SequenceSummary: no visible binding for global variable 'kmer' kmerKLPlot,SequenceSummary: no visible binding for global variable 'position' kmerKLPlot,SequenceSummary: no visible binding for global variable 'kl' kmerKLPlot,list : <anonymous>: no visible binding for global variable 'kmer' kmerKLPlot,list: no visible binding for global variable 'position' kmerKLPlot,list: no visible binding for global variable 'kl' kmerKLPlot,list: no visible binding for global variable 'kmer' plotGC,SequenceSummary : <local>: no visible global function definition for 'aggregate' qualPlot,FASTQSummary: no visible binding for global variable 'position' qualPlot,list: no visible binding for global variable 'position' Undefined global functions or variables: DNAStringSet aggregate base entropy kl kmer na.exclude position quantile write.XStringSet Consider adding importFrom("stats", "aggregate", "na.exclude", "quantile") to your NAMESPACE file.

quadrupen

Version: 0.2-5

checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: libs 7.8Mb

QualInt

Version: 1.0.0

checking R code for possible problems ... NOTE ... powerval: no visible global function definition for ‘qnorm’ powerval: no visible global function definition for ‘pnorm’ print.expplot: no visible global function definition for ‘gray’ print.expplot: no visible binding for global variable ‘coef’ print.outplot: no visible global function definition for ‘gray’ print.outplot: no visible binding for global variable ‘coef’ qualint: no visible global function definition for ‘qnorm’ qualint: no visible global function definition for ‘plot’ qualval: no visible global function definition for ‘qnorm’ qualval: no visible global function definition for ‘plot’ surout: no visible global function definition for ‘tail’ surout: no visible global function definition for ‘coef’ Undefined global functions or variables: coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail Consider adding importFrom("grDevices", "gray") importFrom("graphics", "plot") importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm", "rnorm", "sd") importFrom("utils", "tail") to your NAMESPACE file.

qualvar

Version: 0.1.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Quitting from lines 92-106 (wilcox1973.Rmd) Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics: there is no package called 'webshot' Execution halted

quanteda

Version: 0.99.22

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: all(plot_docnames[order(plot_docnames)] == plot_docnames) isn't false.
1. Failure: test plot.kwic keeps order of keywords passed (@test-plots.R#81) --- as.character(unique(ggplot2::ggplot_build(p)$layout$panel_layout$keyword)) not equal to c("people", "american"). Lengths differ: 0 vs 2
testthat results ================================================================ OK: 1625 SKIPPED: 15 FAILED: 2 1. Failure: test plot.kwic facet order parameter (@test-plots.R#71) 2. Failure: test plot.kwic keeps order of keywords passed (@test-plots.R#81)

Error: testthat unit tests failed Execution halted ```

checking installed package size ... NOTE installed size is 17.6Mb sub-directories of 1Mb or more: libs 15.4Mb
checking data for non-ASCII characters ... NOTE Note: found 1415 marked UTF-8 strings

quickPlot

Version: 0.1.2

checking package dependencies ... NOTE Package suggested but not available for checking: ‘fastshp’
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rgdal’ All declared Imports should be used.

quickpsy

Version: 0.1.4

checking examples ... ERROR ``` Running examples in ‘quickpsy-Ex.R’ failed The error most likely occurred in:

Name: plotcurves

Title: Plot the curves

Aliases: plotcurves

** Examples

library(MPDiR) # contains the Vernier data fit <- quickpsy(Vernier, Phaseshift, NumUpward, N, + grouping = .(Direction, WaveForm, TempFreq), B = 5) plotcurves(fit) Warning: Ignoring unknown aesthetics: x Error: Aesthetics must be either length 1 or the same as the data (8): ymin, ymax, colour, x Execution halted ```

quickReg

Version: 1.5.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘psych’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘PredictABEL’

quokar

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MCMCpack’ ‘gridExtra’ ‘knitr’ All declared Imports should be used.

qvalue

Version: 2.8.0

checking R code for possible problems ... NOTE lfdr: no visible global function definition for ‘qnorm’ lfdr: no visible global function definition for ‘density’ lfdr: no visible global function definition for ‘smooth.spline’ lfdr: no visible global function definition for ‘predict’ lfdr: no visible global function definition for ‘dnorm’ pi0est: no visible global function definition for ‘smooth.spline’ pi0est: no visible global function definition for ‘predict’ pi0est: no visible global function definition for ‘quantile’ plot.qvalue: no visible global function definition for ‘quantile’ write.qvalue: no visible global function definition for ‘write.table’ Undefined global functions or variables: density dnorm predict qnorm quantile smooth.spline write.table Consider adding importFrom("stats", "density", "dnorm", "predict", "qnorm", "quantile", "smooth.spline") importFrom("utils", "write.table") to your NAMESPACE file.

qwraps2

Version: 0.2.4

checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'summary_table': ‘cbind.qwraps2_summary_table’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

r2glmm

Version: 0.1.2

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘data.table’ ‘dplyr’ ‘lmerTest’ All declared Imports should be used.

R3CPET

Version: 1.8.0

checking installed package size ... NOTE installed size is 7.4Mb sub-directories of 1Mb or more: data 3.0Mb example 1.0Mb libs 1.7Mb
checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘methods’ A package should be listed in only one of these fields.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: 'BiocGenerics' All declared Imports should be used.
checking R code for possible problems ... NOTE ... .formatDAVIDResult: no visible global function definition for 'formatList' .formatDAVIDResult: no visible global function definition for 'formatGene2Gene' .formatDAVIDResult: no visible global function definition for 'formatAnnotationReport' .get.NetworksGenes: no visible global function definition for 'annotatePeakInBatch' EnsemblToHGNC: no visible global function definition for 'useMart' EnsemblToHGNC: no visible global function definition for 'useDataset' EnsemblToHGNC: no visible global function definition for 'getBM' EntrezToHGNC: no visible global function definition for 'useMart' EntrezToHGNC: no visible global function definition for 'useDataset' EntrezToHGNC: no visible global function definition for 'getBM' createServer,ChiapetExperimentData-NetworkCollection-ChromMaintainers: no visible global function definition for 'runApp' Undefined global functions or variables: TxDb.Hsapiens.UCSC.hg19.knownGene annotatePeakInBatch formatAnnotationReport formatGene2Gene formatGeneReport formatGeneReportFull formatList getBM org.Hs.eg.db org.Hs.egUCSCKG runApp select toTable useDataset useMart
checking compiled code ... NOTE ``` File ‘R3CPET/libs/R3CPET.so’: Found ‘rand’, possibly from ‘rand’ (C) Object: ‘state.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

radiant.model

Version: 0.8.0

checking data for non-ASCII characters ... NOTE Note: found 2 marked UTF-8 strings

radiant.multivariate

Version: 0.8.0

checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

rags2ridges

Version: 2.2

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: libs 3.7Mb

raincpc

Version: 0.4

checking R code for possible problems ... NOTE cpc_get_rawdata: no visible global function definition for ‘download.file’ Undefined global functions or variables: download.file Consider adding importFrom("utils", "download.file") to your NAMESPACE file.

randomForestExplainer

Version: 0.9

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘MASS’ ‘dtplyr’ All declared Imports should be used.

randomizeR

Version: 1.4

checking re-building of vignette outputs ... WARNING `` ... Loading required package: plotrix Warning: Computation failed instat_boxplot(): there is no package called 'quantreg' Warning: Computation failed instat_boxplot(): there is no package called 'quantreg' Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'comparison-example.tex' failed. LaTeX errors: ! LaTeX Error: Filebiblatex.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.57 \bibliography {vignette}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

randomUniformForest

Version: 1.1.5

checking R code for possible problems ... NOTE ... ‘rnorm’ update.unsupervised: no visible global function definition for ‘predict’ weightedVoteModel: no visible global function definition for ‘lm’ which.is.duplicate: no visible global function definition for ‘na.omit’ Undefined global functions or variables: abline aggregate barplot cor dev.new dev.off dist graphics.off grid head heat.colors kmeans legend lm median memory.limit model.frame model.matrix model.response mosaicplot na.omit par pbinom persp plot points predict qnorm quantile rnorm runif sd title Consider adding importFrom("grDevices", "dev.new", "dev.off", "graphics.off", "heat.colors") importFrom("graphics", "abline", "barplot", "grid", "legend", "mosaicplot", "par", "persp", "plot", "points", "title") importFrom("stats", "aggregate", "cor", "dist", "kmeans", "lm", "median", "model.frame", "model.matrix", "model.response", "na.omit", "pbinom", "predict", "qnorm", "quantile", "rnorm", "runif", "sd") importFrom("utils", "head", "memory.limit") to your NAMESPACE file.

rangeMapper

Version: 0.3-1

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘snow’

raptr

Version: 0.1.1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: done.

Building tree... done. Ball query...

done. Requested probability quantile 0.500000, obtained 0.499612 - setting threshold value 0.084938. For a closer match, you can increase num.thresholds in hypervolume_threshold. testthat results ================================================================ OK: 318 SKIPPED: 18 FAILED: 1 1. Failure: gdal installation checks (@test-02-misc.R#6)

Error: testthat unit tests failed Execution halted ```
checking package dependencies ... NOTE Packages suggested but not available for checking: ‘gurobi’ ‘rgurobi’
checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: data 3.6Mb doc 1.4Mb

Rariant

Version: 1.12.0

checking examples ... WARNING ``` Found the following significant warnings:

Warning: 'rbind_all' is deprecated. Deprecated functions may be defunct as soon as of the next release of R. See ?Deprecated. ```
checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: doc 2.3Mb extdata 5.2Mb
checking R code for possible problems ... NOTE tallyBamRegion: no visible global function definition for 'PileupParam' tallyBamRegion: no visible global function definition for 'ScanBamParam' tallyBamRegion: no visible global function definition for 'pileup' Undefined global functions or variables: PileupParam ScanBamParam pileup
checking installed files from ‘inst/doc’ ... NOTE ``` The following files should probably not be installed: ‘rariant-inspect-ci.png’, ‘rariant-inspect-shift.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’, or move the vignette sources from ‘inst/doc’ to ‘vignettes’. ```

rattle

Version: 5.1.0

checking re-building of vignette outputs ... WARNING `` Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'rattle.tex' failed. LaTeX errors: ! LaTeX Error: Filealgorithm2e.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.14 \usepackage [^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```
checking package dependencies ... NOTE Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘playwith’
checking dependencies in R code ... NOTE ```

(R:36326): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init() ```

rbefdata

Version: 0.3.5

checking R code for possible problems ... NOTE ... bef.portal.get.attachments_for: no visible global function definition for ‘flush.console’ bef.portal.get.categories_for: no visible binding for global variable ‘id’ bef.portal.get.categories_for: no visible global function definition for ‘read.csv’ bef.portal.get.dataset: no visible global function definition for ‘read.csv’ bef.portal.get.dataset_by: no visible global function definition for ‘read.csv’ bef.portal.get.datasets.for_keyword : <anonymous>: no visible global function definition for ‘read.csv’ bef.portal.get.datasets.for_proposal: no visible global function definition for ‘read.csv’ upload_file: no visible global function definition for ‘write.csv’ Undefined global functions or variables: browseURL flush.console id read.csv write.csv Consider adding importFrom("utils", "browseURL", "flush.console", "read.csv", "write.csv") to your NAMESPACE file.

RBesT

Version: 1.2-3

checking installed package size ... NOTE installed size is 27.7Mb sub-directories of 1Mb or more: libs 26.4Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘lme4’ All declared Imports should be used.

rbison

Version: 0.5.4

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:
1. Failure: bison_tax returns the correct ... (@test-bison_tax.R#14) ----------- out3$names$vernacularName not equal to "black bear". Lengths differ: 6 vs 1
testthat results ================================================================ OK: 37 SKIPPED: 0 FAILED: 3 1. Failure: bison returns the correct value (@test-bison.R#16) 2. Failure: bison_tax returns the correct ... (@test-bison_tax.R#12) 3. Failure: bison_tax returns the correct ... (@test-bison_tax.R#14)

Error: testthat unit tests failed Execution halted ```

rbokeh

Version: 0.5.0

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘shiny’
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

rCGH

Version: 1.6.0

checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: data 2.8Mb extdata 1.2Mb

RcmdrPlugin.FuzzyClust

Version: 1.1

R CMD check timed out

RcmdrPlugin.KMggplot2

Version: 0.2-4

checking whether package ‘RcmdrPlugin.KMggplot2’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/RcmdrPlugin.KMggplot2/new/RcmdrPlugin.KMggplot2.Rcheck/00install.out’ for details.

RcmdrPlugin.MA

Version: 0.0-2

checking whether package ‘RcmdrPlugin.MA’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/RcmdrPlugin.MA/new/RcmdrPlugin.MA.Rcheck/00install.out’ for details.

rcongresso

Version: 0.2.1

checking tests ... ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(rcongresso) > > test_check("rcongresso") Error: Column `id` must be a 1d atomic vector or a list In addition: Warning message: Unknown or uninitialised column: 'id'. testthat results ================================================================ OK: 18 SKIPPED: 0 FAILED: 0 Execution halted
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Quitting from lines 45-50 (introducao-rcongresso.Rmd) Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics: Column id must be a 1d atomic vector or a list Execution halted ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘utils’ All declared Imports should be used.

RDAVIDWebService

Version: 1.14.0

checking installed package size ... NOTE installed size is 23.9Mb sub-directories of 1Mb or more: java 21.7Mb
checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period. Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... ‘callNextMethod’ terms,DAVIDGODag: no visible global function definition for ‘nodeData’ terms,DAVIDGODag: no visible global function definition for ‘goDag’ uniqueIds,DAVIDGenes: no visible global function definition for ‘validObject’ upsideDown,graph: no visible global function definition for ‘nodes’ upsideDown,graph: no visible global function definition for ‘edges’ upsideDown,graph : <anonymous>: no visible global function definition for ‘edges’ upsideDown,graph : <anonymous> : <anonymous>: no visible global function definition for ‘addEdge’ Undefined global functions or variables: GOGraph Term addEdge callNextMethod edges fill getFromNamespace goDag inEdges na.omit nodeData nodeData<- nodeDataDefaults<- nodes read.csv removeNode type.convert validObject x y Consider adding importFrom("methods", "callNextMethod", "validObject") importFrom("stats", "na.omit") importFrom("utils", "getFromNamespace", "read.csv", "type.convert") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

rdpla

Version: 0.2.0

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 5 SKIPPED: 0 FAILED: 24
1. Error: dpla_collections basic functionality works (@test-dpla_collections.R#6)
2. Error: dpla_items - pagination works (@test-dpla_collections.R#20)
3. Error: dpla_items - fields requests work (@test-dpla_collections.R#35)
4. Failure: dpla_items fails well (@test-dpla_collections.R#46)
5. Failure: dpla_items fails well (@test-dpla_collections.R#49)
6. Error: dpla_collections_ basic functionality works (@test-dpla_collections_.R#6)
7. Error: dpla_items - pagination works (@test-dpla_collections_.R#22)
8. Error: dpla_items - fields requests work (@test-dpla_collections_.R#37)
9. Failure: dpla_items fails well (@test-dpla_collections_.R#48)
10. ...
Error: testthat unit tests failed Execution halted ```

re2r

Version: 0.2.0

checking installed package size ... NOTE installed size is 13.1Mb sub-directories of 1Mb or more: doc 1.5Mb libs 10.4Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

recoup

Version: 1.4.0

checking re-building of vignette outputs ... WARNING ``` ... • test.exons: A 'GRangesList' containing the exons of the 100 above genes for use with 'recoup' RNA-Seq mode.

Fo_r_m_a_t:
```
 'data.frame' and 'list' objects whose format is accepted by
 recoup.
```
Au_t_h_o_r(_s):
```
 Panagiotis Moulos
```
So_u_r_c_e:
```
 Personal communication with the Talianids lab at BSRC 'Alexander
 Fleming'. Unpublished data.
```
Error: processing vignette 'recoup_intro.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking R code for possible problems ... NOTE ... recoup : <anonymous>: no visible global function definition for ‘runValue’ recoupCorrelation: no visible binding for global variable ‘Index’ recoupCorrelation: no visible binding for global variable ‘Coverage’ recoupCorrelation: no visible binding for global variable ‘Condition’ recoupCorrelation: no visible binding for global variable ‘Design’ recoupHeatmap : <anonymous>: no visible global function definition for ‘grid.text’ recoupProfile: no visible binding for global variable ‘Signal’ recoupProfile: no visible binding for global variable ‘Condition’ recoupProfile: no visible binding for global variable ‘Design’ reduceExons : <anonymous>: no visible global function definition for ‘DataFrame’ splitVector: no visible global function definition for ‘Rle’ Undefined global functions or variables: Condition Coverage DataFrame Design IRanges Index Rle ScanBamParam Seqinfo Signal alphabetFrequency bamWhich<- biocLite dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable flankedSexon gene genomeRanges getBSgenome grid.text indexBam installed.genomes mclapply mcmapply runValue seqlevels seqlevels<- sexon sortBam subjectHits

rEDM

Version: 0.6.5

checking re-building of vignette outputs ... WARNING `` ... Warning in ccm(cbind(thrips_block$Thrips_imaginis, surr_Rain[, i]), E = 8, : Note: CCM results are typically interpreted in the opposite direction of causation. Please see 'Detecting causality in complex ecosystems' (Sugihara et al. 2012) for more details. Warning in model$run() : Found overlap between lib and pred. Enabling cross-validation with exclusion radius = 0. Warning in model$run() : lib size request was larger than maximum available; corrected Error: processing vignette 'rEDM-algorithms.ltx' failed with diagnostics: Running 'texi2dvi' on 'rEDM-algorithms.ltx' failed. LaTeX errors: ! LaTeX Error: Filealgorithm.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.28 \usepackage [noend]{algpseudocode}^^M ! ==> Fatal error occurred, no output PDF file produced! Execution halted ```
checking installed package size ... NOTE installed size is 17.5Mb sub-directories of 1Mb or more: doc 2.1Mb libs 15.1Mb

regionReport

Version: 1.10.2

checking re-building of vignette outputs ... WARNING ... no date field in DESCRIPTION file of package 'BiocStyle' Warning in citation("GenomeInfoDb") : no date field in DESCRIPTION file of package 'GenomeInfoDb' Warning in citation("biovizBase") : no date field in DESCRIPTION file of package 'biovizBase' Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") : no date field in DESCRIPTION file of package 'TxDb.Hsapiens.UCSC.hg19.knownGene' Warning in `[.bibentry`(citation("edgeR"), 5) : subscript out of bounds Warning in citation("DEFormats") : no date field in DESCRIPTION file of package 'DEFormats' Writing 34 Bibtex entries ... OK Results written to file 'regionReportRef.bib' Warning in `[[.BibEntry`(bib, c("edgeR1", "edgeR2", "edgeR5", "edgeR6")) : subscript out of bounds Warning in `[[.BibEntry`(bib, c("edgeR1", "edgeR2", "edgeR5", "edgeR6")) : subscript out of bounds Warning in `[[.BibEntry`(bib, "mgcv") : subscript out of bounds Warning in `[[.BibEntry`(bib, "whisker") : subscript out of bounds Error: processing vignette 'regionReport.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘DESeq2:::pvalueAdjustment’ See the note in ?`:::` about the use of this operator.

ReinforcementLearning

Version: 1.0.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.

repijson

Version: 0.1.0

checking package dependencies ... ERROR ``` Package required but not available: ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

replyr

Version: 0.9.0

checking package dependencies ... NOTE Package suggested but not available for checking: ‘magick’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RSQLite’ ‘dbplyr’ All declared Imports should be used.

ReportingTools

Version: 2.16.0

checking tests ... ``` ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output: ERROR in /home/muelleki/git/R/ggplot2/revdep/checks/ReportingTools/new/ReportingTools.Rcheck/ReportingTools/unitTests/test_DESeqResults.R: Error while sourcing /home/muelleki/git/R/ggplot2/revdep/checks/ReportingTools/new/ReportingTools.Rcheck/ReportingTools/unitTests/test_DESeqResults.R : Error in .requirePackage(package) : unable to find required package 'DESeq'

Test files with failing tests
```
 test_DESeqDataSet.R 
   /home/muelleki/git/R/ggplot2/revdep/checks/ReportingTools/new/ReportingTools.Rcheck/ReportingTools/unitTests/test_DESeqDataSet.R

 test_DESeqResults.R 
   /home/muelleki/git/R/ggplot2/revdep/checks/ReportingTools/new/ReportingTools.Rcheck/ReportingTools/unitTests/test_DESeqResults.R
```
Error in BiocGenerics:::testPackage("ReportingTools") : unit tests failed for package ReportingTools Execution halted ```
checking R code for possible problems ... NOTE ... 'fData' .marrayLM.to.html: no visible global function definition for 'featureNames' .marrayLM.to.html: no visible global function definition for 'fData' check.ids: no visible binding for global variable 'org.Hs.eg.db' check.ids: no visible global function definition for 'keys' custHeaderPanel : <anonymous>: no visible binding for global variable 'tags' custHeaderPanel : <anonymous>: no visible global function definition for 'HTML' custHeaderPanel: no visible global function definition for 'tagList' custHeaderPanel: no visible global function definition for 'tag' custHeaderPanel: no visible global function definition for 'div' custHeaderPanel: no visible global function definition for 'h1' publish,trellis-HTMLReport: no visible binding for global variable 'htmlRep' toReportDF,DESeqDataSet: no visible global function definition for 'mcols' Undefined global functions or variables: HTML columns description div exprs fData featureNames h1 htmlRep keys keytype mcols org.Hs.eg.db tag tagList tags

rerddap

Version: 0.4.2

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 91 SKIPPED: 0 FAILED: 15
1. Failure: ed_search_adv fails well (@test-ed_search_adv.R#58)
2. Failure: ed_search_adv fails well (@test-ed_search_adv.R#59)
3. Error: griddap returns the correct class (@test-griddap.r#6)
4. Error: griddap fixes incorrect user inputs (@test-griddap.r#24)
5. Error: griddap fields parameter works, and fails correctly (@test-griddap.r#65)
6. Failure: griddap fails well, in addition to above failure tests (@test-griddap.r#85)
7. Failure: griddap fails well, in addition to above failure tests (@test-griddap.r#86)
8. Failure: griddap fails well, in addition to above failure tests (@test-griddap.r#89)
9. Error: info returns the correct (@test-info.R#6)
10. ...
Error: testthat unit tests failed Execution halted ```
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘taxize’

rfigshare

Version: 0.3.7

checking R code for possible problems ... NOTE fs_author_ids : <anonymous>: no visible global function definition for ‘select.list’ fs_download : <anonymous>: no visible global function definition for ‘download.file’ Undefined global functions or variables: download.file select.list Consider adding importFrom("utils", "download.file", "select.list") to your NAMESPACE file.

RforProteomics

Version: 1.14.0

checking re-building of vignette outputs ... WARNING ... NetworkAnalysis, GraphsAndNetworks Warning: Dropping unknown biocViews terms: Cancer, StemCells, HIV Warning: Dropping unknown biocViews terms: NoViewProvided Warning: Dropping unknown biocViews terms: Statistics Warning: Dropping unknown biocViews terms: Statistical Method Warning: Dropping unknown biocViews terms: Regulation, HighThroughputSequencing, MultipleComparisons, Bioinformatics Warning: Dropping unknown biocViews terms: HighThroughputSequencing trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/PXD000001_mztab.txt' Content type 'unknown' length 864039 bytes (843 KB) ================================================== Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details. Quitting from lines 414-419 (RProtVis.Rmd) Error: processing vignette 'RProtVis.Rmd' failed with diagnostics: there is no package called 'beanplot' Execution halted
checking installed package size ... NOTE installed size is 8.0Mb sub-directories of 1Mb or more: doc 7.1Mb
checking R code for possible problems ... NOTE RProtVis: no visible global function definition for ‘vignette’ RProtViz: no visible global function definition for ‘vignette’ RforProteomics: no visible global function definition for ‘vignette’ downloadData: no visible global function definition for ‘download.file’ getPackagesInBiocView: no visible global function definition for ‘data’ shinyMA: no visible global function definition for ‘data’ shinyMA : <anonymous>: no visible global function definition for ‘par’ shinyMA : <anonymous>: no visible global function definition for ‘grid’ shinyMA : <anonymous>: no visible global function definition for ‘abline’ shinyMA : <anonymous>: no visible global function definition for ‘points’ Undefined global functions or variables: abline data download.file grid par points vignette Consider adding importFrom("graphics", "abline", "grid", "par", "points") importFrom("utils", "data", "download.file", "vignette") to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE '::' or ':::' import not declared from: ‘AnnotationDbi’

rfPermute

Version: 2.1.5

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘graphics’ All declared Imports should be used.

rgbif

Version: 0.9.9

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: 8: dplyr::collect 9: getExportedValue(pkg, name) 10: asNamespace(ns) 11: getNamespace(ns) 12: tryCatch(loadNamespace(name), error = function(e) stop(e)) 13: tryCatchList(expr, classes, parentenv, handlers) 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 15: value[3L]

testthat results ================================================================ OK: 720 SKIPPED: 0 FAILED: 1 1. Error: gbifmap (@test-gbifmap.r#8)

Error: testthat unit tests failed Execution halted ```

RGCCA

Version: 2.1.2

checking re-building of vignette outputs ... WARNING `` Error in re-building vignettes: ... ! LaTeX Error: Filealgorithm2e.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

Enter file name: ! Emergency stop.

l.128 \usepackage

pandoc: Error producing PDF Error: processing vignette 'vignette_RGCCA.Rmd' failed with diagnostics: pandoc document conversion failed with error 43 Execution halted ```

RGraphics

Version: 2.0-14

checking package dependencies ... NOTE Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘iplots’ ‘playwith’ ‘pmg’ ‘RGraphics’
checking installed package size ... NOTE installed size is 9.7Mb sub-directories of 1Mb or more: extra 9.4Mb

RiboProfiling

Version: 1.6.0

checking whether package ‘RiboProfiling’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘BiocGenerics::Position’ by ‘ggplot2::Position’ when loading ‘RiboProfiling’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/RiboProfiling/new/RiboProfiling.Rcheck/00install.out’ for details.
checking R code for possible problems ... NOTE applyShiftFeature: no visible global function definition for 'is' aroundPromoter: no visible global function definition for 'is' codonInfo: no visible global function definition for 'is' countShiftReads: no visible global function definition for 'is' histMatchLength: no visible global function definition for 'is' orfRelativePos: no visible global function definition for 'is' plotSummarizedCov: no visible global function definition for 'is' readStartCov: no visible global function definition for 'is' readsToStartOrEnd: no visible global function definition for 'is' riboSeqFromBAM: no visible global function definition for 'is' Undefined global functions or variables: is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

riskRegression

Version: 1.4.3

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: libs 5.6Mb

RITAN

Version: 1.0.0

checking R code for possible problems ... NOTE ... summary.term_enrichment_by_subset: no visible global function definition for ‘head’ term.test: no visible global function definition for ‘phyper’ term_enrichment : process_source: no visible binding for global variable ‘active_genesets’ term_enrichment : process_source: no visible global function definition for ‘head’ write_simple_table: no visible global function definition for ‘write.table’ Undefined global functions or variables: Var1 Var2 abline active_genesets all_net all_symbols box density e f geneset_list head hist mad median network_list p.adjust phyper plot polygon read.table rect setTxtProgressBar subSIF txtProgressBar write.table Consider adding importFrom("graphics", "abline", "box", "hist", "plot", "polygon", "rect") importFrom("stats", "density", "mad", "median", "p.adjust", "phyper") importFrom("utils", "head", "read.table", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file.

RIVER

Version: 1.0.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... SubjectID GeneName Feature1 Feature2 Feature3 Feature4 Feature5 Feature6 Feature7 Feature8 Feature9 Feature10 Feature11 Feature12 Feature13 Feature14 Feature15 Feature16 Feature17 Feature18 Zscore N2pair indiv58 gene1614 0.489033798630696 -1.21431829385884 -0.501524068860469 -0.809388087647524 -0.191695708370831 -0.0661469835645102 0.199315319036506 -0.754425337309085 -1.35050355454646 -0.0347771492735548 2.08675351921196 0.728318277270296 0.150747102542626 1.51835790522656 0.222613351767026 1.88846321159354 -0.440823555356033 -0.45581108818362 2.83051056818124 NA Error: processing vignette 'RIVER.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘data.table’

rmcfs

Version: 1.2.6

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: java 4.5Mb

rms

Version: 5.1-1

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘multiwayvcov’, ‘treatSens’

RnBeads

Version: 1.8.0

checking tests ... ``` ERROR Running the tests in ‘tests/runTests.R’ failed. Last 13 lines of output:
```
  ozone
```
The following object is masked from 'package:IRanges':
```
  desc
```
The following object is masked from 'package:S4Vectors':
```
  rename
```
Error in library("RUnit", quietly = TRUE) : there is no package called 'RUnit' Calls: -> library Execution halted ```
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘BiocGenerics’ ‘S4Vectors’ ‘GenomicRanges’ ‘MASS’ ‘cluster’ ‘ff’ ‘fields’ ‘ggplot2’ ‘gplots’ ‘gridExtra’ ‘limma’ ‘matrixStats’ ‘illuminaio’ ‘methylumi’ ‘plyr’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking installed package size ... NOTE installed size is 6.2Mb sub-directories of 1Mb or more: R 1.1Mb bin 1.0Mb doc 3.1Mb
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'Gviz:::.getBMFeatureMap' 'doParallel:::.options' 'grDevices:::.smoothScatterCalcDensity' 'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k' 'minfi:::.normalizeFunnorm450k' See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... BootRefFreeEwasModel ChrNumeric DataTrack Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack ID IdeogramTrack IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICmanifest Index Intensity Measure PairsBootRefFreeEwasModel Probe RGChannelSet RefFreeEwasModel SNP Sample Slide Target Term UcscTrack Value addSex as.profileCGH assayDataElement assayDataElementNames barcode bv chrom color combinedRank comma covgMedian covgPercLow covgPercUp cv.glmnet daglad diffmeth diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency expectedCounts featureData featureData<- featureNames featureNames<- foreach geneCounts genome<- getCN getDoParWorkers getGreen getManifest getMeth getRed getSex getUnmeth getVarCov glmnet grid.draw grid.newpage group group1 group2 i impute.knn intensities is.subsegmentation k letterFrequency lme mapToGenome mean.diff mean.g1 mean.g2 mean.mean.g1 mean.mean.g2 mean.quot.log2 melt muted n.sites num.sites numSites numeric.names oddsRatios pData percent_format phenoData phenoData<- plotOrder plotTracks preprocessSWAN pvalues refText reg.type region.size registerDoParallel relative.coord report samples seqlengths seqlevels<- sigCategories sites2ignore size solve.QP stopCluster sva target tsne type types universeCounts useMart v varLabels x y yint

Rnits

Version: 1.10.0

checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : URL https://ftp.ncbi.nlm.nih.gov/geo/series/GSE4nnn/GSE4158/matrix//geo/series/GSE4nnn/GSE4158/: cannot open destfile '/home/muelleki/tmp/RtmpMRn15c//geo/series/GSE4nnn/GSE4158/', reason 'No such file or directory' Warning in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : download had nonzero exit status Warning in file(con, "r") : cannot open file '/home/muelleki/tmp/RtmpMRn15c//geo/series/GSE4nnn/GSE4158/': No such file or directory Quitting from lines 90-114 (Rnits-vignette.Rnw) Error: processing vignette 'Rnits-vignette.Rnw' failed with diagnostics: cannot open the connection Execution halted ```
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... ‘scale_color_brewer’ plotResults,Rnits: no visible global function definition for ‘facet_wrap’ plotResults,Rnits: no visible global function definition for ‘dev.off’ summary,Rnits: no visible global function definition for ‘hist’ timeAlign,Rnits: no visible global function definition for ‘quantile’ timeAlign,Rnits: no visible global function definition for ‘mvfft’ timeAlign,Rnits: no visible global function definition for ‘abline’ Undefined global functions or variables: Sample Time abline aes dev.off facet_wrap gaussian geom_point geom_smooth glm hat hist kmeans mad median mvfft p.adjust par predict quantile rnorm scale_color_brewer sd setNames setTxtProgressBar smooth.spline theme theme_bw txtProgressBar value ylab Consider adding importFrom("grDevices", "dev.off") importFrom("graphics", "abline", "hist", "par") importFrom("stats", "gaussian", "glm", "hat", "kmeans", "mad", "median", "mvfft", "p.adjust", "predict", "quantile", "rnorm", "sd", "setNames", "smooth.spline") importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file.

rnoaa

Version: 0.7.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 163 SKIPPED: 1 FAILED: 17
1. Failure: buoys fails well (@test-buoy.R#74)
2. Error: check_response returns an error (@test-check_response.r#7)
3. Error: check_response returns the correct error messages (@test-check_response.r#26)
4. Error: gefs time and ensemble selection returns correct indices. (@test-gefs.R#25)
5. Error: gefs_variables returns characters. (@test-gefs.R#52)
6. Error: gefs_latitudes returns numeric. (@test-gefs.R#63)
7. Error: gefs_longitudes returns numeric. (@test-gefs.R#73)
8. Error: gefs_dimensions returns character list. (@test-gefs.R#83)
9. Error: gefs_dimension_values returns numeric array. (@test-gefs.R#93)
10. ...
Error: testthat unit tests failed Execution halted ```

RNOmni

Version: 0.1.4

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘cowplot’ ‘ggplot2’ ‘microbenchmark’ ‘reshape2’ All declared Imports should be used.

rnpn

Version: 0.1.0

checking tests ... `` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: bb$latitude inherits fromnumericnotcharacter`.

testthat results ================================================================ OK: 20 SKIPPED: 0 FAILED: 7 1. Failure: npn_indsatstations works well (@test-npn_indsatstations.R#9) 2. Failure: npn_indspatstations works well (@test-npn_indspatstations.R#9) 3. Error: npn_obsspbyday works well (@test-npn_obsspbyday.R#6) 4. Error: when no match, returns empty data.frame (@test-npn_obsspbyday.R#20) 5. Failure: npn_stationsbystate works well (@test-npn_stationsbystate.R#11) 6. Failure: npn_stationswithspp works well (@test-npn_stationswithspp.R#10) 7. Failure: npn_stationswithspp works well (@test-npn_stationswithspp.R#15)

Error: testthat unit tests failed Execution halted ```

robCompositions

Version: 2.0.6

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘mvoutlier’, ‘StatDA’
checking data for non-ASCII characters ... NOTE Note: found 5701 marked UTF-8 strings

robustbase

Version: 0.92-8

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘matrixStats’, ‘robustX’, ‘quantreg’, ‘Hmisc’
checking re-building of vignette outputs ... NOTE Error in re-building vignettes: ... Loading required package: robustbase Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'fastMcd-kmini.tex' failed. BibTeX errors: The top-level auxiliary file: fastMcd-kmini.aux I couldn't open style file chicago.bst ---line 43 of file fastMcd-kmini.aux : \bibstyle{chicago : } I'm skipping whatever remains of this command I found no style file---while reading file fastMcd-kmini.aux Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted

robustHD

Version: 0.5.1

checking installed package size ... NOTE installed size is 6.4Mb sub-directories of 1Mb or more: libs 5.9Mb

rODE

Version: 0.99.6

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘data.table’ All declared Imports should be used.

Roleswitch

Version: 1.14.0

checking package dependencies ... NOTE Depends: includes the non-default packages: ‘pracma’ ‘reshape’ ‘plotrix’ ‘microRNA’ ‘biomaRt’ ‘Biostrings’ ‘Biobase’ ‘DBI’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking R code for possible problems ... NOTE diagnosticPlot: no visible global function definition for ‘par’ diagnosticPlot: no visible global function definition for ‘axis’ diagnosticPlot: no visible global function definition for ‘plot’ getSeedMatrix: no visible global function definition for ‘data’ getTranscriptIDwithLongest3UTR: no visible global function definition for ‘aggregate’ roleswitch: no visible global function definition for ‘aggregate’ Undefined global functions or variables: aggregate axis data par plot Consider adding importFrom("graphics", "axis", "par", "plot") importFrom("stats", "aggregate") importFrom("utils", "data") to your NAMESPACE file.
checking re-building of vignette outputs ... NOTE ``` ... 3: max(p.x-p.x.prev)=0.00010 4: max(p.x-p.x.prev)=0.00000

Start roleswitch with 365 miRNA and 11016 mRNA 1: max(p.x-p.x.prev)=0.12564 2: max(p.x-p.x.prev)=0.00008 3: max(p.x-p.x.prev)=0.00003 4: max(p.x-p.x.prev)=0.00000 Some genes or miRNA are left out in calculation b/c they have zero target sites or targets! Their probabilities are set to zero in the output matrices Loading required package: ggplot2 Loading required package: hgu95av2.db Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘hgu95av2.db’

Error: processing vignette 'Roleswitch.Rnw' failed with diagnostics: chunk 10 (label = eset) Error in roleswitch(eset, mirna.expr) : hgu95av2.db package must be installed Execution halted ```

rolypoly

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘matrixcalc’ All declared Imports should be used.

rotations

Version: 1.5

checking installed package size ... NOTE installed size is 10.3Mb sub-directories of 1Mb or more: data 2.3Mb libs 6.5Mb

rpdo

Version: 0.2.2

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 15: check_values(data, values = values, unique = TRUE, nulls = FALSE, data_name = data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-data3.R:33 16: check_data_values(data, values, data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-values.R:20 17: vapply(column_names, FUN = check_data_values_column, logical(1), data = data, values = values, data_name = data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-data-values.R:20 18: FUN(X[[i]], ...) 19: check_vector_value_missing(vector, value, column_name, data_name) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-data-values.R:9 20: error(name_info(column_name, data_name), " cannot include missing values") at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/check-vector-value.R:7 21: stop(..., call. = FALSE) at /tmp/RtmpHtcmq3/R.INSTALL6285486ea706/datacheckr/R/utils.R:20

testthat results ================================================================ OK: 1 SKIPPED: 0 FAILED: 1 1. Error: download_pdo (@test-download-pdo.R#4)

Error: testthat unit tests failed Execution halted ```

rpf

Version: 0.55

checking installed package size ... NOTE installed size is 9.3Mb sub-directories of 1Mb or more: libs 8.5Mb

RPPanalyzer

Version: 1.4.4

checking installed package size ... NOTE installed size is 5.4Mb sub-directories of 1Mb or more: extdata 4.5Mb

rPref

Version: 1.2

checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

Rqc

Version: 1.10.2

checking R code for possible problems ... NOTE .ui.Rqc: no visible global function definition for 'packageVersion' rqc: no visible global function definition for 'browseURL' rqcCycleAverageQualityPcaCalc: no visible global function definition for 'prcomp' rqcFileHeatmap: no visible global function definition for 'hclust' stats4trim : <anonymous>: no visible global function definition for 'head' Undefined global functions or variables: browseURL hclust head packageVersion prcomp Consider adding importFrom("stats", "hclust", "prcomp") importFrom("utils", "browseURL", "head", "packageVersion") to your NAMESPACE file.

rrpack

Version: 0.1-6

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: libs 5.1Mb

rrr

Version: 1.0.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘Rcpp’ All declared Imports should be used.

RSA

Version: 0.9.11

checking whether package ‘RSA’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available Warning: loading Rplot failed See ‘/home/muelleki/git/R/ggplot2/revdep/checks/RSA/new/RSA.Rcheck/00install.out’ for details.

rsMove

Version: 0.2.1

checking whether package ‘rsMove’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘rsMove’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/rsMove/new/rsMove.Rcheck/00install.out’ for details.

rsoi

Version: 0.3.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘utils’ All declared Imports should be used.

rSPACE

Version: 1.2.0

checking whether package ‘rSPACE’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/rSPACE/new/rSPACE.Rcheck/00install.out’ for details.

RSSL

Version: 0.6.1

checking installed package size ... NOTE installed size is 5.0Mb sub-directories of 1Mb or more: libs 2.7Mb

rstan

Version: 2.16.2

checking installed package size ... NOTE installed size is 228.9Mb sub-directories of 1Mb or more: libs 226.6Mb
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘coda’, ‘rstanarm’

rstanarm

Version: 2.15.3

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: no valid constructor available for the argument list trying deprecated constructor; please alert package maintainer Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) : no valid constructor available for the argument list trying deprecated constructor; please alert package maintainer Error in new_CppObject_xp(fields$.module, fields$.pointer, ...) : no valid constructor available for the argument list trying deprecated constructor; please alert package maintainer testthat results ================================================================ OK: 1738 SKIPPED: 0 FAILED: 2
1. Error: pp_check.stanreg creates ggplot object (@test_pp_check.R#48)
2. Error: the Stan equivalent of lme4's Z %*% b works (@test_stan_functions.R#408)
Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE installed size is 58.3Mb sub-directories of 1Mb or more: doc 2.2Mb libs 55.0Mb
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘gamm4’, ‘biglm’

RStoolbox

Version: 0.1.10

checking examples ... ERROR ``` ... 49 LC82240632013167LGN00 LC82240632013167LGN00 Download.Link 6 http://earthexplorer.usgs.gov/download/options/4923/LC82240632015157LGN00 27 http://earthexplorer.usgs.gov/download/options/4923/LC82240632014186LGN00 40 http://earthexplorer.usgs.gov/download/options/4923/LC82240632013327LGN00 46 http://earthexplorer.usgs.gov/download/options/4923/LC82240632013215LGN00 49 http://earthexplorer.usgs.gov/download/options/4923/LC82240632013167LGN00 Browse.Link Date Doy Year Satellite Num 6 NA 2015-06-06 157 2015 LS8 8 27 NA 2014-07-05 186 2014 LS8 8 40 NA 2013-11-23 327 2013 LS8 8 46 NA 2013-08-03 215 2013 LS8 8 49 NA 2013-06-16 167 2013 LS8 8 > > ## Available time-series > ggplot(ee) +
- geom_segment(aes(x = Date, xend = Date, y = 0, yend = 100 - Cloud.Cover,
- col = as.factor(Year))) +
- scale_y_continuous(name = "Scene quality (% clear sky)") Error: Columns x, xend are dates/times and must be stored as POSIXct, not POSIXlt Execution halted ```

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: libs 4.3Mb

rsunlight

Version: 0.4.2

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 8 SKIPPED: 0 FAILED: 30
1. Error: returns the correct (@test-amendments.R#6)
2. Error: vectorizing works (@test-amendments.R#29)
3. Error: paging works (@test-amendments.R#37)
4. Error: fails well (@test-amendments.R#47)
5. Error: cg_bills returns the correct (@test-cg_bills.R#6)
6. Error: cg_bills vectorizing works (@test-cg_bills.R#25)
7. Error: cg_bills pagination works (@test-cg_bills.R#35)
8. Failure: cg_bills curl options work (@test-cg_bills.R#44)
9. Failure: cg_bills fails well (@test-cg_bills.R#50)
10. ...
Error: testthat unit tests failed Execution halted ```

RSwissMaps

Version: 0.1.0

checking data for non-ASCII characters ... NOTE Note: found 18627 marked UTF-8 strings

RTCGA

Version: 1.6.0

checking examples ... ERROR ``` ...
- MET = MET|4233) %>%
- cancer samples
- filter(substr(bcr_patient_barcode, 14, 15) == "01") -> ACC_BLCA_BRCA_OV.rnaseq
  
  boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "cohort", "MET") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "cohort", "log1p(MET)") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), max)", "log1p(MET)") boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
- xlab = "Cohort Type", ylab = "Logarithm of MET")
  
  boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
- xlab = "Cohort Type", ylab = "Logarithm of MET", legend.title = "Cohorts")
  
  boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
- xlab = "Cohort Type", ylab = "Logarithm of MET", legend.title = "Cohorts", legend = "bottom")
  
  facet example
  
  library(RTCGA.mutations) Error in library(RTCGA.mutations) : there is no package called ‘RTCGA.mutations’ Execution halted ```
checking package dependencies ... NOTE Packages suggested but not available for checking: ‘RTCGA.clinical’ ‘RTCGA.mutations’ ‘RTCGA.RPPA’ ‘RTCGA.mRNA’ ‘RTCGA.miRNASeq’ ‘RTCGA.methylation’ ‘RTCGA.CNV’
checking R code for possible problems ... NOTE availableDates: no visible binding for global variable ‘.’ downloadTCGA: no visible binding for global variable ‘.’ ggbiplot: no visible binding for global variable ‘xvar’ ggbiplot: no visible binding for global variable ‘yvar’ ggbiplot: no visible global function definition for ‘muted’ ggbiplot: no visible binding for global variable ‘varname’ ggbiplot: no visible binding for global variable ‘angle’ ggbiplot: no visible binding for global variable ‘hjust’ read.mutations: no visible binding for global variable ‘.’ read.rnaseq: no visible binding for global variable ‘.’ survivalTCGA: no visible binding for global variable ‘times’ whichDateToUse: no visible binding for global variable ‘.’ Undefined global functions or variables: . angle hjust muted times varname xvar yvar
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘RTCGA.clinical’, ‘RTCGA.mutations’, ‘RTCGA.CNV’, ‘RTCGA.RPPA’, ‘RTCGA.mRNA’, ‘RTCGA.miRNASeq’, ‘RTCGA.methylation’

rtf

Version: 0.4-11

checking R code for possible problems ... NOTE ... .forest.plot.scale: no visible global function definition for ‘axTicks’ .forest.plot.scale : <anonymous>: no visible global function definition for ‘lines’ .forest.plot.scale: no visible global function definition for ‘lines’ .forest.plot.scale: no visible global function definition for ‘text’ .rtf.plot: no visible global function definition for ‘png’ .rtf.plot: no visible global function definition for ‘dev.off’ .rtf.trellis.object: no visible global function definition for ‘png’ .rtf.trellis.object: no visible global function definition for ‘dev.off’ addSessionInfo.RTF: no visible global function definition for ‘sessionInfo’ Undefined global functions or variables: abline arrows axTicks dev.off lines par plot png points sessionInfo text Consider adding importFrom("grDevices", "dev.off", "png") importFrom("graphics", "abline", "arrows", "axTicks", "lines", "par", "plot", "points", "text") importFrom("utils", "sessionInfo") to your NAMESPACE file.

rtimes

Version: 0.5.0

checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output: 6: Filter(Negate(is.null), x) 7: unlist(lapply(x, f)) 8: lapply(x, f) 9: check_key(key) 10: stop("need an API key for ", y, call. = FALSE)

testthat results ================================================================ OK: 2 SKIPPED: 0 FAILED: 4 1. Error: returns the correct stuff (@test-as_search.R#8) 2. Error: returns the correct stuff (@test-geo_search.R#8) 3. Failure: fails well (@test-geo_search.R#48) 4. Error: fails well (@test-geo_search.R#50)

Error: testthat unit tests failed Execution halted ```

rtimicropem

Version: 1.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R6’ All declared Imports should be used.

rtweet

Version: 0.6.0

checking data for non-ASCII characters ... NOTE Note: found 113868 marked UTF-8 strings

rvertnet

Version: 0.6.2

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: grepl("Bufo debilis", aa$data$scientificname) isn't true.
1. Failure: vert_id works (@test-vert_id.R#33) --------------------------------- any(grepl("Bufo", aa$data$scientificname)) isn't true.
testthat results ================================================================ OK: 107 SKIPPED: 0 FAILED: 3 1. Failure: searchbyterm works correctly (@test-searchbyterm.R#12) 2. Failure: vert_id works (@test-vert_id.R#15) 3. Failure: vert_id works (@test-vert_id.R#33)

Error: testthat unit tests failed Execution halted ```

rvinecopulib

Version: 0.2.3.1.0

checking installed package size ... NOTE installed size is 49.2Mb sub-directories of 1Mb or more: libs 48.4Mb

rWBclimate

Version: 0.1.3

checking R code for possible problems ... NOTE check_ISO_code: no visible binding for global variable ‘NoAm_country’ check_ISO_code: no visible binding for global variable ‘SoAm_country’ check_ISO_code: no visible binding for global variable ‘Oceana_country’ check_ISO_code: no visible binding for global variable ‘Africa_country’ check_ISO_code: no visible binding for global variable ‘Asia_country’ check_ISO_code: no visible binding for global variable ‘Eur_country’ climate_map: no visible binding for global variable ‘data’ date_correct: no visible global function definition for ‘tail’ Undefined global functions or variables: Africa_country Asia_country Eur_country NoAm_country Oceana_country SoAm_country data tail Consider adding importFrom("utils", "data", "tail") to your NAMESPACE file.

Rz

Version: 0.9-1

checking dependencies in R code ... NOTE 'library' or 'require' call to ‘vcd’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘foreign’ ‘ggplot2’ ‘grid’ ‘psych’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported object imported by a ':::' call: ‘foreign:::adQuote’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ... for ‘rgb’ gtkColorSelectionWidgetNew: no visible global function definition for ‘colors’ gtkFileChooserDialogFilteredActivate: no visible binding for global variable ‘theme_grey’ localize: no visible global function definition for ‘localeToCharset’ summary.CrossTable : twoDimTable: no visible global function definition for ‘addmargins’ summary.CrossTable: no visible global function definition for ‘assocstats’ write.spss: no visible global function definition for ‘write.table’ write.stata: no visible global function definition for ‘write.table’ Undefined global functions or variables: addmargins as.formula assocstats colors localeToCharset nclass.FD nclass.Sturges nclass.scott rgb theme_grey write.table Consider adding importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges", "nclass.scott", "rgb") importFrom("stats", "addmargins", "as.formula") importFrom("utils", "localeToCharset", "write.table") to your NAMESPACE file.

samExploreR

Version: 1.0.0

checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE plotsamExplorer: no visible binding for global variable ‘f’ plotsamExplorer: no visible binding for global variable ‘value’ plotsamExplorer: no visible binding for global variable ‘group’ Undefined global functions or variables: f group value

sand

Version: 1.0.3

checking data for non-ASCII characters ... NOTE Note: found 6 marked UTF-8 strings

savR

Version: 1.14.0

checking R code for possible problems ... NOTE buildReports,savProject-character: no visible global function definition for ‘dev.off’ qualityHeatmap,savProject-integer-integer-logical: no visible global function definition for ‘quantile’ Undefined global functions or variables: dev.off quantile Consider adding importFrom("grDevices", "dev.off") importFrom("stats", "quantile") to your NAMESPACE file.

SC3

Version: 1.4.2

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'my-vignette.Rmd' failed with diagnostics: there is no package called ‘BiocStyle’ Execution halted

scanstatistics

Version: 1.0.0

checking installed package size ... NOTE installed size is 6.9Mb sub-directories of 1Mb or more: libs 6.3Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gamlss.dist’ All declared Imports should be used.

scater

Version: 1.4.0

checking installed package size ... NOTE installed size is 8.7Mb sub-directories of 1Mb or more: doc 5.7Mb
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'arrange': ‘arrange.SCESet’

S3 methods shown with full name in documentation object 'filter': ‘filter.SCESet’

S3 methods shown with full name in documentation object 'mutate': ‘mutate.SCESet’

S3 methods shown with full name in documentation object 'rename': ‘rename.SCESet’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

scDD

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘grDevices’ ‘graphics’ ‘stats’ All declared Imports should be used.
checking R code for possible problems ... NOTE ... testZeroes: no visible global function definition for ‘anova’ validation : <anonymous>: no visible global function definition for ‘var’ validation: no visible binding for global variable ‘var’ validation: no visible global function definition for ‘par’ validation: no visible global function definition for ‘plot’ validation: no visible global function definition for ‘abline’ validation: no visible global function definition for ‘points’ Undefined global functions or variables: abline anova axis binomial density dev.off fisher.test hcl hist ks.test lines lm model.matrix p.adjust par pdf plot points quantile rbinom rect residuals rnbinom rt runif t.test var Consider adding importFrom("grDevices", "dev.off", "hcl", "pdf") importFrom("graphics", "abline", "axis", "hist", "lines", "par", "plot", "points", "rect") importFrom("stats", "anova", "binomial", "density", "fisher.test", "ks.test", "lm", "model.matrix", "p.adjust", "quantile", "rbinom", "residuals", "rnbinom", "rt", "runif", "t.test", "var") to your NAMESPACE file.

SciencesPo

Version: 1.4.1

checking examples ... ERROR ``` ... > ### Title: Automatically enclose points in a polygon > ### Aliases: GeomSpotlight geom_spotlight > ### Keywords: datasets ggplot2 > > ### * Examples > > d <- data.frame(x=c(1,1,2),y=c(1,2,2)100) > > gg <- ggplot(d,aes(x,y)) > gg <- gg + scale_x_continuous(expand=c(0.5,1)) > gg <- gg + scale_y_continuous(expand=c(0.5,1)) > gg + geom_spotlight(s_shape=1, expand=0) + geom_point() > > > gg <- ggplot(mpg, aes(displ, hwy)) > ss <- subset(mpg,hwy>29 & displ<3) > gg + geom_spotlight(data=ss, colour="blue", s_shape=.8, expand=0) +
- geom_point() + geom_point(data=ss, colour="blue") Error in loadNamespace(name) : there is no package called ‘dplyr’ Calls: geom_spotlight ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted ```

checking re-building of vignette outputs ... WARNING ... Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: New theme missing the following elements: axis.title.x.top, axis.title.y.right, axis.text.x.top, axis.text.y.right, axis.line.x, axis.line.y, legend.spacing.x, legend.spacing.y, legend.box.margin, legend.box.background, legend.box.spacing, panel.spacing.x, panel.spacing.y, panel.grid.major, panel.grid.minor, plot.subtitle, plot.caption, strip.placement Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead Quitting from lines 1090-1091 (SciencesPo.Rmd) Error: processing vignette 'SciencesPo.Rmd' failed with diagnostics: invalid 'times' argument Execution halted
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘gmodels’

scone

Version: 1.0.0

checking re-building of vignette outputs ... WARNING ``` ...

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':
```
anyMissing, rowMedians
```
Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':
```
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
```
The following object is masked from 'package:base':
```
apply
```
Error: processing vignette 'sconeTutorial.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘EDASeq’ All declared Imports should be used.

SCORPIUS

Version: 1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Rcpp’ ‘testthat’ All declared Imports should be used.

scsR

Version: 1.12.0

checking whether package ‘scsR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/scsR/new/scsR.Rcheck/00install.out’ for details.
checking package dependencies ... NOTE Depends: includes the non-default packages: ‘STRINGdb’ ‘BiocGenerics’ ‘Biostrings’ ‘IRanges’ ‘plyr’ ‘tcltk’ Adding so many packages to the search path is excessive and importing selectively is preferable.
checking R code for possible problems ... NOTE ... seed_correction_pooled: no visible global function definition for ‘txtProgressBar’ seed_correction_pooled: no visible global function definition for ‘setTxtProgressBar’ seed_removal: no visible global function definition for ‘txtProgressBar’ seed_removal: no visible global function definition for ‘setTxtProgressBar’ seeds_analysis : <anonymous>: no visible global function definition for ‘ks.test’ seeds_analysis: no visible global function definition for ‘phyper’ transcribe_seqs: no visible global function definition for ‘txtProgressBar’ transcribe_seqs: no visible global function definition for ‘setTxtProgressBar’ Undefined global functions or variables: cor.test heatmap.2 ks.test lm phyper setTxtProgressBar txtProgressBar Consider adding importFrom("stats", "cor.test", "ks.test", "lm", "phyper") importFrom("utils", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file.

SDaA

Version: 0.1-3

checking R code for possible problems ... NOTE lahiri.design: no visible global function definition for ‘runif’ Undefined global functions or variables: runif Consider adding importFrom("stats", "runif") to your NAMESPACE file.

sdcMicro

Version: 5.0.4

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: libs 2.1Mb

SDEFSR

Version: 0.7.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘grDevices’ All declared Imports should be used.

season

Version: 0.3-5

checking R code for possible problems ... NOTE ... sinusoid: no visible global function definition for ‘par’ sinusoid: no visible global function definition for ‘plot’ sinusoid: no visible global function definition for ‘lines’ sinusoid: no visible global function definition for ‘axis’ summary.monthglm: no visible global function definition for ‘qnorm’ wtest: no visible global function definition for ‘qchisq’ wtest: no visible global function definition for ‘pchisq’ Undefined global functions or variables: acf as.formula axis box cpgram fitted gaussian glm gray hist lines median model.frame na.omit par pchisq plot points polygon qchisq qnorm quantile relevel resid residuals rgamma rnorm rug runif sd text time Consider adding importFrom("grDevices", "gray") importFrom("graphics", "axis", "box", "hist", "lines", "par", "plot", "points", "polygon", "rug", "text") importFrom("stats", "acf", "as.formula", "cpgram", "fitted", "gaussian", "glm", "median", "model.frame", "na.omit", "pchisq", "qchisq", "qnorm", "quantile", "relevel", "resid", "residuals", "rgamma", "rnorm", "runif", "sd", "time") to your NAMESPACE file.

seewave

Version: 2.0.5

checking package dependencies ... NOTE Package suggested but not available for checking: ‘rpanel’

selfea

Version: 1.0.1

checking R code for possible problems ... NOTE get_statistics_from_file: no visible global function definition for ‘read.csv’ glm_anova: no visible global function definition for ‘aov’ glm_anova: no visible global function definition for ‘glm’ glm_anova: no visible global function definition for ‘gaussian’ glm_anova: no visible global function definition for ‘anova’ glm_anova: no visible global function definition for ‘quasipoisson’ glm_anova: no visible global function definition for ‘sd’ glm_anova: no visible global function definition for ‘p.adjust’ ttest_cohens_d: no visible global function definition for ‘t.test’ ttest_cohens_d: no visible global function definition for ‘sd’ Undefined global functions or variables: anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test Consider adding importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust", "quasipoisson", "sd", "t.test") importFrom("utils", "read.csv") to your NAMESPACE file.

sensitivity

Version: 1.15.0

checking package dependencies ... NOTE Package suggested but not available for checking: ‘fanovaGraph’

SensusR

Version: 2.2.0

checking examples ... ERROR ... [1] "93% done merging data for SpeedDatum (15 of 16)." [1] "100% done merging data for SpeedDatum (16 of 16)." [1] "Creating data frame for SpeedDatum." [1] "100% done merging data for TelephonyDatum (1 of 1)." [1] "Creating data frame for TelephonyDatum." [1] "14% done merging data for WlanDatum (1 of 7)." [1] "28% done merging data for WlanDatum (2 of 7)." [1] "42% done merging data for WlanDatum (3 of 7)." [1] "57% done merging data for WlanDatum (4 of 7)." [1] "71% done merging data for WlanDatum (5 of 7)." [1] "85% done merging data for WlanDatum (6 of 7)." [1] "100% done merging data for WlanDatum (7 of 7)." [1] "Creating data frame for WlanDatum." > plot(data$LocationDatum) Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=38.0676352725243,-78.9510441850485&zoom=10&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=38.0676352725243,-78.9510441850485&sensor=false Warning: geocode failed with status OVER_QUERY_LIMIT, location = "38.0676352725243,-78.9510441850485" Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : arguments imply differing number of rows: 0, 1 Calls: plot ... <Anonymous> -> ggmap -> get_map -> get_googlemap -> data.frame Execution halted

SentimentAnalysis

Version: 1.3-0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘SnowballC’ ‘XML’ ‘mgcv’ All declared Imports should be used.

sentimentr

Version: 1.0.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘lexicon’ ‘syuzhet’ All declared Imports should be used.

sentometrics

Version: 0.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘compiler’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 6339 marked UTF-8 strings

SEPA

Version: 1.6.0

checking R code for possible problems ... NOTE ... definition for ‘t.test’ truetimepattern : <anonymous>: no visible global function definition for ‘p.adjust’ truetimevisualize : <anonymous> : <anonymous>: no visible global function definition for ‘median’ truetimevisualize: no visible binding for global variable ‘time’ truetimevisualize: no visible binding for global variable ‘expmean’ truetimevisualize: no visible binding for global variable ‘Gene’ windowGOanalysis: no visible global function definition for ‘new’ windowGOvisualize: no visible binding for global variable ‘Var1’ windowGOvisualize: no visible binding for global variable ‘value’ Undefined global functions or variables: Gene Var1 Var2 confint expmean fitted lines lm median new p.adjust pseudotime t.test time value xend yend Consider adding importFrom("graphics", "lines") importFrom("methods", "new") importFrom("stats", "confint", "fitted", "lm", "median", "p.adjust", "t.test", "time") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

seqbias

Version: 1.24.0

checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: libs 7.3Mb
checking DESCRIPTION meta-information ... NOTE Versioned 'LinkingTo' value for ‘Rsamtools’ is only usable in R >= 3.0.2
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends. Please remove these calls from your code. Packages in Depends field not imported from: ‘Biostrings’ ‘GenomicRanges’ ‘methods’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... function definition for ‘runif’ random.intervals: no visible global function definition for ‘GRanges’ random.intervals: no visible global function definition for ‘IRanges’ seqbias.fit: no visible global function definition for ‘new’ seqbias.load: no visible global function definition for ‘new’ seqbias.predict: no visible global function definition for ‘is’ seqbias.predict : <anonymous>: no visible global function definition for ‘seqnames’ seqbias.predict : <anonymous>: no visible global function definition for ‘start’ seqbias.predict : <anonymous>: no visible global function definition for ‘end’ seqbias.predict : <anonymous>: no visible global function definition for ‘strand’ Undefined global functions or variables: GRanges IRanges end is new runif seqnames start strand Consider adding importFrom("methods", "is", "new") importFrom("stats", "end", "runif", "start") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').
checking compiled code ... NOTE ``` File ‘seqbias/libs/seqbias.so’: Found ‘rand’, possibly from ‘rand’ (C) Objects: ‘sequencing_bias.o’, ‘twobitseq.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

SeqFeatR

Version: 0.2.4

checking whether package ‘SeqFeatR’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/SeqFeatR/new/SeqFeatR.Rcheck/00install.out’ for details.
checking re-building of vignette outputs ... WARNING `` Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'SeqFeatR_tutorial.tex' failed. LaTeX errors: ! LaTeX Error: Filealgorithm2e.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.6 ^^M

! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

seqplots

Version: 1.14.1

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error in rep("../", npos) : invalid 'times' argument Error: processing vignette 'QuickStart.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking installed package size ... NOTE installed size is 13.7Mb sub-directories of 1Mb or more: doc 2.6Mb seqplots 10.3Mb
checking foreign function calls ... NOTE Foreign function call to a different package: .Call("BWGFile_summary", ..., PACKAGE = "rtracklayer") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... plotHeatmap,list: no visible global function definition for ‘kmeans’ plotHeatmap,list: no visible global function definition for ‘hclust’ plotHeatmap,list: no visible global function definition for ‘dist’ plotHeatmap,list: no visible global function definition for ‘cutree’ plotHeatmap,list: no visible global function definition for ‘as.dendrogram’ plotHeatmap,list: no visible global function definition for ‘title’ Undefined global functions or variables: Var1 Var2 abline adjustcolor approx as.dendrogram axis box capture.output colorRampPalette cutree dist hclust image kmeans layout lines mtext par plot.new qt rainbow rect rgb text title value Consider adding importFrom("grDevices", "adjustcolor", "colorRampPalette", "rainbow", "rgb") importFrom("graphics", "abline", "axis", "box", "image", "layout", "lines", "mtext", "par", "plot.new", "rect", "text", "title") importFrom("stats", "approx", "as.dendrogram", "cutree", "dist", "hclust", "kmeans", "qt") importFrom("utils", "capture.output") to your NAMESPACE file.

Seurat

Version: 2.1.0

checking examples ... ERROR ``` Running examples in ‘Seurat-Ex.R’ failed The error most likely occurred in:

Name: DarkTheme

Title: Dark Theme

Aliases: DarkTheme

** Examples

df <- data.frame(x = rnorm(n = 100, mean = 20, sd = 2), y = rbinom(n = 100, size = 100, prob = 0.2)) p <- ggplot(data = df, mapping = aes(x = x, y = y)) + geom_point(mapping = aes(color = 'red')) p + DarkTheme(legend.position = 'none') Theme element panel.border missing Error in if (theme$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: | |=================================================================== | 96% | |==================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% testthat results ================================================================ OK: 210 SKIPPED: 0 FAILED: 2
1. Failure: tSNE plots correctly (@test_seurat_object.R#115)
2. Error: tSNE plots correctly (@test_seurat_object.R#116)
Error: testthat unit tests failed Execution halted ```

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: libs 5.0Mb

sf

Version: 0.5-5

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Quitting from lines 194-197 (sf5.Rmd) Error: processing vignette 'sf5.Rmd' failed with diagnostics: cannot open the connection Execution halted
checking installed package size ... NOTE installed size is 20.2Mb sub-directories of 1Mb or more: doc 10.7Mb libs 5.7Mb sqlite 1.5Mb

sgd

Version: 1.1

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 13 SKIPPED: 0 FAILED: 10
1. Error: MSE converges for linear regression with lasso (@test-lasso.R#6)
2. Failure: MSE converges for linear models (@test-linear.R#37)
3. Failure: MSE converges for linear models (@test-linear.R#40)
4. Failure: MSE converges for linear models (@test-linear.R#42)
5. Failure: MSE converges for linear models (@test-linear.R#55)
6. Failure: MSE converges for linear models (@test-linear.R#56)
7. Failure: MSE converges for linear models (@test-linear.R#57)
8. Failure: MSE converges for linear models (@test-linear.R#60)
9. Failure: MSE converges for linear models (@test-linear.R#61)
10. Failure: MSE converges for linear models (@test-linear.R#62)
Error: testthat unit tests failed Execution halted ```

sglr

Version: 0.7

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE .computePStar: no visible global function definition for ‘uniroot’ plotBoundary: no visible global function definition for ‘scale_y_continuous’ Undefined global functions or variables: scale_y_continuous uniroot Consider adding importFrom("stats", "uniroot") to your NAMESPACE file.

shazam

Version: 0.1.8

checking data for non-ASCII characters ... NOTE Note: found 2 marked UTF-8 strings

shiny

Version: 1.0.5

checking installed package size ... NOTE installed size is 7.8Mb sub-directories of 1Mb or more: www 6.5Mb

ShinyItemAnalysis

Version: 1.2.3

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’ ‘xtable’ All declared Imports should be used.

shinyKGode

Version: 1.0.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’ ‘tools’ All declared Imports should be used.

SIBER

Version: 2.1.3

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dplyr’ ‘ggplot2’ ‘viridis’ All declared Imports should be used.

sicegar

Version: 0.2.2

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘dplyr’ All declared Imports should be used.

SigFuge

Version: 1.14.0

checking R code for possible problems ... NOTE ... SFfigure: no visible global function definition for ‘hcl’ SFfigure: no visible binding for global variable ‘cluster’ SFfigure: no visible binding for global variable ‘median’ SFfigure: no visible binding for global variable ‘x’ SFfigure: no visible binding for global variable ‘y1’ SFfigure: no visible binding for global variable ‘label’ SFfigure: no visible binding for global variable ‘value’ SFfigure: no visible binding for global variable ‘Clusters’ SFfigure: no visible binding for global variable ‘y2’ SFfigure: no visible global function definition for ‘pdf’ SFfigure: no visible global function definition for ‘dev.off’ SFlabels: no visible global function definition for ‘kmeans’ SFnormalize : <anonymous>: no visible global function definition for ‘median’ Undefined global functions or variables: Clusters base cluster dev.off e hcl kmeans label median pdf rgb s value x y1 y2 Consider adding importFrom("grDevices", "dev.off", "hcl", "pdf", "rgb") importFrom("stats", "kmeans", "median") to your NAMESPACE file.

SIMAT

Version: 1.8.0

checking examples ... ERROR ... > ### Name: plotEIC > ### Title: Plotting EIC of one peak > ### Aliases: plotEIC > > ### ** Examples > > # load an RData file including a single run data acquired by readCDF > data("Run") > > # load targets information > data(Targets) > > # get all the corresponding peaks of the target list > runPeaks <- getPeak(Run = Run, Targets = Targets) > > # plot the EIC of the first target > plotEIC(runPeaks[[1]]) Error in if (ggplot_build(mainPlot)$layout$panel_ranges[[1]]$y.range[2] > : argument is of length zero Calls: plotEIC Execution halted
checking re-building of vignette outputs ... NOTE ``` Error in re-building vignettes: ... Loading required package: Rcpp

Error: processing vignette 'SIMAT-vignette.Rnw' failed with diagnostics: chunk 9 (label = plotEIC) Error in if (ggplot_build(mainPlot)$layout$panel_ranges[[1]]$y.range[2] > : argument is of length zero Execution halted ```

checking R code for possible problems ... NOTE getRIStandard: no visible global function definition for ‘read.csv’ plotEIC: no visible global function definition for ‘stack’ plotEIC: no visible global function definition for ‘dnorm’ plotEIC: no visible global function definition for ‘dev.copy’ plotEIC: no visible binding for global variable ‘pdf’ plotEIC: no visible global function definition for ‘dev.off’ plotTIC: no visible binding for global variable ‘rt’ Undefined global functions or variables: dev.copy dev.off dnorm pdf read.csv rt stack Consider adding importFrom("grDevices", "dev.copy", "dev.off", "pdf") importFrom("stats", "dnorm", "rt") importFrom("utils", "read.csv", "stack") to your NAMESPACE file.

simcausal

Version: 0.5.4

checking package dependencies ... NOTE Package suggested but not available for checking: ‘tmlenet’

SimMultiCorrData

Version: 0.2.1

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’

simTool

Version: 1.0.3

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking R code for possible problems ... NOTE evalGrids: no visible global function definition for ‘sessionInfo’ meanAndNormCI: no visible global function definition for ‘sd’ Undefined global functions or variables: sd sessionInfo Consider adding importFrom("stats", "sd") importFrom("utils", "sessionInfo") to your NAMESPACE file.

sincell

Version: 1.8.0

checking R code for possible problems ... NOTE ... sc_InitializingSincellObject: no visible binding for global variable ‘var’ sc_StatisticalSupportByGeneSubsampling: no visible global function definition for ‘cor’ sc_StatisticalSupportByReplacementWithInSilicoCellsReplicates: no visible global function definition for ‘cor’ sc_clusterObj: no visible global function definition for ‘hclust’ sc_clusterObj: no visible global function definition for ‘cutree’ sc_distanceObj: no visible global function definition for ‘cor’ sc_marker2color: no visible global function definition for ‘colorRampPalette’ Undefined global functions or variables: cmdscale colorRampPalette combn cor cutree hclust plot prcomp quantile rnbinom rnorm runif var Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "plot") importFrom("stats", "cmdscale", "cor", "cutree", "hclust", "prcomp", "quantile", "rnbinom", "rnorm", "runif", "var") importFrom("utils", "combn") to your NAMESPACE file.
checking compiled code ... NOTE ``` File ‘sincell/libs/sincell.so’: Found ‘rand’, possibly from ‘rand’ (C) Objects: ‘pseudoreplicatesbymodel.o’, ‘pseudoreplicatesbynoise.o’, ‘pseudoreplicatesbynoise_cv2.o’ Found ‘srand’, possibly from ‘srand’ (C) Objects: ‘pseudoreplicatesbymodel.o’, ‘pseudoreplicatesbynoise.o’, ‘pseudoreplicatesbynoise_cv2.o’

Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

Single.mTEC.Transcriptomes

Version: 1.4.0

checking data for ASCII and uncompressed saves ... WARNING Warning: package needs dependence on R (>= 2.10)
checking installed package size ... NOTE installed size is 911.9Mb sub-directories of 1Mb or more: data 895.1Mb doc 16.6Mb

SISPA

Version: 1.6.0

checking files in ‘vignettes’ ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': ‘SISPA.Rmd’, ‘SISPA.md’, ‘SISPA_data.Rda’, ‘SISPA_files/figure-html/unnamed-chunk-2-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-3-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-4-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-5-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-6-1.png’, ‘SISPA_files/figure-html/unnamed-chunk-7-1.png’, ‘sispa_overview.png’ The following directory looks like a leftover from 'knitr': ‘figure’ Please remove from your package.
checking R code for possible problems ... NOTE cptSamples : cptsPlot: no visible global function definition for ‘abline’ cptSamples : cptsPlot: no visible global function definition for ‘text’ Undefined global functions or variables: abline text Consider adding importFrom("graphics", "abline", "text") to your NAMESPACE file.

sjlabelled

Version: 1.0.5

checking package dependencies ... NOTE Package suggested but not available for checking: ‘sjPlot’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘sjPlot’

sjmisc

Version: 2.6.2

checking package dependencies ... NOTE Package suggested but not available for checking: ‘sjPlot’

sjPlot

Version: 2.4.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘prediction’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘plm’

sjstats

Version: 0.12.0

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘sjPlot’, ‘MuMIn’, ‘piecewiseSEM’

SmarterPoland

Version: 1.7

checking installed package size ... NOTE installed size is 8.2Mb sub-directories of 1Mb or more: data 8.1Mb
checking data for non-ASCII characters ... NOTE Note: found 1122 marked UTF-8 strings

SMFI5

Version: 1.0

checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘ggplot2’ ‘reshape’ Please remove these calls from your code. Packages in Depends field not imported from: ‘corpcor’ ‘ggplot2’ ‘reshape’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... sim.cir: no visible global function definition for ‘aes’ sim.cir: no visible global function definition for ‘geom_line’ sim.cir: no visible global function definition for ‘ggtitle’ sim.n.chi2: no visible global function definition for ‘rchisq’ sim.n.chi2: no visible global function definition for ‘rnorm’ sim.n.chi2: no visible global function definition for ‘rpois’ sim.vasicek: no visible global function definition for ‘rnorm’ sim.vasicek: no visible global function definition for ‘melt’ sim.vasicek: no visible global function definition for ‘ggplot’ sim.vasicek: no visible global function definition for ‘aes’ sim.vasicek: no visible global function definition for ‘geom_line’ sim.vasicek: no visible global function definition for ‘ggtitle’ Undefined global functions or variables: acf aes cor cov dchisq geom_line ggplot ggtitle head melt optim plot pseudoinverse qnorm rchisq rnorm rpois sd title Consider adding importFrom("graphics", "plot", "title") importFrom("stats", "acf", "cor", "cov", "dchisq", "optim", "qnorm", "rchisq", "rnorm", "rpois", "sd") importFrom("utils", "head") to your NAMESPACE file.

smoof

Version: 1.5.1

checking package dependencies ... NOTE Package suggested but not available for checking: ‘rPython’

snht

Version: 1.0.5

checking re-building of vignette outputs ... WARNING `` Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'pairwiseSNHT.tex' failed. LaTeX errors: ! LaTeX Error: Filealgorithm2e.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.63 \usepackage {mathtools}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

SNPhood

Version: 1.6.1

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'IntroductionToSNPhood.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: data 3.8Mb doc 3.8Mb
checking DESCRIPTION meta-information ... NOTE BugReports field is not a suitable URL but appears to contain an email address not specified by mailto: nor contained in < >
checking R code for possible problems ... NOTE .calcBinomTestVector: no visible binding for global variable ‘pp’ Undefined global functions or variables: pp

soc.ca

Version: 0.7.3

checking data for non-ASCII characters ... NOTE Note: found 833 marked UTF-8 strings

soGGi

Version: 1.8.0

checking whether package ‘soGGi’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/soGGi/new/soGGi.Rcheck/00install.out’ for details.
checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'c,ChIPprofile-method': \S4method{c}{ChIPprofile} Code: function(x, ...) Docs: function(x, ..., recursive = FALSE) Argument names in docs not in code: recursive
checking foreign function calls ... NOTE Foreign function call to a different package: .Call("rle_sum_any", ..., PACKAGE = "chipseq") See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual.
checking R code for possible problems ... NOTE ... definition for ‘weighted.mean’ getShifts: no visible global function definition for ‘readGAlignmentsFromBam’ getSummitScore: no visible global function definition for ‘readGAlignmentsFromBam’ plotRegion.ChIPprofile: no visible global function definition for ‘formula’ runFindSummit: no visible global function definition for ‘readGAlignmentsFromBam’ runRegionPlot : <anonymous>: no visible global function definition for ‘spline’ summitPipeline: no visible global function definition for ‘readGAlignmentsFromBam’ plotRegion,ChIPprofile: no visible global function definition for ‘formula’ Undefined global functions or variables: formula read.delim readGAlignmentsFromBam spline weighted.mean Consider adding importFrom("stats", "formula", "spline", "weighted.mean") importFrom("utils", "read.delim") to your NAMESPACE file.

soilcarbon

Version: 1.2.0

checking data for non-ASCII characters ... NOTE Note: found 145 marked UTF-8 strings

SomaticCancerAlterations

Version: 1.12.0

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE ... .load_dataset: no visible global function definition for ‘data’ .maf2gr: no visible binding for global variable ‘Chromosome’ .maf2gr: no visible binding for global variable ‘Start_position’ .maf2gr: no visible binding for global variable ‘End_position’ .read_maf: no visible global function definition for ‘read.delim’ hg2ncbi: no visible global function definition for ‘seqnameStyle<-’ hg2ncbi: no visible global function definition for ‘genome<-’ mutationDensity: no visible global function definition for ‘keepSeqlevels’ mutationDensity: no visible global function definition for ‘as’ ncbi2hg: no visible global function definition for ‘seqnameStyle<-’ ncbi2hg: no visible global function definition for ‘genome<-’ scaListDatasets: no visible global function definition for ‘data’ Undefined global functions or variables: Chromosome End_position Start_position as data genome<- keepSeqlevels read.delim seqnameStyle<- Consider adding importFrom("methods", "as") importFrom("utils", "data", "read.delim") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

SomaticSignatures

Version: 2.12.1

checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘NMF’ A package should be listed in only one of these fields.

sorvi

Version: 0.7.26

checking R code for possible problems ... NOTE ... regression_plot: no visible global function definition for ‘colorRampPalette’ regression_plot: no visible global function definition for ‘loess.control’ regression_plot: no visible global function definition for ‘predict’ regression_plot : <anonymous>: no visible global function definition for ‘quantile’ regression_plot : <anonymous>: no visible global function definition for ‘pnorm’ regression_plot: no visible global function definition for ‘flush.console’ regression_plot: no visible global function definition for ‘density’ Undefined global functions or variables: colorRampPalette density flush.console loess loess.control pnorm predict quantile read.csv Consider adding importFrom("grDevices", "colorRampPalette") importFrom("stats", "density", "loess", "loess.control", "pnorm", "predict", "quantile") importFrom("utils", "flush.console", "read.csv") to your NAMESPACE file.

sparklyr

Version: 0.6.4

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > Sys.setenv("R_TESTS" = "") > library(testthat) > library(sparklyr) > > if (identical(Sys.getenv("NOT_CRAN"), "true")) {
- test_check("sparklyr")
- on.exit({ spark_disconnect_all() ; livy_service_stop() })
- } Error in if (is.na(a)) return(-1L) : argument is of length zero Calls: test_check ... spark_install_find -> spark_versions -> lapply -> FUN -> compareVersion testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 0 Execution halted ```

SpatialEpiApp

Version: 0.3

checking package dependencies ... NOTE Package suggested but not available for checking: ‘INLA’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’ ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’ All declared Imports should be used.

spatialwarnings

Version: 1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘moments’ ‘poweRlaw’ All declared Imports should be used.

specmine

Version: 1.0

checking examples ... ERROR ``` Running examples in ‘specmine-Ex.R’ failed The error most likely occurred in:

Name: impute_nas_linapprox

Title: Impute missing values with linear approximation

Aliases: impute_nas_linapprox

Keywords: missing values

** Examples

## Example of NA imputation with linear approximation data(propolis) dataset = impute_nas_linapprox(propolis) Error: 'spc.NA.linapprox' is not an exported object from 'namespace:hyperSpec' Execution halted ```
checking dependencies in R code ... NOTE Missing or unexported objects: ‘ChemoSpec::readJDX’ ‘hyperSpec::spc.NA.linapprox’

spew

Version: 1.3.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘maptools’ All declared Imports should be used.

SpidermiR

Version: 1.7.4

checking R code for possible problems ... NOTE .SpidermiRvisualize_gene: possible error in simpleNetwork(NetworkData, linkColour = "gray", textColour = "black", zoom = TRUE): unused argument (textColour = "black") SpidermiRvisualize_plot_target: no visible binding for global variable ‘miRNAs’ SpidermiRvisualize_plot_target: no visible binding for global variable ‘mRNA_target’ Undefined global functions or variables: mRNA_target miRNAs

spikeSlabGAM

Version: 1.1-11

checking re-building of vignette outputs ... NOTE `` ... Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used. Warning in (function (xnew) : predictions outside fitted range for lin(glucose). Warning in (function (xnew) : predictions outside fitted range for sm(glucose). Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed. LaTeX errors: ! LaTeX Error: Filealgorithmic.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.12 \usepackage {algorithm}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

spind

Version: 2.1.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘sp’ All declared Imports should be used.

splatter

Version: 1.0.3

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'splatter.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

sppmix

Version: 1.0.2

checking installed package size ... NOTE installed size is 15.3Mb sub-directories of 1Mb or more: data 5.4Mb libs 9.3Mb
checking data for non-ASCII characters ... NOTE Note: found 17 marked UTF-8 strings

ss3sim

Version: 0.9.5

checking whether package ‘ss3sim’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/ss3sim/new/ss3sim.Rcheck/00install.out’ for details.

ssviz

Version: 1.10.0

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.

stacomiR

Version: 0.5.3

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

starmie

Version: 0.1.2

checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: doc 1.1Mb extdata 4.9Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘MCMCpack’ All declared Imports should be used.

statcheck

Version: 1.2.2

checking whether package ‘statcheck’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/statcheck/new/statcheck.Rcheck/00install.out’ for details.

STATegRa

Version: 1.10.0

checking re-building of vignette outputs ... WARNING ... Warning in cor.test.default(getDist(listDistW[[i]])[referenceFeatures, referenceFeatures], : Cannot compute exact p-value with ties Warning in plot.window(...) : relative range of values = 18 * EPS, is small (axis 2) Warning in plot.window(...) : relative range of values = 18 * EPS, is small (axis 2) Warning in plot.window(...) : relative range of values = 18 * EPS, is small (axis 2) Warning in plot.window(...) : relative range of values = 18 * EPS, is small (axis 2) Warning in replayPlot(x) : relative range of values = 18 * EPS, is small (axis 2) Warning in replayPlot(x) : relative range of values = 18 * EPS, is small (axis 2) Warning in replayPlot(x) : relative range of values = 18 * EPS, is small (axis 2) Warning in replayPlot(x) : relative range of values = 18 * EPS, is small (axis 2) Error: processing vignette 'STATegRa.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: data 2.4Mb doc 2.4Mb
checking R code for possible problems ... NOTE biplotRes,caClass-character-numeric-character: no visible binding for global variable ‘values.1’ biplotRes,caClass-character-numeric-character: no visible binding for global variable ‘values.2’ biplotRes,caClass-character-numeric-character: no visible binding for global variable ‘color’ plotVAF,caClass: no visible binding for global variable ‘comp’ plotVAF,caClass: no visible binding for global variable ‘VAF’ plotVAF,caClass: no visible binding for global variable ‘block’ selectCommonComps,matrix-matrix-numeric: no visible binding for global variable ‘comps’ selectCommonComps,matrix-matrix-numeric: no visible binding for global variable ‘block’ selectCommonComps,matrix-matrix-numeric: no visible binding for global variable ‘comp’ selectCommonComps,matrix-matrix-numeric: no visible binding for global variable ‘ratio’ Undefined global functions or variables: VAF block color comp comps ratio values.1 values.2

statisticalModeling

Version: 0.3.0

checking tests ... ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(statisticalModeling) Loading required package: ggplot2 > > test_check("statisticalModeling") Error: gwm() has been removed from `mosaic'. It will be replaced by better tools in `mosaicModel'. testthat results ================================================================ OK: 21 SKIPPED: 0 FAILED: 0 Execution halted
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 303-306 (modeling.Rmd) Error: processing vignette 'modeling.Rmd' failed with diagnostics: Invalid formula type for gf_point. Execution halted
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘magrittr’ ‘rpart’ All declared Imports should be used.

statsDK

Version: 0.1.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dplyr’ ‘ggplot2’ ‘stringr’ All declared Imports should be used.

strataG

Version: 2.0.2

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: libs 4.2Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘survival’ All declared Imports should be used.

StroupGLMM

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’ All declared Imports should be used.

structSSI

Version: 1.1.1

checking R code for possible problems ... NOTE PlotHypTree: no visible global function definition for ‘browseURL’ treePValues: no visible global function definition for ‘lm’ treePValues: no visible global function definition for ‘pf’ plot,GBH-ANY: no visible binding for global variable ‘sorted.hyp’ plot,GBH-ANY: no visible binding for global variable ‘pval’ plot,GBH-ANY: no visible binding for global variable ‘group’ plot,GBH-ANY: no visible binding for global variable ‘type’ Undefined global functions or variables: browseURL group lm pf pval sorted.hyp type Consider adding importFrom("stats", "lm", "pf") importFrom("utils", "browseURL") to your NAMESPACE file.

subSeq

Version: 1.6.0

checking R code for possible problems ... NOTE ... summary.subsamples: no visible binding for global variable ‘o.padj’ summary.subsamples: no visible binding for global variable ‘significant’ summary.subsamples: no visible binding for global variable ‘estFDP’ summary.subsamples: no visible binding for global variable ‘rFDP’ summary.subsamples: no visible binding for global variable ‘metric’ summary.subsamples: no visible binding for global variable ‘value’ summary.subsamples: no visible binding for global variable ‘percent’ voomLimma: no visible global function definition for ‘model.matrix’ Undefined global functions or variables: . ID average.depth average.value coefficient cor count cov depth estFDP method metric model.matrix o.coefficient o.lfdr o.padj p.adjust padj percent plot proportion pvalue rFDP rbinom replication selectMethod significant valid value var Consider adding importFrom("graphics", "plot") importFrom("methods", "selectMethod") importFrom("stats", "cor", "cov", "model.matrix", "p.adjust", "rbinom", "var") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

subspaceMOA

Version: 0.6.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘fields’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘subspace’

sure

Version: 0.2.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘truncdist’

surveillance

Version: 1.15.0

checking package dependencies ... NOTE Packages suggested but not available for checking: ‘hhh4contacts’ ‘INLA’
checking installed package size ... NOTE installed size is 7.3Mb sub-directories of 1Mb or more: doc 2.3Mb help 1.0Mb libs 1.7Mb
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘coin’, ‘VGAM’

survivALL

Version: 0.9.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘Biobase’ ‘broom’ ‘data.table’ ‘magrittr’ ‘pander’ ‘png’ ‘readr’ ‘survsim’ ‘testthat’ All declared Imports should be used.

survminer

Version: 0.4.1

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: doc 4.9Mb

SWATH2stats

Version: 1.6.1

checking package dependencies ... NOTE Packages which this enhances but not available for checking: ‘imsbInfer’ ‘MSstats’
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘MSstats’

swfdr

Version: 1.0.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'swfdrTutorial.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

switchde

Version: 1.2.0

checking re-building of vignette outputs ... WARNING ``` ...

The following object is masked from 'package:Biobase':
```
combine
```
The following objects are masked from 'package:BiocGenerics':
```
combine, intersect, setdiff, union
```
The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Warning: Removed 68 rows containing missing values (geom_path). Error: processing vignette 'switchde_vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

synlet

Version: 1.6.0

checking R code for possible problems ... NOTE ... siRNAPlot: no visible global function definition for ‘pdf’ siRNAPlot: no visible global function definition for ‘dev.off’ tTest: no visible global function definition for ‘p.adjust’ zFactor: no visible binding for global variable ‘condition’ zFactor: no visible binding for global variable ‘sd’ zFactor: no visible binding for global variable ‘median’ zFactor: no visible global function definition for ‘complete.cases’ Undefined global functions or variables: COL_NAME EXPERIMENT_MODIFICATION EXPERIMENT_TYPE MASTER_PLATE PLATE READOUT ROW_NAME Var1 WELL_CONTENT_NAME colorRampPalette complete.cases condition dev.off experiments is mad median medpolish p.adjust pdf phyper rainbow sd siRNA t.test value write.table Consider adding importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "rainbow") importFrom("methods", "is") importFrom("stats", "complete.cases", "mad", "median", "medpolish", "p.adjust", "phyper", "sd", "t.test") importFrom("utils", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

synthpop

Version: 1.4-0

checking re-building of vignette outputs ... NOTE `` ... ... Loading required package: lattice Loading required package: MASS Loading required package: nnet Loading required package: ggplot2 Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'inference.tex' failed. LaTeX errors: ! LaTeX Error: Filealgorithm.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.25 \usepackage {algpseudocode}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

systemPipeR

Version: 1.10.2

checking package subdirectories ... WARNING Invalid citation information in ‘inst/CITATION’: Error in library(knitcitations): there is no package called ‘knitcitations’
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'systemPipeR.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking for hidden files and directories ... NOTE Found the following hidden files and directories: inst/extdata/.BatchJobs.R These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: doc 3.0Mb extdata 1.7Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘BiocGenerics’ ‘VariantAnnotation’ All declared Imports should be used.
checking R code for possible problems ... NOTE ... ‘close.screen’ writeTargetsRef: no visible global function definition for ‘read.delim’ show,INTERSECTset: no visible binding for global variable ‘vennset’ Undefined global functions or variables: AllVariants Base Comparisons Counts Coverage Cycle DataFrame Feature Frequency IRanges Intersect_Sets Length Level Method Outliers Percent Quality RelDiv Rle Sample SampleMatch Strand Type aggregate alt altDepth<- asVCF boxplot chunk close.screen combn dev.off first import.bed last locateVariants low mid minQuality model.matrix na.omit pdf phyper plot predictCoding qwidth read.delim readGAlignmentPairs readGAlignments readVcf ref refDepth<- screen seqlengths seqlengths<- split.screen subsetByOverlaps summarizeOverlaps symbols test_sample text top tophatargs totalDepth<- vennset write.table writeVcf Consider adding importFrom("grDevices", "dev.off", "pdf") importFrom("graphics", "boxplot", "close.screen", "plot", "screen", "split.screen", "symbols", "text") importFrom("stats", "aggregate", "model.matrix", "na.omit", "phyper") importFrom("utils", "combn", "read.delim", "write.table") to your NAMESPACE file.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘GenomicAlignments’

tadaatoolbox

Version: 0.14.0

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘rmdformats’
checking data for non-ASCII characters ... NOTE Note: found 3 marked UTF-8 strings

taRifx

Version: 1.0.6

checking DESCRIPTION meta-information ... NOTE Malformed Title field: should not end in a period.
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... xtable.summary.lme: no visible global function definition for ‘align<-’ xtable.summary.lme: no visible global function definition for ‘digits<-’ xtable.summary.lme: no visible global function definition for ‘display<-’ xtablelm: no visible global function definition for ‘xtable’ xtablelm: no visible global function definition for ‘pf’ Undefined global functions or variables: aes align<- barplot caption<- convertUnit coord_cartesian digits<- display<- ecdf ggplot gpar grid.layout grid.lines grid.newpage grid.points grid.polyline grid.rect grid.segments grid.text interleave label<- latticeParseFormula median na.omit opts panel.densityplot panel.lines panel.xyplot par pf plot.new popViewport pushViewport quantile sd seekViewport stat_summary terms text theme_text time unit upViewport viewport write.csv xtable Consider adding importFrom("graphics", "barplot", "par", "plot.new", "text") importFrom("stats", "ecdf", "median", "na.omit", "pf", "quantile", "sd", "terms", "time") importFrom("utils", "write.csv") to your NAMESPACE file.

TCGAbiolinks

Version: 2.5.9

checking examples ... ERROR ... |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA |NA Error in checkProjectInput(project) Please set a valid project Calls: GDCquery -> checkProje Execution halted |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | |NA |NA | : argument from the column id above. Project TCGA-ACC was not found. ctInput
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 123 SKIPPED: 0 FAILED: 15
1. Error: TCGAanalyze_survival creates pdf (@test-analyse.R#4)
2. Error: GDCdownload API method for two files is working (@test-prepare-download.R#4)
3. Error: GDCdownload API method for one files is working (@test-prepare-download.R#20)
4. Error: GDCprepare accepts more than one project (@test-prepare-download.R#50)
5. Error: Accecpts more than one platform (@test-prepare-download.R#68)
6. Error: GDCquery can filter by data.category (@test-query.R#5)
7. Error: GDCquery accepts more than one project (@test-query.R#11)
8. Error: GDCquery can filter by sample.type (@test-query.R#23)
9. Error: GDCquery can filter by barcode (@test-query.R#46)
10. ...
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ...

The following objects are masked from 'package:S4Vectors':
```
first, intersect, rename, setdiff, setequal, union
```
The following objects are masked from 'package:BiocGenerics':
```
combine, intersect, setdiff, union
```
The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Quitting from lines 16-20 (clinical.Rmd) Error: processing vignette 'clinical.Rmd' failed with diagnostics: there is no package called 'DT' Execution halted ```
checking installed package size ... NOTE installed size is 61.0Mb sub-directories of 1Mb or more: R 1.1Mb data 2.3Mb doc 57.4Mb
checking R code for possible problems ... NOTE ... ‘limmacontrasts.fit’ TCGAanalyze_analyseGRN: no visible global function definition for ‘knnmi.cross’ TCGAanalyze_networkInference: no visible global function definition for ‘c3net’ TCGAanalyze_networkInference: no visible global function definition for ‘minet’ TCGAvisualize_SurvivalCoxNET: no visible global function definition for ‘dNetInduce’ TCGAvisualize_SurvivalCoxNET: no visible global function definition for ‘dNetPipeline’ TCGAvisualize_SurvivalCoxNET: no visible global function definition for ‘dCommSignif’ TCGAvisualize_SurvivalCoxNET: no visible global function definition for ‘visNet’ TCGAvisualize_oncoprint: no visible binding for global variable ‘value’ getTSS: no visible global function definition for ‘promoters’ Undefined global functions or variables: c3net dCommSignif dNetInduce dNetPipeline knnmi.cross limmacontrasts.fit limmamakeContrasts minet portions promoters value visNet
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘DT’

TCGAbiolinksGUI

Version: 1.2.1

checking re-building of vignette outputs ... WARNING ``` ...

The following objects are masked from 'package:S4Vectors':
```
first, intersect, rename, setdiff, setequal, union
```
The following objects are masked from 'package:BiocGenerics':
```
combine, intersect, setdiff, union
```
The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Quitting from lines 11-15 (data.Rmd) Error: processing vignette 'data.Rmd' failed with diagnostics: there is no package called 'DT' Execution halted ```
checking installed package size ... NOTE installed size is 30.3Mb sub-directories of 1Mb or more: app 1.1Mb doc 28.9Mb
checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' calls not declared from: ‘DT’ ‘dplyr’

tcR

Version: 2.2.1.11

checking installed package size ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: data 1.2Mb doc 3.9Mb libs 1.1Mb
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘scales’ All declared Imports should be used.
checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'top.fun': ‘slice.fun’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

TCseq

Version: 1.0.0

checking R code for possible problems ... NOTE DBresult: no visible global function definition for ‘as’ DBresult.cluster: no visible global function definition for ‘as’ TCA: no visible global function definition for ‘is’ TCA: no visible global function definition for ‘as’ TCAFromSummarizedExperiment: no visible global function definition for ‘is’ TCAFromSummarizedExperiment: no visible global function definition for ‘as’ countReads: no visible global function definition for ‘createAnnotationFile’ countReads: no visible global function definition for ‘featureCounts’ timeclustplot: no visible binding for global variable ‘group’ timecourseTable: no visible global function definition for ‘as’ Undefined global functions or variables: as createAnnotationFile featureCounts group is Consider adding importFrom("methods", "as", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

tdr

Version: 0.11

checking R code for possible problems ... NOTE makeCircles: no visible global function definition for ‘quantile’ targetDiagram: no visible global function definition for ‘as.formula’ targetDiagram: no visible global function definition for ‘modifyList’ targetDiagram: no visible global function definition for ‘extendrange’ tdStats : sdo: no visible global function definition for ‘sd’ tdStats : sdm: no visible global function definition for ‘sd’ tdStats : r2: no visible global function definition for ‘cor’ Undefined global functions or variables: as.formula cor extendrange modifyList quantile sd Consider adding importFrom("grDevices", "extendrange") importFrom("stats", "as.formula", "cor", "quantile", "sd") importFrom("utils", "modifyList") to your NAMESPACE file.

teachingApps

Version: 1.0.2

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: apps 2.6Mb libs 2.1Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘data.table’ ‘datasets’ ‘stats’ All declared Imports should be used.

TeachingDemos

Version: 2.10

R CMD check timed out
checking package dependencies ... NOTE Package suggested but not available for checking: ‘R2wd’

TELP

Version: 1.0

checking examples ... ERROR ``` Running examples in ‘TELP-Ex.R’ failed The error most likely occurred in:

Name: telp

Title: The Base Function of This Package The Free Evocation of Words

Technique

Aliases: telp

Keywords: function

** Examples

telp() Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : [tcl] invalid command name "toplevel". Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure Execution halted ```
checking whether package ‘TELP’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/TELP/new/TELP.Rcheck/00install.out’ for details.

texmexseq

Version: 0.3

checking examples ... ERROR ... > > # make up some data > sim.data <- function() rpoilog(1000, 1.0, 1.0, condS=TRUE) > otu <- data.frame(sample0=sim.data()) > for (i in 1:10) otu[[paste('sample', i, sep='')]] <- sim.data() > otu.ids <- paste('otu', seq(1:1000), sep='') > rownames(otu) <- otu.ids > z.table <- z.transform.table(otu) Warning in value[[3L]](cond) : fit 1 failed Warning in value[[3L]](cond) : fit 1 failed Warning in value[[3L]](cond) : fit 2 failed > > # pull out a quad, imagining that samples 1 and 2 were the control samples > # and 3 and 4 were the treatment > q <- quad.table(z.table, 'sample1', 'sample2', 'sample3', 'sample4') > > # plot it > p <- quad.plot(q) Error in get("d.control") : object 'd.control' not found Calls: quad.plot ... lapply -> FUN -> overscope_eval_next -> .Call -> get Execution halted

tidyjson

Version: 0.2.2

checking examples ... ERROR ``` ... > # companies[[1]] %>% prettify > > # Get the key employees data > key_employees <- companies %>%
- spread_values(
- name = jstring("name")
- ) %>%
- mutate(
- company.sort_order = rank(name)
- ) %>%
- enter_object("relationships") %>%
- gather_array("relationship.index") %>%
- spread_values(
- is.past = jlogical("is_past"),
- name = jstring("person", "permalink"),
- title = jstring("title")
- ) Error in eval(assertion, env) : argument "json.column" is missing, with no default Calls: %>% ... tryCatchList -> tryCatchOne -> doTryCatch -> eval -> eval Execution halted ```

tidyquant

Version: 0.5.3

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:

testthat results ================================================================ OK: 179 SKIPPED: 0 FAILED: 3 1. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#15) 2. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#17) 3. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#19)

Error: testthat unit tests failed In addition: Warning messages: 1: In download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' 2: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv'

Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv'

Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing AAPL. Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=FB&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'FB', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=FB&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing FB. Warning in download.file(url, destfile = tmp, quiet = TRUE) : cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOG&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' Warning: x = 'GOOG', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOG&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing GOOG. Warning in value[3L] : Returning as nested data frame. Quitting from lines 211-214 (TQ01-core-functions-in-tidyquant.Rmd) Error: processing vignette 'TQ01-core-functions-in-tidyquant.Rmd' failed with diagnostics: object 'Ask' not found Execution halted ```
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’ All declared Imports should be used.

tidyverse

Version: 1.2.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dbplyr’ ‘reprex’ ‘rlang’ All declared Imports should be used.

tikzDevice

Version: 0.10-1

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 675-675 (tikzDevice.Rnw) Error: processing vignette 'tikzDevice.Rnw' failed with diagnostics: there is no package called 'formatR' Execution halted

timeline

Version: 0.9

checking dependencies in R code ... NOTE 'library' or 'require' call to ‘shiny’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘ggplot2’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE timeline: no visible global function definition for ‘ggplot’ timeline: no visible global function definition for ‘geom_segment’ timeline: no visible global function definition for ‘aes_string’ timeline: no visible global function definition for ‘geom_rect’ timeline: no visible global function definition for ‘geom_text’ timeline: no visible global function definition for ‘theme’ timeline: no visible global function definition for ‘element_blank’ timeline: no visible global function definition for ‘xlab’ timeline: no visible global function definition for ‘ylab’ timeline: no visible global function definition for ‘xlim’ timeline: no visible global function definition for ‘scale_y_continuous’ timeline: no visible global function definition for ‘geom_point’ timeline: no visible global function definition for ‘scale_color_grey’ timeline: no visible global function definition for ‘geom_hline’ Undefined global functions or variables: aes_string element_blank geom_hline geom_point geom_rect geom_segment geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim ylab

timelineS

Version: 0.1.1

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘base’ All declared Imports should be used.

TimeProjection

Version: 0.2.0

checking examples ... ERROR ``` Running examples in ‘TimeProjection-Ex.R’ failed The error most likely occurred in:

Name: projectDate

Title: Time Projection

Aliases: projectDate

** Examples

dates = timeSequence(from = "2001-01-01", to = "2004-01-01", by = "day") projectDate(as.Date(dates)) Error in if (all(diff(as.numeric(raw[, i])) == 0)) redundantCols[i] = T : missing value where TRUE/FALSE needed Calls: projectDate Execution halted ```
checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘ggplot2’ ‘plyr’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘Matrix’ ‘lubridate’ ‘timeDate’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... plotCalendarHeatmap: no visible global function definition for ‘ddply’ plotCalendarHeatmap: no visible global function definition for ‘.’ plotCalendarHeatmap: no visible binding for global variable ‘year’ plotCalendarHeatmap: no visible binding for global variable ‘month’ plotCalendarHeatmap: no visible binding for global variable ‘week’ plotCalendarHeatmap: no visible global function definition for ‘ggplot’ plotCalendarHeatmap: no visible global function definition for ‘aes’ plotCalendarHeatmap: no visible binding for global variable ‘monthweek’ plotCalendarHeatmap: no visible binding for global variable ‘weekday’ plotCalendarHeatmap: no visible global function definition for ‘geom_tile’ plotCalendarHeatmap: no visible global function definition for ‘facet_grid’ plotCalendarHeatmap: no visible global function definition for ‘scale_fill_gradientn’ projectDate: no visible global function definition for ‘holidayNYSE’ projectDate: no visible global function definition for ‘sparse.model.matrix’ Undefined global functions or variables: . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month monthweek scale_fill_gradientn sparse.model.matrix week weekday year

TimerQuant

Version: 1.6.0

checking R code for possible problems ... NOTE ... ‘rainbow’ plotPrimordiumProfile: no visible binding for global variable ‘median’ plotPrimordiumProfile: no visible binding for global variable ‘mad’ plotPrimordiumProfile: no visible global function definition for ‘par’ plotPrimordiumProfile: no visible global function definition for ‘plot’ plotPrimordiumProfile: no visible global function definition for ‘axis’ plotPrimordiumProfile: no visible global function definition for ‘points’ plotPrimordiumProfile: no visible global function definition for ‘polygon’ plotPrimordiumProfile: no visible global function definition for ‘rgb’ simulatedRatio: no visible global function definition for ‘rnorm’ Undefined global functions or variables: approxfun axis mad median optimize par plot points polygon predict rainbow rgb rnorm Consider adding importFrom("grDevices", "rainbow", "rgb") importFrom("graphics", "axis", "par", "plot", "points", "polygon") importFrom("stats", "approxfun", "mad", "median", "optimize", "predict", "rnorm") to your NAMESPACE file.

tis

Version: 1.32

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘zoo’

tmap

Version: 1.10

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: data 1.5Mb doc 3.3Mb

toaster

Version: 0.5.5

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: target is NULL, current is character
1. Failure: format 'boxplot' with facets works (@test-showData.R#21) ----------- nrow(p$layout$panel_layout) not equal to length(cols). target is NULL, current is numeric
testthat results ================================================================ OK: 496 SKIPPED: 0 FAILED: 2 1. Failure: format 'boxplot' works (@test-showData.R#12) 2. Failure: format 'boxplot' with facets works (@test-showData.R#21)

Error: testthat unit tests failed Execution halted ```

checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘igraph’

TOSTER

Version: 0.3

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R6’ ‘jmvcore’ All declared Imports should be used.

tourrGui

Version: 0.4

checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': MIT
checking dependencies in R code ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘TeachingDemos’ ‘ash’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Packages in Depends field not imported from: ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached.
checking R code for possible problems ... NOTE ... ‘gmessage’ gui_xy: no visible global function definition for ‘dev.cur’ gui_xy: no visible global function definition for ‘CairoX11’ gui_xy: no visible global function definition for ‘dev.list’ gui_xy: no visible global function definition for ‘dev.new’ gui_xy: no visible global function definition for ‘dev.control’ gui_xy: no visible global function definition for ‘visible<-’ Undefined global functions or variables: CairoX11 basis_init cmass dev.control dev.cur dev.list dev.new display_andrews display_dist display_faces display_image display_pcp display_scatmat display_stars display_stereo display_xy dispose find_platform flea gIdleAdd gbutton gcheckbox gcheckboxgroup gdroplist ggroup glayout gmessage gnotebook gradio grand_tour gslider gtable gtkIdleRemove guided_tour gwindow holes lda_pp little_tour local_tour ozone par pda_pp rainbow_hcl rescale rgb sphere svalue svalue<- tooltip<- visible<- Consider adding importFrom("grDevices", "dev.control", "dev.cur", "dev.list", "dev.new", "rgb") importFrom("graphics", "par") to your NAMESPACE file.

toxboot

Version: 0.1.1

checking package dependencies ... NOTE Package suggested but not available for checking: ‘rmongodb’

toxplot

Version: 0.1.0

checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':
```
filter, lag
```
The following objects are masked from 'package:base':
```
intersect, setdiff, setequal, union
```
Quitting from lines 48-52 (Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd) Error: processing vignette 'Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd' failed with diagnostics: 'roxygen2' >= 5.0.0 must be installed for this functionality. Execution halted ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘tidyr’ All declared Imports should be used.

TPP

Version: 3.4.3

checking installed package size ... NOTE installed size is 13.3Mb sub-directories of 1Mb or more: data 1.9Mb example_data 8.0Mb test_data 1.9Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘doParallel:::.options’ ‘mefa:::rep.data.frame’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE ``` File ‘TPP/R/TPP.R’: .onLoad calls: packageStartupMessage(msgText, "\n")

See section ‘Good practice’ in '?.onAttach'.

plot_fSta_distribution: no visible binding for global variable ‘..density..’ plot_pVal_distribution: no visible binding for global variable ‘..density..’ Undefined global functions or variables: ..density.. ```

trackeR

Version: 0.0.5

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘colorspace’ All declared Imports should be used.

trapezoid

Version: 2.0-0

checking R code for possible problems ... NOTE rtrapezoid: no visible global function definition for ‘runif’ Undefined global functions or variables: runif Consider adding importFrom("stats", "runif") to your NAMESPACE file.

treeclim

Version: 2.0.0

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: libs 5.0Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘dplR’

treeDA

Version: 0.0.2

checking examples ... ERROR ``` Running examples in ‘treeDA-Ex.R’ failed The error most likely occurred in:

Name: plot_coefficients

Title: Plot the discriminating axes from treeda

Aliases: plot_coefficients

** Examples

data(treeda_example) out.treeda = treeda(response = treeda_example$response, + predictors = treeda_example$predictors, + tree = treeda_example$tree, + p = 1) plot_coefficients(out.treeda) Error in .C(ape:::node_depth_edgelength, PACKAGE = "ape", as.integer(Ntip), : Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength' Calls: plot_coefficients ... plot_tree -> tree_layout -> ape_node_depth_edge_length -> .C Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. Quitting from lines 190-191 (treeda-vignette.Rmd) Error: processing vignette 'treeda-vignette.Rmd' failed with diagnostics: Incorrect number of arguments (7), expecting 5 for 'node_depth_edgelength' Execution halted

treespace

Version: 1.0.0

checking whether package ‘treespace’ can be installed ... WARNING Found the following significant warnings: Warning: namespace ‘DBI’ is not available and has been replaced See ‘/home/muelleki/git/R/ggplot2/revdep/checks/treespace/new/treespace.Rcheck/00install.out’ for details.

TSCAN

Version: 1.14.0

checking R code for possible problems ... NOTE ... ‘lm’ exprmclust: no visible global function definition for ‘dist’ plotmclust: no visible binding for global variable ‘pca_dim_1’ plotmclust: no visible binding for global variable ‘pca_dim_2’ plotmclust: no visible binding for global variable ‘sample_name’ preprocess: no visible binding for global variable ‘sd’ preprocess: no visible global function definition for ‘hclust’ preprocess: no visible global function definition for ‘dist’ preprocess: no visible global function definition for ‘cutree’ preprocess: no visible global function definition for ‘aggregate’ singlegeneplot: no visible global function definition for ‘fitted.values’ singlegeneplot: no visible binding for global variable ‘predict’ Undefined global functions or variables: aggregate cutree dist fitted.values hclust lm p.adjust pca_dim_1 pca_dim_2 pchisq prcomp predict sample_name sd Consider adding importFrom("stats", "aggregate", "cutree", "dist", "fitted.values", "hclust", "lm", "p.adjust", "pchisq", "prcomp", "predict", "sd") to your NAMESPACE file.

TSMining

Version: 1.0

checking R code for possible problems ... NOTE Func.SAX: no visible global function definition for ‘sd’ Func.SAX: no visible global function definition for ‘qnorm’ Func.matrix: no visible global function definition for ‘qnorm’ Func.motif: no visible global function definition for ‘sd’ Func.motif: no visible global function definition for ‘na.omit’ Func.motif: no visible global function definition for ‘combn’ Func.motif.multivariate: no visible global function definition for ‘txtProgressBar’ Func.motif.multivariate: no visible global function definition for ‘setTxtProgressBar’ Undefined global functions or variables: combn na.omit qnorm sd setTxtProgressBar txtProgressBar Consider adding importFrom("stats", "na.omit", "qnorm", "sd") importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar") to your NAMESPACE file.

TSRchitect

Version: 1.2.0

checking top-level files ... NOTE File inst/LICENSE will install at top-level and is not mentioned in the DESCRIPTION file.

TSS.RESTREND

Version: 0.1.02

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘ggplot2’ All declared Imports should be used.
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘gimms’

tufterhandout

Version: 1.2.1

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.

TVTB

Version: 1.2.0

checking examples ... ERROR ``` ... > # Pre-process variants > vcf <- VariantAnnotation::readVcf(
- vcfFile, param = tparam, colData = phenotypes)
  
  vcf <- VariantAnnotation::expand(vcf, row.names = TRUE) vcf <- addFrequencies(vcf, "super_pop")
  
  Example usage ----
  
  if (requireNamespace("EnsDb.Hsapiens.v75")){
- plotInfo(
- vcf, "MAF",
- range(GenomicRanges::granges(vcf)),
- EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75,
- "super_pop"
- )
- } Loading required namespace: EnsDb.Hsapiens.v75 Error in validObject(.Object) : invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class Calls: plotInfo ... .AnnotationFilterList -> new -> initialize -> initialize -> validObject Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: rs1426654 rs150379789 rs570906312 rs538198029 rs553496066 rs574775672 TRUE TRUE FALSE FALSE TRUE FALSE rs140666229 rs556950130 rs575303689 rs147513140 rs187525777 rs192454382 TRUE FALSE TRUE TRUE FALSE FALSE rs184818838 rs566886499 rs199924625 rs555872528 rs531820822 rs201353600 FALSE FALSE FALSE FALSE FALSE FALSE rs550201688 rs565338261 rs201239799 rs200461129 rs146726548 FALSE FALSE FALSE FALSE TRUE testthat results ================================================================ OK: 229 SKIPPED: 0 FAILED: 2
1. Error: all signatures work to completion (@test_plotInfo-methods.R#25)
2. Error: invalid metric/phenotype combination is detected (@test_plotInfo-methods.R#50)
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... Overwriting INFO keys in data:
- REF
- HET
- ALT
- AAF
- MAF Overwriting INFO keys in header:
- REF
- HET
- ALT
- AAF
- MAF Quitting from lines 570-577 (Introduction.Rmd) Error: processing vignette 'Introduction.Rmd' failed with diagnostics: invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class Execution halted ```

twoddpcr

Version: 1.0.6

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'twoddpcr.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted

ukbtools

Version: 0.9.0

checking data for non-ASCII characters ... NOTE Note: found 5 marked UTF-8 strings

ukgasapi

Version: 0.13

checking examples ... ERROR ``` Running examples in ‘ukgasapi-Ex.R’ failed The error most likely occurred in:

Name: dataItemExplorer

Title: Data Item Explorer API

Aliases: dataItemExplorer

** Examples

Specify the data item(s) to enquire from API

dataitems <- c('Storage Injection, Actual', + 'Storage Withdrawal, Actual')

Initialise API (requires internet connection for this step)

response <- dataItemExplorer(dataitems, + fromdate = '2013-10-01', + todate='2015-09-30') ```

unvotes

Version: 0.2.0

checking data for non-ASCII characters ... NOTE Note: found 4494 marked UTF-8 strings

UpSetR

Version: 1.3.3

checking installed package size ... NOTE installed size is 8.4Mb sub-directories of 1Mb or more: doc 7.9Mb

usmap

Version: 0.2.1

checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: extdata 6.2Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘ggthemes’
checking data for non-ASCII characters ... NOTE Note: found 1 marked UTF-8 string

uSORT

Version: 1.2.0

checking whether package ‘uSORT’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/uSORT/new/uSORT.Rcheck/00install.out’ for details.

valr

Version: 0.3.1

checking installed package size ... NOTE installed size is 15.5Mb sub-directories of 1Mb or more: libs 14.1Mb

vanddraabe

Version: 1.0.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check("vanddraabe") Loading required package: vanddraabe
1. Failure: FileTimeStamp returns the correct formatted date and time (@test-utilities.R#87) FileTimeStamp(current.time) not equal to "may042016_1234". 1/1 mismatches x[1]: "mai042016_1234" y[1]: "may042016_1234"
testthat results ================================================================ OK: 64 SKIPPED: 0 FAILED: 1 1. Failure: FileTimeStamp returns the correct formatted date and time (@test-utilities.R#87)

Error: testthat unit tests failed Execution halted ```

variancePartition

Version: 1.6.0

checking re-building of vignette outputs ... WARNING ``` ...
```
anyMissing, rowMedians
```
Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':
```
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
```
The following object is masked from 'package:base':
```
apply
```
converting counts to integer mode Note: importing abundance.h5 is typically faster than abundance.tsv reading in files with read_tsv 1 Quitting from lines 529-565 (variancePartition.Rnw) Error: processing vignette 'variancePartition.Rnw' failed with diagnostics: reading kallisto results from hdf5 files requires Bioconductor package rhdf5 Execution halted ```

VariantAnnotation

Version: 1.22.3

checking dependencies in R code ... NOTE 'library' or 'require' call to ‘snpStats’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported objects imported by ':::' calls: ‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’ ‘Rsamtools:::.RsamtoolsFile’ ‘Rsamtools:::.RsamtoolsFileList’ ‘Rsamtools:::.io_check_exists’ ‘S4Vectors:::expandByColumnSet’ ‘S4Vectors:::labeledLine’ ‘S4Vectors:::recycleVector’ ‘S4Vectors:::selectSome’ ‘SummarizedExperiment:::.SummarizedExperiment.charbound’ ‘SummarizedExperiment:::.cbind.DataFrame’ See the note in ?`:::` about the use of this operator.
checking R code for possible problems ... NOTE .predictCodingGRangesList: no visible binding for global variable ‘GENETIC_CODE’ VRangesForMatching: no visible binding for global variable ‘REF’ VRangesForMatching: no visible binding for global variable ‘ALT’ probabilityToSnpMatrix: no visible global function definition for ‘post2g’ import,VcfFile-ANY-ANY: no visible global function definition for ‘checkArgFormat’ Undefined global functions or variables: ALT GENETIC_CODE REF checkArgFormat post2g
checking compiled code ... NOTE ``` File ‘VariantAnnotation/libs/VariantAnnotation.so’: Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ```

vcdExtra

Version: 0.7-1

checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘coin’, ‘alr3’, ‘Hmisc’

vcfR

Version: 1.5.0

checking installed package size ... NOTE installed size is 11.3Mb sub-directories of 1Mb or more: doc 3.0Mb libs 7.5Mb

vdg

Version: 1.2.0

checking re-building of vignette outputs ... WARNING `` Error in re-building vignettes: ... Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'vdg.tex' failed. LaTeX errors: ! LaTeX Error: Filealgorithm.sty' not found.

Type X to quit or to proceed, or enter new name. (Default extension: sty)

! Emergency stop.

l.75 \usepackage {algorithmic}^^M ! ==> Fatal error occurred, no output PDF file produced! Calls: buildVignettes -> texi2pdf -> texi2dvi Execution halted ```

vdmR

Version: 0.2.4

checking examples ... ERROR ``` Running examples in ‘vdmR-Ex.R’ failed The error most likely occurred in:

Name: vhist

Title: Generate histogram with interactive functions

Aliases: vhist

** Examples

data(vsfuk2012) vhist(FertilityRate, vsfuk2012, "hist1", "vsfuk2012", fill=Type) stat_bin() using bins = 30. Pick better value with binwidth. Error in histparam$xmax : $ operator is invalid for atomic vectors Calls: vhist -> unique Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/run-all.R’ failed. Last 13 lines of output: with 72 features It has 3 fields Integer64 fields read as strings: CityCode .. Failed -------------------------------------------------------------------------
1. Error: check vhist (@test-vdmR.R#7) ----------------------------------------- $ operator is invalid for atomic vectors 1: vhist(Sepal.Length, iris, "hist01", "iris", fill = Species) at /home/muelleki/git/R/ggplot2/revdep/checks/vdmR/new/vdmR.Rcheck/vdmR/tests/test-vdmR.R:7 2: unique(histparam$xmax)
DONE =========================================================================== Error: Test failures In addition: Warning message: Placing tests in inst/tests/ is deprecated. Please use tests/testthat/ instead Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... `stat_bin()` using `bins = 30`. Pick better value with `binwidth`. Quitting from lines 40-42 (vdmR-vignette.Rnw) Error: processing vignette 'vdmR-vignette.Rnw' failed with diagnostics: $ operator is invalid for atomic vectors Execution halted

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘maptools’ ‘rgeos’ All declared Imports should be used.

VetResearchLMM

Version: 0.2.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘nlme’ All declared Imports should be used.

viridis

Version: 0.4.0

checking re-building of vignette outputs ... WARNING ``` ...
```
RGB
```
The following object is masked from 'package:ggplot2':
```
calc
```
Loading required package: lattice Loading required package: latticeExtra Loading required package: RColorBrewer

Attaching package: 'latticeExtra'

The following object is masked from 'package:ggplot2':
```
layer
```
Quitting from lines 204-213 (intro-to-viridis.Rmd) Error: processing vignette 'intro-to-viridis.Rmd' failed with diagnostics: Cannot create RasterLayer object from this file; perhaps you need to install rgdal first Execution halted ```
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘stats’ All declared Imports should be used.

vmsbase

Version: 2.1.3

checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

voxel

Version: 1.3.2

checking examples ... ERROR ``` ...

Name: plotGAMM

Title: GAMM plotting using ggplot2

Aliases: plotGAMM

** Examples

set.seed(1) data <- data.frame(x = (seq(.25,25, .25) +rnorm(100)), group = rep(1:2, 5), z=rnorm(100), + index.rnorm = rep(rnorm(50, sd = 50), 2), index.var = rep(1:50, 2)) data$y <- (data$x)data$group10 + rnorm(100, sd = 700) + data$index.rnorm + data$z data$group <- ordered(data$group) gamm <- gamm4::gamm4(y ~ + s(x) + s(x, by=group) + z + group, data=data, random = ~ (1|index.var)) plot <- plotGAMM(gammFit <- gamm, smooth.cov <- "x", groupCovs = "group", + plotCI <- T, rawOrFitted = "raw", grouping = "index.var") [1] "Working with a GAMM4 object" [1] "orderedAsFactor functionality temporally disabled" plot Error: Column x must be a 1d atomic vector or a list Execution halted ```

vqtl

Version: 1.2.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘iterators’ ‘knitr’ ‘testthat’ All declared Imports should be used.

vsn

Version: 3.44.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘hexbin’ All declared Imports should be used.
checking R code for possible problems ... NOTE meanSdPlot,matrix: no visible binding for global variable ‘y’ Undefined global functions or variables: y

walker

Version: 0.2.0

checking installed package size ... NOTE installed size is 46.9Mb sub-directories of 1Mb or more: libs 46.2Mb

walkr

Version: 0.3.4

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: libs 5.0Mb

walrus

Version: 1.0.1

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘R6’ ‘WRS2’ ‘ggplot2’ All declared Imports should be used.

warbleR

Version: 1.1.9

checking package dependencies ... ERROR ``` Packages required but not available: ‘seewave’ ‘fftw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```

Wats

Version: 0.10.3

checking installed package size ... NOTE installed size is 12.3Mb sub-directories of 1Mb or more: doc 12.1Mb

wavClusteR

Version: 2.10.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Error: processing vignette 'wavCluster_vignette.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted
checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘doMC’
checking dependencies in R code ... NOTE 'library' or 'require' call to ‘doMC’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.
checking R code for possible problems ... NOTE ... plotSubstitutions: no visible global function definition for ‘barplot’ processChunk: no visible global function definition for ‘extractAt’ processMD: no visible global function definition for ‘registerDoMC’ readSortedBam: no visible global function definition for ‘scanBamFlag’ readSortedBam : <anonymous>: no visible binding for global variable ‘rname’ readSortedBam : <anonymous>: no visible binding for global variable ‘qwidth’ Undefined global functions or variables: Compartment DNAString DNAStringSet Percentage abline axis barplot dbinom extractAt grid hist legend lines pairs panel.smooth par polygon qwidth rect registerDoMC rname scanBamFlag seqlevels setTxtProgressBar strwidth text txtProgressBar write.table Consider adding importFrom("graphics", "abline", "axis", "barplot", "grid", "hist", "legend", "lines", "pairs", "panel.smooth", "par", "polygon", "rect", "strwidth", "text") importFrom("stats", "dbinom") importFrom("utils", "setTxtProgressBar", "txtProgressBar", "write.table") to your NAMESPACE file.

wbstats

Version: 0.1.1

checking data for non-ASCII characters ... NOTE Note: found 1371 marked UTF-8 strings

wesanderson

Version: 0.3.2

checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences.
checking R code for possible problems ... NOTE print.palette: no visible global function definition for ‘par’ print.palette: no visible global function definition for ‘image’ print.palette: no visible global function definition for ‘rect’ print.palette: no visible global function definition for ‘rgb’ print.palette: no visible global function definition for ‘text’ wes_palette: no visible global function definition for ‘colorRampPalette’ Undefined global functions or variables: colorRampPalette image par rect rgb text Consider adding importFrom("grDevices", "colorRampPalette", "rgb") importFrom("graphics", "image", "par", "rect", "text") to your NAMESPACE file.

widyr

Version: 0.1.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘methods’ All declared Imports should be used.

wiggleplotr

Version: 1.0.0

checking examples ... ERROR ``` ... The following object is masked from 'package:base':
```
expand.grid
```
Loading required package: IRanges Loading required package: GenomeInfoDb Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor
```
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
```
Loading required package: AnnotationFilter

plotTranscriptsFromEnsembldb(EnsDb.Hsapiens.v86, "NCOA7", transcript_ids = c("ENST00000438495", "ENST00000392477")) Error in validObject(.Object) : invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class Calls: plotTranscriptsFromEnsembldb ... .AnnotationFilterList -> new -> initialize -> initialize -> validObject Execution halted ```
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 148-152 (wiggleplotr.Rmd) Error: processing vignette 'wiggleplotr.Rmd' failed with diagnostics: invalid class "AnnotationFilterList" object: superclass "vectorORfactor" not defined in the environment of the object's class Execution halted

windfarmGA

Version: 1.1.1

checking whether package ‘windfarmGA’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/windfarmGA/new/windfarmGA.Rcheck/00install.out’ for details.
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘RandomFields’ All declared Imports should be used.

wordbankr

Version: 0.2.0

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 27-31 (wordbankr.Rmd) Error: processing vignette 'wordbankr.Rmd' failed with diagnostics: Condition message must be a string Execution halted
checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘RMySQL’ All declared Imports should be used.

wrswoR

Version: 1.0-1

checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... Quitting from lines 622-635 (wrswoR.Rmd) Error: processing vignette 'wrswoR.Rmd' failed with diagnostics:

TeX was unable to calculate metrics for the following string or character:
```
77
```
Common reasons for failure include: * The string contains a character which is special to LaTeX unless escaped properly, such as % or $. * The string makes use of LaTeX commands provided by a package and the tikzDevice was not told to load the package.

The contents of the LaTeX log of the aborted run have been printed above, it may contain additional details as to why the metric calculation failed. Execution halted ```

WRTDStidal

Version: 1.1.0

checking whether package ‘WRTDStidal’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘forecast::autolayer’ by ‘ggplot2::autolayer’ when loading ‘WRTDStidal’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/WRTDStidal/new/WRTDStidal.Rcheck/00install.out’ for details.

WVPlots

Version: 0.2.6

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘mgcv’ All declared Imports should be used.

XBSeq

Version: 1.6.0

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':
```
  apply

  Welcome to 'XBSeq'.
```
test_check("XBSeq") estimating parameters using MLE for group one estimating parameters using MLE for group two Error: XBplot(XB, Samplenum = "Sample_54_WT") did not throw an error. testthat results ================================================================ OK: 0 SKIPPED: 0 FAILED: 0 Execution halted ```
checking re-building of vignette outputs ... WARNING ``` ... Attaching package: 'DESeq'

The following object is masked from 'package:XBSeq':
```
fitInfo
```
The following objects are masked from 'package:DESeq2':
```
estimateSizeFactorsForMatrix, getVarianceStabilizedData,
varianceStabilizingTransformation
```
Warning in block_exec(params) : failed to tidy R code in chunk reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning: Transformation introduced infinite values in continuous x-axis Warning: Removed 17 rows containing missing values (geom_point). Warning: Removed 2 rows containing missing values (geom_point). Error: processing vignette 'XBSeq.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```
checking whether the namespace can be loaded with stated dependencies ... NOTE ``` Warning: no function found corresponding to methods exports from ‘XBSeq’ for: ‘conditions’, ‘conditions<-’, ‘dispTable’

A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file. ```
checking R code for possible problems ... NOTE ... estimateRealCount,XBSeqDataSet: no visible global function definition for ‘assay’ estimateRealCount,XBSeqDataSet: no visible global function definition for ‘assay<-’ estimateSCV,XBSeqDataSet: no visible global function definition for ‘conditions’ estimateSCV,XBSeqDataSet: no visible global function definition for ‘dispTable<-’ Undefined global functions or variables: ..count.. DataFrame Gamma Group Sample SummarizedExperiment assay assay<- assays baseMean coefficients complete.cases conditions cor data ddelap dispTable dispTable<- dnbinom dpois formula glm log2FoldChange median optim p.adjust pbeta predict qbeta quantile rnbinom scvBiasCorrectionFits Consider adding importFrom("stats", "Gamma", "coefficients", "complete.cases", "cor", "dnbinom", "dpois", "formula", "glm", "median", "optim", "p.adjust", "pbeta", "predict", "qbeta", "quantile", "rnbinom") importFrom("utils", "data") to your NAMESPACE file.

xgboost

Version: 0.6-4

checking installed package size ... NOTE installed size is 11.9Mb sub-directories of 1Mb or more: libs 11.3Mb

XLConnect

Version: 0.2-13

checking installed package size ... NOTE installed size is 11.7Mb sub-directories of 1Mb or more: java 9.7Mb

xpose

Version: 0.4.0

checking examples ... ERROR ``` Running examples in ‘xpose-Ex.R’ failed The error most likely occurred in:

Name: amt_vs_idv

Title: Compartment kinetics

Aliases: amt_vs_idv

** Examples

amt_vs_idv(xpdb_ex_pk) Using data from $prob no.1 Tidying data by ID, SEX, MED1, MED2, AMT ... and 20 more variables Error in 1:page_tot : argument of length 0 Calls: -> print.xpose_plot Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 3: grid.draw(plot) 4: grid.draw.ggplot(plot) 5: print(x) 6: print.xpose_plot(x)

testthat results ================================================================ OK: 520 SKIPPED: 0 FAILED: 5 1. Error: warnings and errors are properly returned (@test-print_xpose_plots.R#19) 2. Error: properly creates the xpdb when using the file argument (@test-xpose_data.R#39) 3. Error: properly creates the xpdb when using the runno argument (@test-xpose_data.R#52) 4. Error: common graphical device work properly (@test-xpose_save.R#45) 5. Error: template filenames and auto file extension work properly (@test-xpose_save.R#67)

Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ... Returning parameter estimates from $prob no.1, subprob no.0, method foce Using data from $prob no.1 Filtering data by EVID == 0 Using data from $prob no.1 Filtering data by EVID == 0 Using data from $prob no.1 Filtering data by EVID == 0 Using data from $prob no.1 Filtering data by EVID == 0 Using data from $prob no.1 Filtering data by EVID == 0 Using data from $prob no.1 Filtering data by EVID == 0 Using data from $prob no.1 Filtering data by EVID == 0 Using data from $prob no.1 Filtering data by EVID == 0 Quitting from lines 76-87 (customize_plots.Rmd) Error: processing vignette 'customize_plots.Rmd' failed with diagnostics: argument is of length zero Execution halted

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘gridExtra’ All declared Imports should be used.

xtractomatic

Version: 3.3.2

checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Warning in engine$weave(file, quiet = quiet, encoding = enc) : The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. date lon lat lowLon higLon lowLat higLat 4/23/2003 203.899 19.664 203.899 203.899 19.664 19.664 4/24/2003 204.151 19.821 203.912597 204.389403 18.78051934 20.86148066 4/30/2003 203.919 20.351 203.6793669 204.1586331 18.79728188 21.90471812 5/1/2003 204.229 20.305 203.9943343 204.4636657 18.90440013 21.70559987 Quitting from lines 1044-1046 (Usingxtractomatic.Rmd) Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics: there is no package called 'webshot' Execution halted

xxIRT

Version: 2.0.3

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘graphics’ All declared Imports should be used.

YAPSA

Version: 1.2.0

checking re-building of vignette outputs ... WARNING ``` ...

The following object is masked from 'package:base':
```
strsplit
```
Loading required package: rtracklayer Warning in posthoc.kruskal.nemenyi.test.default(x = sig_exposures_vector, : Ties are present, p-values are not corrected. Warning in posthoc.kruskal.nemenyi.test.default(x = sig_exposures_vector, : Ties are present, p-values are not corrected. Warning in posthoc.kruskal.nemenyi.test.default(x = sig_exposures_vector, : Ties are present, p-values are not corrected. Warning in posthoc.kruskal.nemenyi.test.default(x = sig_exposures_vector, : Ties are present, p-values are not corrected. Warning in posthoc.kruskal.nemenyi.test.default(x = sig_exposures_vector, : Ties are present, p-values are not corrected. Warning in posthoc.kruskal.nemenyi.test.default(x = sig_exposures_vector, : Ties are present, p-values are not corrected. Error: processing vignette 'YAPSA.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted ```

zenplots

Version: 0.0-1

checking whether package ‘zenplots’ can be installed ... WARNING Found the following significant warnings: Warning: no DISPLAY variable so Tk is not available See ‘/home/muelleki/git/R/ggplot2/revdep/checks/zenplots/new/zenplots.Rcheck/00install.out’ for details.

zFactor

Version: 0.1.7

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘rootSolve’ All declared Imports should be used.

zonator

Version: 0.5.8

checking whether package ‘zonator’ can be installed ... WARNING Found the following significant warnings: Warning: replacing previous import ‘ggplot2::calc’ by ‘raster::calc’ when loading ‘zonator’ See ‘/home/muelleki/git/R/ggplot2/revdep/checks/zonator/new/zonator.Rcheck/00install.out’ for details.

checking package dependencies ... NOTE Package suggested but not available for checking: ‘zdat’

zoo

Version: 1.8-0

checking tests ... ``` ERROR Running the tests in ‘tests/vignette-zoo-quickref.R’ failed. Last 13 lines of output:

library("tseries") online <- FALSE ## if set to FALSE the local copy of ## is used instead of get.hist.quote() options(prompt = "R> ") R> Sys.setenv(TZ = "GMT") R> R> R> ################################################### R> ### chunk number 2: read.zoo R> ################################################### R> inrusd <- read.zoo(system.file("doc", "demo1.txt", package = "zoo"), sep = "|", format="%d %b %Y") Error in read.zoo(system.file("doc", "demo1.txt", package = "zoo"), sep = "|", : index has bad entries at data rows: 14 15 16 17 18 19 20 Execution halted ```
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘stinepack’

zooaRchGUI

Version: 1.0.2

R CMD check timed out

zoocat

Version: 0.2.0

checking Rd \usage sections ... NOTE ``` S3 methods shown with full name in documentation object 'merge': ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. ```

ztype

Version: 0.1.0

checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘dplyr’ ‘ggplot2’ ‘lubridate’ All declared Imports should be used.

SahaRahul/ggplot2 documentation built on May 17, 2019, 1:46 p.m.

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SahaRahul/ggplot2 Create Elegant Data Visualisations Using the Grammar of Graphics

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SahaRahul/ggplot2
Create Elegant Data Visualisations Using the Grammar of Graphics

revdep/problems.md
In SahaRahul/ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics