Version: 1.0.0
Namespaces in Imports field not imported from:
‘rARPACK’ ‘sparseLDA’
All declared Imports should be used.
Version: 1.0.2
Namespaces in Imports field not imported from:
‘plotly’ ‘shinydashboard’
All declared Imports should be used.
Version: 1.48.0
Package unavailable to check Rd xrefs: ‘oligo’
Version: 0.0.1
Namespaces in Imports field not imported from:
‘DBI’ ‘assertthat’ ‘tibble’
All declared Imports should be used.
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
Version: 0.2.8
installed size is 15.7Mb
sub-directories of 1Mb or more:
data 15.6Mb
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').
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.
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',
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
Version: 1.4.0
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’
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:
.
Version: 0.2.4
Namespace in Imports field not imported from: ‘caret’
All declared Imports should be used.
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').
Version: 1.2
Packages unavailable to check Rd xrefs: ‘sensitivity’, ‘APSIMBatch’
Version: 1.3
Namespace in Imports field not imported from: ‘DT’
All declared Imports should be used.
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.
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’
Version: 1.1
...
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.
Version: 2.0-12
Package which this enhances but not available for checking: ‘asreml’
Version: 1.0.2
...
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.
Version: 2.0
Package unavailable to check Rd xrefs: ‘akima’
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').
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
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
Version: 0.1.4.2
Packages unavailable to check Rd xrefs: ‘InvariantCausalPrediction’, ‘CompareCausalNetworks’
Version: 1.4.0
.hist: no visible binding for global variable ‘..density..’
.qq: no visible binding for global variable ‘column’
Undefined global functions or variables:
..density.. column
Version: 0.1.0
Namespaces in Imports field not imported from:
‘XML’ ‘devtools’ ‘ggplot2’ ‘scales’
All declared Imports should be used.
Version: 1.0.2.0
installed size is 5.2Mb
sub-directories of 1Mb or more:
libs 4.2Mb
Version: 1.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
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 ```
Version: 1.2.2
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
Version: 1.4.0
installed size is 5.8Mb
sub-directories of 1Mb or more:
R 1.6Mb
doc 3.6Mb
Version: 2.2-5
Package suggested but not available for checking: ‘INLA’
Version: 3.1.2
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
Version: 4.0.0
installed size is 5.4Mb
sub-directories of 1Mb or more:
libs 5.1Mb
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’
Version: 1.0.1
...
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.
Version: 1.0.2
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.
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').
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').
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
Error: testthat unit tests failed Execution halted ```
Version: 0.4
installed size is 5.7Mb
sub-directories of 1Mb or more:
data 2.1Mb
libs 3.3Mb
Version: 2.0.4
installed size is 5.1Mb
sub-directories of 1Mb or more:
libs 4.8Mb
Version: 1.1.0
...
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
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
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
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.
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').
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
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: File
mhchem.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 ```
Version: 1.4
Package unavailable to check Rd xrefs: ‘seqinr’
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
Version: 0.0.1
Package has no Sweave vignette sources and no VignetteBuilder field.
Version: 2.0.0
...
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.
Version: 1.0.4
Namespaces in Imports field not imported from:
‘Matrix’ ‘SuperLearner’ ‘biotmleData’
All declared Imports should be used.
Version: 0.4.3
Namespace in Imports field not imported from: ‘knitr’
All declared Imports should be used.
Version: 0.1
Namespace in Imports field not imported from: ‘rJava’
All declared Imports should be used.
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’
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.
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.
Version: 0.1
installed size is 8.9Mb
sub-directories of 1Mb or more:
data 8.7Mb
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
Error: testthat unit tests failed Execution halted ```
Version: 0.1.0
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.
Namespaces in Imports field not imported from:
‘rgdal’ ‘tidyr’
All declared Imports should be used.
Version: 0.1.0
installed size is 6.5Mb
sub-directories of 1Mb or more:
libs 6.1Mb
Version: 0.26.0
Package suggested but not available for checking: ‘installr’
Version: 1.0.0
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’
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’
Version: 0.4.0
Package unavailable to check Rd xrefs: ‘breathteststan’
Version: 0.4.0
installed size is 28.9Mb
sub-directories of 1Mb or more:
libs 28.7Mb
Version: 1.10.2
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
Version: 0.4.2
checking examples ... ERROR ``` ...
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
Version: 1.0
installed size is 5.8Mb
sub-directories of 1Mb or more:
bin 2.3Mb
doc 1.2Mb
libs 2.2Mb
Version: 1.1.2
Namespaces in Imports field not imported from:
‘rworldxtra’ ‘sp’
All declared Imports should be used.
Version: 0.1.1-1
installed size is 29.4Mb
sub-directories of 1Mb or more:
libs 28.5Mb
Version: 1.9.0
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.
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.
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
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.
Version: 0.2.2
Namespace in Imports field not imported from: ‘markdown’
All declared Imports should be used.
Version: 1.8.0
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.
Version: 6.0-77
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.5Mb
models 2.4Mb
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 ```
Version: 1.1.1
installed size is 11.2Mb
sub-directories of 1Mb or more:
data 2.3Mb
doc 8.5Mb
Version: 1.0.4
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
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.
Version: 2.0.0
installed size is 7.9Mb
sub-directories of 1Mb or more:
libs 7.6Mb
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’
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 ```
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').
Version: 1.0.0
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
Version: 0.2.0
Namespace in Imports field not imported from: ‘data.table’
All declared Imports should be used.
Version: 1.1
Checking should be performed on sources prepared by ‘R CMD build’.
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. ```
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
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
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 ```
Version: 0.1.0
Namespaces in Imports field not imported from:
‘knitr’ ‘tools’
All declared Imports should be used.
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 ```
Version: 1.1.1
installed size is 18.0Mb
sub-directories of 1Mb or more:
data 17.9Mb
Version: 1.2.0
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’
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’
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 ```
Version: 2.0
...
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.
Version: 1.3.3
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
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.
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.
Version: 0.1-2
.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.
Version: 0.1
Namespace in Imports field not imported from: ‘stats’
All declared Imports should be used.
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.
Version: 1.0.8
installed size is 7.4Mb
sub-directories of 1Mb or more:
libs 6.4Mb
Version: 1.4.1
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.
Version: 0.1.0
Namespace in Imports field not imported from: ‘tidyr’
All declared Imports should be used.
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.
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
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 ```
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').
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’
Version: 0.1.1
mapping_rf: Error while checking: there is no package called
‘randomForest’
Version: 0.3.1
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
Version: 1.2.4
Packages which this enhances but not available for checking:
‘glmnet’ ‘maxLik’
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
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’
Version: 0.1.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 2.3-1
...
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.
Version: 0.1.2
Namespaces in Imports field not imported from:
‘grid’ ‘gridExtra’
All declared Imports should be used.
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').
Version: 0.1.1
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.
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.
Version: 1.12.0
...
‘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.
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. ```
Version: 1.1-2
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.
Version: 0.1.1
Note: found 1 marked UTF-8 string
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 ```
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.
Version: 1.0.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ******
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 ```
Version: 1.1
...
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.
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
```
Version: 0.1
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.
Version: 1.3.0
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’
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.
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 ```
Version: 0.1.0
Note: found 1 marked UTF-8 string
Version: 0.4.1
installed size is 9.7Mb
sub-directories of 1Mb or more:
libs 9.1Mb
Version: 0.1.0
Namespaces in Imports field not imported from:
‘ggplot2’ ‘misc3d’
All declared Imports should be used.
Version: 0.9.1
Package suggested but not available for checking: ‘magick’
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.
Version: 2.1.1
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 6.5Mb
Version: 0.0.14
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.
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’
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 ```
Version: 1.0.0
Namespace in Imports field not imported from: ‘qte’
All declared Imports should be used.
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
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 ```
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 ```
Version: 2.4.0
installed size is 283.1Mb
sub-directories of 1Mb or more:
data 282.7Mb
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
Version: 1.0
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.
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.
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.
Version: 1.3.0
installed size is 23.2Mb
sub-directories of 1Mb or more:
libs 22.5Mb
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
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.
Version: 1.0.0
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
Version: 1.8.7
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
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’
Version: 1.3.0
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:
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 ```
Version: 0.93
Namespaces in Imports field not imported from:
‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’
All declared Imports should be used.
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 ```
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")
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 ```
Version: 2.7.1
Namespace in Imports field not imported from: ‘curl’
All declared Imports should be used.
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.
Version: 1.0
...
‘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.
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
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.
Version: 0.7-9
...
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)
Version: 1.2.10
deepblue_enrich_region_overlap(
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
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. ```
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’. ```
Version: 1.1.2
...
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.
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’
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 ```
Version: 2.0.2
installed size is 6.9Mb
sub-directories of 1Mb or more:
libs 5.4Mb
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’
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’
Version: 1.16.1
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: > test_check("DESeq2")
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
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
Version: 0.2.0
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
Version: 0.2.1
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.
Version: 3.4.0
installed size is 43.2Mb
sub-directories of 1Mb or more:
libs 42.8Mb
Version: 2.0.1
installed size is 27.5Mb
sub-directories of 1Mb or more:
doc 1.9Mb
libs 25.2Mb
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
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').
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
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)
Version: 1.4.0
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.
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:
Version: 1.9.90
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 5.9Mb
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
Version: 0.4
Package suggested but not available for checking: ‘rPython’
Version: 1.0.0
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 4.9Mb
Version: 4.5-15
Package unavailable to check Rd xrefs: ‘gdata’
Version: 0.0.3
installed size is 9.7Mb
sub-directories of 1Mb or more:
doc 3.4Mb
libs 6.1Mb
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
Version: 0.3.0
Package unavailable to check Rd xrefs: ‘arm’
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
Version: 1.0.0
Namespaces in Imports field not imported from:
‘devtools’ ‘drc’ ‘testthat’
All declared Imports should be used.
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",
plotProportions(d, gene_id = top_gene_id, group_variable = "group",
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
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
Version: 2.2.15
Error in .requirePackage(package) : unable to find required package 'sp'
Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
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
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
Version: 0.2.3
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 ```
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: File
apacite.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 ```
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.
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.
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.
Version: 0.1.0
Namespaces in Imports field not imported from:
‘corrplot’ ‘scorer’
All declared Imports should be used.
Version: 1.11.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 1.2.1-2
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.
Version: 2.8.0
...
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.
Version: 1.1
installed size is 6.3Mb
sub-directories of 1Mb or more:
data 4.9Mb
doc 1.2Mb
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’
Version: 1.1.0
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
Version: 0.1.1
.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').
Version: 1.4.1
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.
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.
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
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.
Version: 2.2.8
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
Version: 0.9.1
Packages which this enhances but not available for checking:
‘CARBayes’ ‘coxme’ ‘gee’ ‘geepack’ ‘glmmADMB’ ‘MCMCglmm’ ‘MCMCpack’
‘pscl’ ‘rstanarm’
Version: 0.5.1
installed size is 7.6Mb
sub-directories of 1Mb or more:
emoji_fonts 6.5Mb
Version: 0.1
Package unavailable to check Rd xrefs: ‘betareg’
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’
Version: 0.9.2
Namespaces in Imports field not imported from:
‘llogistic’ ‘logitnorm’
All declared Imports should be used.
Version: 1.10.0
dynRangePlot: no visible binding for global variable ‘value’
dynRangePlot: no visible binding for global variable ‘Rep’
Undefined global functions or variables:
Rep value
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
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’
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.
Version: 0.0.3
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.
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.
Version: 0.1.0
Namespaces in Imports field not imported from:
‘ggalt’ ‘pander’ ‘psych’
All declared Imports should be used.
Missing or unexported object: ‘purrr::by_row’
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.
Version: 0.2-5
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
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,
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.
Version: 0.6-3
...
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.
Version: 0.1.6
checking examples ... ERROR ``` ...
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,
response_time <- make_time_sequence_data(response_window, time_bin_size = 500, aois = "Animate",
time_cluster_data <- make_time_cluster_data(data = response_time, predictor_column = "SexM",
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
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.
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.
Version: 1.0.5
Package unavailable to check Rd xrefs: ‘NbClust’
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
Version: 0.2.0
Namespace in Imports field not imported from: ‘magrittr’
All declared Imports should be used.
Version: 1.2.0
fccac: no visible binding for global variable ‘variables’
Undefined global functions or variables:
variables
Version: 0.2
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.
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.
Version: 0.9.4
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.
Version: 1.2.1
gmtPathways: no visible binding for global variable ‘head’
Undefined global functions or variables:
head
Consider adding
importFrom("utils", "head")
to your NAMESPACE file.
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.
Version: 0.3-3
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').
Version: 0.1.8
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
Version: 1.0-9
Package unavailable to check Rd xrefs: ‘Hmisc’
Version: 0.4.6
Namespace in Imports field not imported from: ‘rgdal’
All declared Imports should be used.
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. ```
Version: 0.1.1
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
Version: 0.1.1
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
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’
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').
Version: 0.2.2
installed size is 5.0Mb
sub-directories of 1Mb or more:
libs 4.5Mb
Version: 2.1
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.
Version: 1.0.4
Package unavailable to check Rd xrefs: ‘Hmisc’
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
Version: 1.2
...
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.
Version: 0.1.8
installed size is 11.1Mb
sub-directories of 1Mb or more:
doc 2.2Mb
libs 8.7Mb
Version: 0.6.4
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.
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.
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. ```
Version: 1.0.0
installed size is 5.3Mb
sub-directories of 1Mb or more:
libs 5.0Mb
Version: 2.1-1
Namespace in Imports field not imported from: ‘scales’
All declared Imports should be used.
Version: 0.0.2
Namespaces in Imports field not imported from:
‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
All declared Imports should be used.
Version: 0.9.5-3
Packages which this enhances but not available for checking:
‘raster’ ‘doParallel’ ‘doMPI’
Version: 0.4.01
installed size is 58.6Mb
sub-directories of 1Mb or more:
libs 58.2Mb
Version: 1.6.1
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.
Version: 1.4.0
installed size is 9.2Mb
sub-directories of 1Mb or more:
data 2.3Mb
doc 1.1Mb
Version: 1.4.2
installed size is 6.2Mb
sub-directories of 1Mb or more:
libs 5.7Mb
Version: 1.2.0
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.
Version: 0.5.1
Package suggested but not available for checking: ‘genderdata’
Version: 0.9.5
Package suggested but not available for checking: ‘ProjectionBasedClustering’
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. ```
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.
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. ```
Version: 1.10.0
installed size is 11.0Mb
sub-directories of 1Mb or more:
doc 2.0Mb
extdata 7.9Mb
Version: 1.8.0
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.
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: File
algorithm2e.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 ```
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'
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
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
Version: 1.0
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.
Version: 1.0
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.
Version: 0.11.2
installed size is 5.1Mb
sub-directories of 1Mb or more:
libs 4.2Mb
Version: 1.2
Namespaces in Imports field not imported from:
‘DT’ ‘shinydashboard’
All declared Imports should be used.
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.
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
Version: 3.2
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.
Version: 0.1.9
Namespace in Imports field not imported from: ‘tidyr’
All declared Imports should be used.
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
```
Version: 0.4.0
Namespace in Imports field not imported from: ‘plotly’
All declared Imports should be used.
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.
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.
Version: 0.1
Namespace in Imports field not imported from: ‘tibble’
All declared Imports should be used.
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.
Version: 0.1.3.9
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 8.9Mb
Version: 0.1.1
Namespaces in Imports field not imported from:
‘GGEBiplotGUI’ ‘gge’ ‘utils’
All declared Imports should be used.
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
Version: 0.7
Namespace in Imports field not imported from: ‘grDevices’
All declared Imports should be used.
Version: 0.1.0
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
Namespaces in Imports field not imported from:
‘colorspace’ ‘grid’
All declared Imports should be used.
Version: 0.1.1
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
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 ```
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 wantstats::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
Version: 0.1.1
Namespaces in Imports field not imported from:
‘gridExtra’ ‘lazyeval’ ‘readr’
All declared Imports should be used.
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. ```
Version: 0.1.0
Namespaces in Imports field not imported from:
‘XML’ ‘mapproj’ ‘moonBook’
All declared Imports should be used.
Version: 0.1.3
Namespace in Imports field not imported from: ‘knitr’
All declared Imports should be used.
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 usepanel.spacing
property instead Error in if (theme$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```
Version: 0.1.2
checking examples ... ERROR ``` Running examples in ‘ggmosaic-Ex.R’ failed The error most likely occurred in:
Name: geom_mosaic
Title: Mosaic plots.
Aliases: geom_mosaic stat_mosaic
** Examples
data(Titanic) titanic <- as.data.frame(Titanic) titanic$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. ```
Namespaces in Imports field not imported from:
‘NHANES’ ‘gridExtra’
All declared Imports should be used.
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
```
Version: 0.1.3
Namespaces in Imports field not imported from:
‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
All declared Imports should be used.
Version: 0.1.6
Package unavailable to check Rd xrefs: ‘FactoMineR’
Version: 0.0.1
Namespaces in Imports field not imported from:
‘plyr’ ‘reshape2’
All declared Imports should be used.
Version: 2.0.1
Namespace in Imports field not imported from: ‘randomForest’
All declared Imports should be used.
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.
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
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.
Version: 0.7.0
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
Version: 0.4.1
Note: found 6242 marked UTF-8 strings
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
Version: 0.3
checking tests ... ``` ...
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*()
```
Namespace in Imports field not imported from: ‘lazyeval’
All declared Imports should be used.
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’
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
Package unavailable to check Rd xrefs: ‘latticeExtra’
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 ```
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
```
installed size is 11.1Mb
sub-directories of 1Mb or more:
doc 6.8Mb
examples 3.7Mb
Version: 0.1.0
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
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. ```
Version: 0.1-3
Package which this enhances but not available for checking: ‘sp’
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
Version: 0.2.1
installed size is 20.9Mb
sub-directories of 1Mb or more:
libs 19.9Mb
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’
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
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")) {
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
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 ```
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.
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.
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’
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.
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. ```
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
Version: 0.7-1
accrualReport: multiple local function definitions for ‘gg’ with
different formal arguments
Version: 0.6
Namespace in Imports field not imported from: ‘BiasedUrn’
All declared Imports should be used.
Version: 1.2.0
Error in re-building vignettes:
...
Error: processing vignette 'GRmetrics-vignette.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
Version: 0.2.4.1
installed size is 18.5Mb
sub-directories of 1Mb or more:
libs 18.0Mb
Version: 0.13
installed size is 13.2Mb
sub-directories of 1Mb or more:
libs 12.8Mb
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.
Version: 3.0-1
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
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.
Version: 0.1
checking package dependencies ... ERROR ``` Package required but not available: ‘rpanel’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
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.
Version: 0.1.3
Note: found 13617 marked UTF-8 strings
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 ```
Version: 3.14.0.3
installed size is 86.4Mb
sub-directories of 1Mb or more:
java 85.1Mb
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’
Version: 0.2.2
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
Version: 0.1
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.
Version: 0.4.0
Namespace in Imports field not imported from: ‘rstantools’
All declared Imports should be used.
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
Version: 0.13.0
Package unavailable to check Rd xrefs: ‘d3heatmap’
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. ```
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.
Version: 2.9
...
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.
Version: 1.0.2
Unexported objects imported by ':::' calls:
‘ggplot2:::build_guides’ ‘ggplot2:::guide_axis’
‘ggplot2:::scales_list’
See the note in ?`:::` about the use of this operator.
Version: 0.5.0
installed size is 16.5Mb
sub-directories of 1Mb or more:
doc 13.7Mb
htmlwidgets 1.9Mb
Version: 1.0.0
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.
Version: 0.8-2
Packages unavailable to check Rd xrefs: ‘psych’, ‘Guerry’, ‘alr3’, ‘agridat’, ‘coin’
Version: 1.5
Package unavailable to check Rd xrefs: ‘genalg’
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.
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() ```
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
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.
Version: 1.7
installed size is 13.8Mb
sub-directories of 1Mb or more:
data 12.3Mb
doc 1.0Mb
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 usepanel.spacing
property instead Theme element panel.border missing Error in if (theme$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```
Package suggested but not available for checking: ‘hurricaneexposuredata’
Version: 1.1.0
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message) 5: withVisible(code) 6: rmarkdown::render("table-tester-2.Rmd", quiet = TRUE, output_format = "pdf_document") 7: convert(output_file, run_citeproc) 8: pandoc_convert(utf8_input, pandoc_to, output_format$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’
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’
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
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.
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
Version: 0.3
Package unavailable to check Rd xrefs: ‘fICA’
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
Version: 0.3.5
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.
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. ```
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.
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
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
Version: 1.6.0
Error in re-building vignettes:
...
Error: processing vignette 'imetagene.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
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. ```
Version: 1.0.0
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
Version: 3.0.1
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.
Version: 1.2.1
checking examples ... ERROR ``` ...
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
Version: 1.2.3
BugReports field should be the URL of a single webpage
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’
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’
Version: 0.0.2
Namespace in Imports field not imported from: ‘prodlim’
All declared Imports should be used.
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.
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
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 ```
Version: 0.7.0
installed size is 10.1Mb
sub-directories of 1Mb or more:
doc 1.1Mb
libs 8.7Mb
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.
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
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 ```
...
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
Version: 0.6
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.
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 ```
Version: 0.8
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.
Version: 0.8.1.6
Package suggested but not available for checking: ‘RProtoBuf’
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: File
biblatex.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
Version: 0.2.0
Note: found 188 marked UTF-8 strings
Version: 0.9.0
Packages unavailable to check Rd xrefs: ‘effects’, ‘ReporteRs’, ‘arm’, ‘rockchalk’, ‘pequod’, ‘MuMIn’
Version: 0.1.5
...
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.
Version: 0.5.0
...
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.
Version: 1.3.2
...
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.
Version: 0.2.0
Namespaces in Imports field not imported from:
‘dplyr’ ‘tibble’
All declared Imports should be used.
Version: 6.0-0
installed size is 7.5Mb
sub-directories of 1Mb or more:
data 7.2Mb
Version: 1.1.0
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').
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
Version: 1.1.1
Namespaces in Imports field not imported from:
‘gridExtra’ ‘scales’ ‘tidyverse’
All declared Imports should be used.
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.
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.
Version: 1.6.1
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.
Version: 6.2.1
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.
Version: 1.3.5
Note: found 7 marked UTF-8 strings
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 ```
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
Version: 1.1-14
installed size is 26.8Mb
sub-directories of 1Mb or more:
doc 1.5Mb
libs 21.7Mb
testdata 1.5Mb
Version: 1.0.0
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.
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.
Version: 1.4.1
installed size is 8.3Mb
sub-directories of 1Mb or more:
doc 2.6Mb
extdata 5.5Mb
Version: 1.0
Namespaces in Imports field not imported from:
‘e1071’ ‘utils’
All declared Imports should be used.
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.
Version: 0.3.1
Namespace in Imports field not imported from: ‘DBI’
All declared Imports should be used.
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.
Version: 0.0.3
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.
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.
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’
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’
Version: 0.2.0
Package unavailable to check Rd xrefs: ‘qqman’
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
Version: 0.9.6
Package unavailable to check Rd xrefs: ‘maptools’
Version: 1.2.1
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 3.7Mb
doc 1.9Mb
Version: 0.52.2
installed size is 8.3Mb
sub-directories of 1Mb or more:
libs 7.6Mb
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. ```
Version: 1.0.1
installed size is 9.0Mb
sub-directories of 1Mb or more:
data 3.2Mb
doc 4.9Mb
Version: 1.0.1
Namespaces in Imports field not imported from:
‘parallelMap’ ‘reshape2’
All declared Imports should be used.
Version: 1.0.1
Namespace in Imports field not imported from: ‘glmnet’
All declared Imports should be used.
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
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
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
Version: 1.0.0
Namespaces in Imports field not imported from:
‘R6’ ‘ggplot2’ ‘lavaan’
All declared Imports should be used.
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.
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. ```
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. ```
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.
Version: 1.0
...
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.
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').
Version: 1.0.3
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
Version: 0.2
...
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.
Version: 1.0
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.
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.
Version: 1.10.0
Package suggested but not available for checking: ‘MethylAidData’
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 ```
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 ```
Namespace in Imports field not imported from: ‘digest’
All declared Imports should be used.
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’
Version: 1.4-2.1
GNU make is a SystemRequirements.
Version: 1.9.2
...
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.
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 ```
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').
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').
Version: 1.0.0
Namespaces in Imports field not imported from:
‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
All declared Imports should be used.
Version: 1.6.0
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').
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. ```
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.
Version: 0.2
...
‘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.
Version: 1.0
checking examples ... ERROR ``` ...
system.time(testfun()) Error in prep_call_sampler(object) : the compiled object from C++ code for this model is invalid, possible reasons:
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.
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’
Version: 1.1.0
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.
Version: 3.2.0
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.
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').
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. ```
Version: 2.16-4
...
‘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.
Version: 0.1.1
Packages unavailable to check Rd xrefs: ‘lme4’, ‘rstanarm’
Version: 0.1.3
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
Version: 1.2.0
installed size is 7.7Mb
sub-directories of 1Mb or more:
data 2.0Mb
doc 1.8Mb
libs 3.4Mb
Version: 1.2.2
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 2.3Mb
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
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.
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’
Version: 0.14.0
Note: found 7 marked UTF-8 strings
Version: 0.3.0
Namespaces in Imports field not imported from:
‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
All declared Imports should be used.
Version: 3.1.0
installed size is 6.9Mb
sub-directories of 1Mb or more:
data 2.0Mb
libs 4.5Mb
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 ```
installed size is 15.9Mb
sub-directories of 1Mb or more:
libs 15.1Mb
Version: 2.1
checking package dependencies ... ERROR ``` Package required but not available: ‘gWidgetsRGtk2’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. ```
Version: 1.3.0
Namespace in Imports field not imported from: ‘Rdpack’
All declared Imports should be used.
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.
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.
Version: 1.10.0
...
.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.
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.
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
Version: 1.0.0
Namespaces in Imports field not imported from:
‘hms’ ‘methods’
All declared Imports should be used.
Version: 0.2.0
installed size is 9.5Mb
sub-directories of 1Mb or more:
libs 7.9Mb
Version: 1.2.4
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
Version: 0.1
...
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.
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()
andcoord_flip()
Execution halted ```
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: File
apacite.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 ```
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 ```
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
Version: 0.6.0
installed size is 5.8Mb
sub-directories of 1Mb or more:
data 2.0Mb
doc 2.7Mb
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. ```
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 ```
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. ```
Version: 1.8.0
...
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.
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 ```
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. ```
Version: 0.3
Namespace in Imports field not imported from: ‘abind’
All declared Imports should be used.
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
```
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 ```
Namespace in Imports field not imported from: ‘devtools’
All declared Imports should be used.
Version: 0.5.0
Namespaces in Imports field not imported from:
‘htmlTable’ ‘lme4’ ‘stringi’
All declared Imports should be used.
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
Version: 0.4.5
Namespace in Imports field not imported from: ‘survival’
All declared Imports should be used.
Version: 0.6-7
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
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
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.
Version: 2.0.6
installed size is 8.6Mb
sub-directories of 1Mb or more:
data 4.3Mb
reports 2.3Mb
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: File
biblatex.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
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.
Version: 0.22
installed size is 9.2Mb
sub-directories of 1Mb or more:
doc 8.6Mb
Version: 1.0.0
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.
Version: 0.13.1
installed size is 10.8Mb
sub-directories of 1Mb or more:
libs 10.4Mb
Version: 0.3.1
...
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.
Version: 0.4.0
Note: found 6409 marked UTF-8 strings
Version: 2.0.23
installed size is 27.4Mb
sub-directories of 1Mb or more:
libs 27.3Mb
Version: 0.1.2
Packages unavailable to check Rd xrefs: ‘ensurer’, ‘validate’
Version: 1.0.0
checking examples ... ERROR ``` ...
insert first odds ratios to plot
plot_object <- insert_or(plot_object, or_object1, or_yloc = 3,
calculate second odds ratio
or_object2 <- or_gam(data = data_gam, model = fit_gam, pred = "x2",
add or_object2 into plot
insert_or(plot_object, or_object2, or_yloc = 2.1, values_yloc = 2,
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
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 ```
Version: 2.6.0
installed size is 11.0Mb
sub-directories of 1Mb or more:
doc 5.4Mb
libs 4.9Mb
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.
Version: 0.1.0
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
Version: 1.8.0
...
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.
Version: 0.37.3
checking tests ...
``
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
check1inherits from
ggplot_builtnot
list`.
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 ```
Version: 1.0.0
installed size is 8.0Mb
sub-directories of 1Mb or more:
extdata 1.8Mb
libs 5.5Mb
Version: 1.7
...
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.
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.
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.
Version: 0.3.0
installed size is 6.4Mb
sub-directories of 1Mb or more:
doc 5.9Mb
Version: 0.2.0
Namespace in Imports field not imported from: ‘quantreg’
All declared Imports should be used.
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. ```
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.
Version: 0.2.2
installed size is 7.1Mb
sub-directories of 1Mb or more:
libs 6.9Mb
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.
Version: 1.2.0
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 ```
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. ```
Version: 0.2.0
installed size is 5.1Mb
sub-directories of 1Mb or more:
libs 4.8Mb
Version: 0.2.1
Note: found 13 marked UTF-8 strings
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 with
install.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.
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 ```
Version: 1.2.1
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
Version: 1.6.0
...
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
Version: 1.1.0
Checking should be performed on sources prepared by ‘R CMD build’.
Version: 0.2
GNU make is a SystemRequirements.
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.
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').
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]
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 ```
Version: 3.0.4
installed size is 5.1Mb
sub-directories of 1Mb or more:
doc 1.9Mb
extdata 1.6Mb
libs 1.5Mb
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’
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
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’
Version: 0.1.0
Namespace in Imports field not imported from: ‘glmnet’
All declared Imports should be used.
Version: 0.6.0
Package unavailable to check Rd xrefs: ‘ICEbox’
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.
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.
Version: 1.0.0
Namespaces in Imports field not imported from:
‘MASS’ ‘devtools’ ‘ggplot2’ ‘haven’ ‘tidyverse’
All declared Imports should be used.
Version: 0.2.0
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
getS3method
Consider adding
importFrom("utils", "getS3method")
to your NAMESPACE file.
Version: 0.1.1
Namespaces in Imports field not imported from:
‘Rgraphviz’ ‘cluster’ ‘graph’
All declared Imports should be used.
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
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. ```
Version: 0.2.3.2
Package unavailable to check Rd xrefs: ‘RecordLinkage’
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. ```
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. ```
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’
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.
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
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.
Version: 1.4.0
installed size is 6.1Mb
sub-directories of 1Mb or more:
doc 5.2Mb
Version: 1.0.1
Namespace in Imports field not imported from: ‘gridExtra’
All declared Imports should be used.
Version: 1.8.2
Package suggested but not available for checking: ‘ggsubplot’
Version: 0.2.2
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
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. ```
Version: 2.0.0
Namespace in Imports field not imported from: ‘purrr’
All declared Imports should be used.
Version: 1.5
...
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.
Version: 1.6
installed size is 5.9Mb
sub-directories of 1Mb or more:
libs 5.4Mb
Version: 0.0.2
df02 <- data.frame(well = num_to_well(1:96),
df <- rbind(df01, df02)
b_grid(data = df$vals,
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
```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. ```
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.
Version: 1.1.0
Namespaces in Imports field not imported from:
‘hexbin’ ‘quantreg’
All declared Imports should be used.
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
Error: testthat unit tests failed Execution halted ```
Version: 0.1.1
Namespace in Imports field not imported from: ‘ROCR’
All declared Imports should be used.
Version: 0.4.4
Version: 3.0.0
Package unavailable to check Rd xrefs: ‘ecodist’
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 ```
Version: 1.8
installed size is 6.4Mb
sub-directories of 1Mb or more:
java 5.1Mb
Version: 1.3.2
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
Version: 0.1.0
Namespace in Imports field not imported from: ‘testthat’
All declared Imports should be used.
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 ```
Version: 2.0.1
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
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.
Version: 0.9.1
installed size is 9.4Mb
sub-directories of 1Mb or more:
doc 1.2Mb
libs 7.4Mb
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 ```
...
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').
Version: 1.1.3
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.
prediction_errors: possible error in psf(data = dataIn1, n.ahead =
nextVal): unused argument (n.ahead = nextVal)
Version: 3.1.6
installed size is 13.3Mb
sub-directories of 1Mb or more:
libs 13.1Mb
Version: 0.2.0
Namespace in Imports field not imported from: ‘e1071’
All declared Imports should be used.
Version: 3.3
Package unavailable to check Rd xrefs: ‘sparr’
Version: 1.0.3
Error in .requirePackage(package) :
unable to find required package 'RCurl'
Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
Execution halted
Version: 0.0.7
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.
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.
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.
Version: 0.1.0
Namespace in Imports field not imported from: ‘R6’
All declared Imports should be used.
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.
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.
Version: 0.2.1
installed size is 22.9Mb
sub-directories of 1Mb or more:
libs 21.7Mb
Version: 2.0.0
Packages unavailable to check Rd xrefs: ‘binom’, ‘PropCIs’, ‘BlakerCI’, ‘prevalence’
Version: 3.1.1
installed size is 5.5Mb
sub-directories of 1Mb or more:
data 1.5Mb
libs 2.8Mb
Version: 0.2
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.
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
Version: 1.1.4
Note: found 4 marked UTF-8 strings
Version: 0.1-2
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.
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.
Version: 1.0.0
Namespace in Imports field not imported from: ‘raster’
All declared Imports should be used.
Version: 0.1.2
Note: found 5 marked UTF-8 strings
Version: 0.0.2
Namespaces in Imports field not imported from:
‘rtf’ ‘tidyverse’
All declared Imports should be used.
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').
Version: 0.92.0
installed size is 6.9Mb
sub-directories of 1Mb or more:
doc 3.8Mb
examples 2.3Mb
Version: 1.6.3
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 1.6Mb
extdata 2.7Mb
Version: 0.6.3
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output:
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 ```
Version: 1.14.0
...
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.
Version: 2.2.9
Package unavailable to check Rd xrefs: ‘gplots’
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.
Version: 0.2-5
installed size is 8.2Mb
sub-directories of 1Mb or more:
libs 7.8Mb
Version: 1.0.0
...
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.
Version: 0.1.0
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
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.
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
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.
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 ```
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’
Version: 0.1.0
Namespaces in Imports field not imported from:
‘MCMCpack’ ‘gridExtra’ ‘knitr’
All declared Imports should be used.
Version: 2.8.0
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.
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. ```
Version: 0.1.2
Namespaces in Imports field not imported from:
‘data.table’ ‘dplyr’ ‘lmerTest’
All declared Imports should be used.
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. ```
Version: 0.8.0
Note: found 2 marked UTF-8 strings
Version: 0.8.0
Note: found 1 marked UTF-8 string
Version: 2.2
installed size is 5.2Mb
sub-directories of 1Mb or more:
libs 3.7Mb
Version: 0.4
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.
Version: 0.9
Namespaces in Imports field not imported from:
‘MASS’ ‘dtplyr’
All declared Imports should be used.
Version: 1.4
checking re-building of vignette outputs ... WARNING
``
...
Loading required package: plotrix
Warning: Computation failed in
stat_boxplot():
there is no package called 'quantreg'
Warning: Computation failed in
stat_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: File
biblatex.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 ```
Version: 1.1.5
...
‘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.
Version: 0.3-1
Package unavailable to check Rd xrefs: ‘snow’
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
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’. ```
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: File
algorithm2e.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() ```
Version: 0.3.5
...
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.
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.
Version: 0.5.4
checking tests ... ``` ERROR Running the tests in ‘tests/test-all.R’ failed. Last 13 lines of output:
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 ```
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.
Version: 1.6.0
installed size is 5.0Mb
sub-directories of 1Mb or more:
data 2.8Mb
extdata 1.2Mb
Version: 1.1
Version: 0.2-4
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.
Version: 0.0-2
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.
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.
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').
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
Error: testthat unit tests failed Execution halted ```
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.
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
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: File
algorithm.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
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.
Version: 1.0.1
Namespace in Imports field not imported from: ‘ggplot2’
All declared Imports should be used.
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. ```
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.
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
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
Error: testthat unit tests failed Execution halted ```
checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘taxize’
Version: 0.3.7
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.
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’
Version: 2.1.5
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
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 ```
Version: 2.1.2
checking re-building of vignette outputs ... WARNING
``
Error in re-building vignettes:
...
! LaTeX Error: File
algorithm2e.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 ```
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
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').
Version: 1.4.3
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.6Mb
Version: 1.0.0
...
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.
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’
Version: 1.2.6
installed size is 5.2Mb
sub-directories of 1Mb or more:
java 4.5Mb
Version: 5.1-1
Packages unavailable to check Rd xrefs: ‘multiwayvcov’, ‘treatSens’
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
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.
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
Error: testthat unit tests failed Execution halted ```
Version: 0.1.4
Namespaces in Imports field not imported from:
‘cowplot’ ‘ggplot2’ ‘microbenchmark’ ‘reshape2’
All declared Imports should be used.
Version: 0.1.0
checking tests ...
``
ERROR
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
bb$latitude inherits from
numericnot
character`.
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 ```
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
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
Version: 0.5.1
installed size is 6.4Mb
sub-directories of 1Mb or more:
libs 5.9Mb
Version: 0.99.6
Namespace in Imports field not imported from: ‘data.table’
All declared Imports should be used.
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 ```
Version: 0.1.0
Namespace in Imports field not imported from: ‘matrixcalc’
All declared Imports should be used.
Version: 1.5
installed size is 10.3Mb
sub-directories of 1Mb or more:
data 2.3Mb
libs 6.5Mb
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 ```
Version: 0.55
installed size is 9.3Mb
sub-directories of 1Mb or more:
libs 8.5Mb
Version: 1.4.4
installed size is 5.4Mb
sub-directories of 1Mb or more:
extdata 4.5Mb
Version: 1.2
GNU make is a SystemRequirements.
Version: 1.10.2
.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.
Version: 0.1-6
installed size is 5.3Mb
sub-directories of 1Mb or more:
libs 5.1Mb
Version: 1.0.0
Namespace in Imports field not imported from: ‘Rcpp’
All declared Imports should be used.
Version: 0.9.11
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.
Version: 0.2.1
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.
Version: 0.3.0
Namespace in Imports field not imported from: ‘utils’
All declared Imports should be used.
Version: 1.2.0
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.
Version: 0.6.1
installed size is 5.0Mb
sub-directories of 1Mb or more:
libs 2.7Mb
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’
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
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’
Version: 0.1.10
x
, xend
are dates/times and must be stored as POSIXct, not POSIXlt
Execution halted
```installed size is 5.6Mb
sub-directories of 1Mb or more:
libs 4.3Mb
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
Error: testthat unit tests failed Execution halted ```
Version: 0.1.0
Note: found 18627 marked UTF-8 strings
Version: 1.6.0
checking examples ... ERROR ``` ...
MET|4233
) %>% 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)",
boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
boxplotTCGA(ACC_BLCA_BRCA_OV.rnaseq, "reorder(cohort,log1p(MET), median)", "log1p(MET)",
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’
Version: 0.4-11
...
.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.
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 ```
Version: 1.3
Namespace in Imports field not imported from: ‘R6’
All declared Imports should be used.
Version: 0.6.0
Note: found 113868 marked UTF-8 strings
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.
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 ```
Version: 0.2.3.1.0
installed size is 49.2Mb
sub-directories of 1Mb or more:
libs 48.4Mb
Version: 0.1.3
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.
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.
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
Version: 1.0.3
Note: found 6 marked UTF-8 strings
Version: 1.14.0
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.
Version: 1.4.2
Error in re-building vignettes:
...
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
there is no package called ‘BiocStyle’
Execution halted
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.
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. ```
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.
Version: 1.4.1
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’
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.
Version: 1.0
Namespaces in Imports field not imported from:
‘Rcpp’ ‘testthat’
All declared Imports should be used.
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.
Version: 0.1-3
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
runif
Consider adding
importFrom("stats", "runif")
to your NAMESPACE file.
Version: 5.0.4
installed size is 5.3Mb
sub-directories of 1Mb or more:
libs 2.1Mb
Version: 0.7.1.0
Namespace in Imports field not imported from: ‘grDevices’
All declared Imports should be used.
Version: 0.3-5
...
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.
Version: 2.0.5
Package suggested but not available for checking: ‘rpanel’
Version: 1.0.1
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.
Version: 1.15.0
Package suggested but not available for checking: ‘fanovaGraph’
Version: 2.2.0
...
[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
Version: 1.3-0
Namespaces in Imports field not imported from:
‘SnowballC’ ‘XML’ ‘mgcv’
All declared Imports should be used.
Version: 1.0.0
Namespaces in Imports field not imported from:
‘lexicon’ ‘syuzhet’
All declared Imports should be used.
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
Version: 1.6.0
...
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').
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. ```
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: File
algorithm2e.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 ```
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.
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$panel.ontop) { : argument is of length zero Calls: ... print.ggplot -> ggplot_gtable -> -> f -> lapply -> FUN Execution halted ```
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: | |=================================================================== | 96% | |==================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 100% testthat results ================================================================ OK: 210 SKIPPED: 0 FAILED: 2
Error: testthat unit tests failed Execution halted ```
installed size is 6.0Mb
sub-directories of 1Mb or more:
libs 5.0Mb
Version: 0.5-5
checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
...
Warning in engine$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
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
Error: testthat unit tests failed Execution halted ```
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.
Version: 0.1.8
Note: found 2 marked UTF-8 strings
Version: 1.0.5
installed size is 7.8Mb
sub-directories of 1Mb or more:
www 6.5Mb
Version: 1.2.3
Namespaces in Imports field not imported from:
‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
‘xtable’
All declared Imports should be used.
Version: 1.0.1
Namespaces in Imports field not imported from:
‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
‘tools’
All declared Imports should be used.
Version: 2.1.3
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggplot2’ ‘viridis’
All declared Imports should be used.
Version: 0.2.2
Namespace in Imports field not imported from: ‘dplyr’
All declared Imports should be used.
Version: 1.14.0
...
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.
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 ```
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.
Version: 0.5.4
Package suggested but not available for checking: ‘tmlenet’
Version: 0.2.1
Packages unavailable to check Rd xrefs: ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’
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.
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. ```
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
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.
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’
Version: 2.6.2
Package suggested but not available for checking: ‘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’
Version: 0.12.0
Packages unavailable to check Rd xrefs: ‘sjPlot’, ‘MuMIn’, ‘piecewiseSEM’
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
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.
Version: 1.5.1
Package suggested but not available for checking: ‘rPython’
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: File
algorithm2e.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 ```
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
Version: 0.7.3
Note: found 833 marked UTF-8 strings
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.
Version: 1.2.0
Note: found 145 marked UTF-8 strings
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').
Version: 2.12.1
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘NMF’
A package should be listed in only one of these fields.
Version: 0.7.26
...
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.
Version: 0.6.4
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.
Version: 1.0
Namespaces in Imports field not imported from:
‘moments’ ‘poweRlaw’
All declared Imports should be used.
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’
Version: 1.3.0
Namespace in Imports field not imported from: ‘maptools’
All declared Imports should be used.
Version: 1.7.4
.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
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: File
algorithmic.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 ```
Version: 2.1.1
Namespace in Imports field not imported from: ‘sp’
All declared Imports should be used.
Version: 1.0.3
Error in re-building vignettes:
...
Error: processing vignette 'splatter.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
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
Version: 0.9.5
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.
Version: 1.10.0
Malformed Description field: should contain one or more complete sentences.
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. ```
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.
Version: 1.2.2
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.
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
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.
Version: 0.1.1
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggplot2’ ‘stringr’
All declared Imports should be used.
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.
Version: 0.1.0
Namespaces in Imports field not imported from:
‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
All declared Imports should be used.
Version: 1.1.1
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.
Version: 1.6.0
...
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').
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’
Version: 0.2.0
Package unavailable to check Rd xrefs: ‘truncdist’
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’
Version: 0.9.1
Namespaces in Imports field not imported from:
‘Biobase’ ‘broom’ ‘data.table’ ‘magrittr’ ‘pander’ ‘png’ ‘readr’
‘survsim’ ‘testthat’
All declared Imports should be used.
Version: 0.4.1
installed size is 5.2Mb
sub-directories of 1Mb or more:
doc 4.9Mb
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’
Version: 1.0.0
Error in re-building vignettes:
...
Error: processing vignette 'swfdrTutorial.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
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 ```
Version: 1.6.0
...
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').
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: File
algorithm.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 ```
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’
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
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.
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 |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 argument from the column id above. Project TCGA-ACC was not found.
Calls: GDCquery -> checkProjectInput
Execution halted
checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: testthat results ================================================================ OK: 123 SKIPPED: 0 FAILED: 15
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’
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’
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. ```
Version: 1.0.0
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').
Version: 0.11
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.
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.
Version: 2.10
R CMD check timed out
checking package dependencies ... NOTE
Package suggested but not available for checking: ‘R2wd’
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.
Version: 0.3
...
>
> # 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
Version: 0.2.2
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.
Version: 1.2.1
Namespaces in Imports field not imported from:
‘dbplyr’ ‘reprex’ ‘rlang’
All declared Imports should be used.
Version: 0.10-1
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
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
Version: 0.1.1
Namespace in Imports field not imported from: ‘base’
All declared Imports should be used.
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
Version: 1.6.0
...
‘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.
Version: 1.32
Package which this enhances but not available for checking: ‘zoo’
Version: 1.10
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.5Mb
doc 3.3Mb
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
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 ```
Package unavailable to check Rd xrefs: ‘igraph’
Version: 0.3
Namespaces in Imports field not imported from:
‘R6’ ‘jmvcore’
All declared Imports should be used.
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.
Version: 0.1.1
Package suggested but not available for checking: ‘rmongodb’
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.
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.. ```
Version: 0.0.5
Namespace in Imports field not imported from: ‘colorspace’
All declared Imports should be used.
Version: 2.0-0
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
runif
Consider adding
importFrom("stats", "runif")
to your NAMESPACE file.
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’
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
Version: 1.0.0
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.
Version: 1.14.0
...
‘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.
Version: 1.0
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.
Version: 1.2.0
File
inst/LICENSE
will install at top-level and is not mentioned in the DESCRIPTION file.
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’
Version: 1.2.1
Malformed Description field: should contain one or more complete sentences.
Version: 1.2.0
checking examples ... ERROR ``` ... > # Pre-process variants > vcf <- VariantAnnotation::readVcf(
vcf <- VariantAnnotation::expand(vcf, row.names = TRUE) vcf <- addFrequencies(vcf, "super_pop")
Example usage ----
if (requireNamespace("EnsDb.Hsapiens.v75")){
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
Error: testthat unit tests failed Execution halted ```
checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... Overwriting INFO keys in data:
Version: 1.0.6
Error in re-building vignettes:
...
Error: processing vignette 'twoddpcr.Rmd' failed with diagnostics:
path for html_dependency not found:
Execution halted
Version: 0.9.0
Note: found 5 marked UTF-8 strings
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') ```
Version: 0.2.0
Note: found 4494 marked UTF-8 strings
Version: 1.3.3
installed size is 8.4Mb
sub-directories of 1Mb or more:
doc 7.9Mb
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
Version: 1.2.0
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.
Version: 0.3.1
installed size is 15.5Mb
sub-directories of 1Mb or more:
libs 14.1Mb
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
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 ```
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
```
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. ```
Version: 0.7-1
Packages unavailable to check Rd xrefs: ‘coin’, ‘alr3’, ‘Hmisc’
Version: 1.5.0
installed size is 11.3Mb
sub-directories of 1Mb or more:
doc 3.0Mb
libs 7.5Mb
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: File
algorithm.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 ```
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()
usingbins = 30
. Pick better value withbinwidth
. 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 -------------------------------------------------------------------------
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
Namespaces in Imports field not imported from:
‘maptools’ ‘rgeos’
All declared Imports should be used.
Version: 0.2.0
Namespace in Imports field not imported from: ‘nlme’
All declared Imports should be used.
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.
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. ```
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 ```
Version: 1.2.0
Namespaces in Imports field not imported from:
‘iterators’ ‘knitr’ ‘testthat’
All declared Imports should be used.
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
Version: 0.2.0
installed size is 46.9Mb
sub-directories of 1Mb or more:
libs 46.2Mb
Version: 0.3.4
installed size is 5.6Mb
sub-directories of 1Mb or more:
libs 5.0Mb
Version: 1.0.1
Namespaces in Imports field not imported from:
‘R6’ ‘WRS2’ ‘ggplot2’
All declared Imports should be used.
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. ```
Version: 0.10.3
installed size is 12.3Mb
sub-directories of 1Mb or more:
doc 12.1Mb
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.
Version: 0.1.1
Note: found 1371 marked UTF-8 strings
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.
Version: 0.1.0
Namespace in Imports field not imported from: ‘methods’
All declared Imports should be used.
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
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.
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.
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 ```
Version: 1.1.0
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.
Version: 0.2.6
Namespace in Imports field not imported from: ‘mgcv’
All declared Imports should be used.
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.
Version: 0.6-4
installed size is 11.9Mb
sub-directories of 1Mb or more:
libs 11.3Mb
Version: 0.2-13
installed size is 11.7Mb
sub-directories of 1Mb or more:
java 9.7Mb
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 $prob no.1
Filtering data by EVID == 0
Quitting from lines 76-87 (customize_plots.Rmd)
Error: processing vignette 'customize_plots.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Namespace in Imports field not imported from: ‘gridExtra’
All declared Imports should be used.
Version: 3.3.2
Error in re-building vignettes:
...
Warning in engine$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
Version: 2.0.3
Namespace in Imports field not imported from: ‘graphics’
All declared Imports should be used.
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 ```
Version: 0.0-1
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.
Version: 0.1.7
Namespace in Imports field not imported from: ‘rootSolve’
All declared Imports should be used.
Version: 0.5.8
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.
Package suggested but not available for checking: ‘zdat’
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’
Version: 1.0.2
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. ```
Version: 0.1.0
Namespaces in Imports field not imported from:
‘dplyr’ ‘ggplot2’ ‘lubridate’
All declared Imports should be used.
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