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revdep/problems.md

assertthat: Easy Pre and Post Assertions

afmToolkit

Version: 0.0.1

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

antaresViz

Version: 0.15.0

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: R 2.1Mb doc 2.0Mb htmlwidgets 1.1Mb

AntWeb

Version: 0.7

checking R code for possible problems ... NOTE aw_map: no visible global function definition for ‘browseURL’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/AntWeb/new/AntWeb.Rcheck/00_pkg_src/AntWeb/R/aw_map.R:52) Undefined global functions or variables: browseURL Consider adding importFrom("utils", "browseURL") to your NAMESPACE file.

auk

Version: 0.3.2

checking data for non-ASCII characters ... NOTE Note: found 552 marked UTF-8 strings

awsjavasdk

Version: 0.2.0

checking whether package ‘awsjavasdk’ can be installed ... ERROR Installation failed. See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/awsjavasdk/new/awsjavasdk.Rcheck/00install.out’ for details.

* installing *source* package ‘awsjavasdk’ ...
** package ‘awsjavasdk’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so':
  dlopen(/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so
  Reason: image not found
ERROR: lazy loading failed for package ‘awsjavasdk’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/awsjavasdk/new/awsjavasdk.Rcheck/awsjavasdk’

* installing *source* package ‘awsjavasdk’ ...
** package ‘awsjavasdk’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error : .onLoad failed in loadNamespace() for 'rJava', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so':
  dlopen(/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so, 6): Library not loaded: /Library/Java/JavaVirtualMachines/jdk-11.0.1.jdk/Contents/Home/lib/server/libjvm.dylib
  Referenced from: /Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/awsjavasdk/rJava/libs/rJava.so
  Reason: image not found
ERROR: lazy loading failed for package ‘awsjavasdk’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/awsjavasdk/old/awsjavasdk.Rcheck/awsjavasdk’

bigQueryR

Version: 0.4.0

checking package dependencies ... ERROR ``` Packages required but not available: ‘googleAuthR’ ‘googleCloudStorageR’

Packages suggested but not available for checking: ‘shiny’ ‘data.table’

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

binman

Version: 0.1.1

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

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

biofiles

Version: 1.0.0

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

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

BPRMeth

Version: 1.8.1

checking whether package ‘BPRMeth’ can be installed ... ERROR Installation failed. See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/BPRMeth/new/BPRMeth.Rcheck/00install.out’ for details.

* installing *source* package ‘BPRMeth’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘BPRMeth’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/BPRMeth/new/BPRMeth.Rcheck/BPRMeth’

* installing *source* package ‘BPRMeth’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/BPRMeth/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘BPRMeth’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/BPRMeth/old/BPRMeth.Rcheck/BPRMeth’

breathtestcore

Version: 0.4.6

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

bulletcp

Version: 1.0.0

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

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

CAGEfightR

Version: 1.2.0

checking package dependencies ... ERROR ``` Packages required but not available: ‘Matrix.utils’ ‘grr’ ‘GenomicFeatures’ ‘InteractionSet’ ‘GenomicInteractions’

Packages suggested but not available for checking: ‘org.Mm.eg.db’ ‘TxDb.Mmusculus.UCSC.mm9.knownGene’

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

CausalImpact

Version: 1.2.3

checking R code for possible problems ... NOTE ConstructModel: warning in AddDynamicRegression(ss, formula, data = data, sigma.mean.prior = sigma.mean.prior): partial argument match of 'sigma.mean.prior' to 'sigma.mean.prior.DEPRECATED' (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/CausalImpact/new/CausalImpact.Rcheck/00_pkg_src/CausalImpact/R/impact_model.R:232-233)

cicero

Version: 1.0.15

R CMD check timed out

checking R code for possible problems ... NOTE aggregate_nearby_peaks: no visible binding for global variable 'val' (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/aggregate.R:37) assemble_connections: no visible binding for global variable 'value' (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/runCicero.R:640-641) find_overlapping_ccans: no visible binding for global variable 'CCAN' (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/runCicero.R:919-922) generate_windows: no visible binding for global variable 'V1' (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/runCicero.R:663-667) plot_accessibility_in_pseudotime: no visible binding for global variable 'f_id' (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/cicero/new/cicero.Rcheck/00_pkg_src/cicero/R/plotting.R:676-695) Undefined global functions or variables: CCAN V1 f_id val value

circumplex

Version: 0.2.1

checking whether package ‘circumplex’ can be installed ... ERROR Installation failed. See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/circumplex/new/circumplex.Rcheck/00install.out’ for details.

* installing *source* package ‘circumplex’ ...
** package ‘circumplex’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘circumplex’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/circumplex/new/circumplex.Rcheck/circumplex’

* installing *source* package ‘circumplex’ ...
** package ‘circumplex’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/circumplex/RcppArmadillo/include" -I/usr/local/include  -fopenmp  -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘circumplex’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/circumplex/old/circumplex.Rcheck/circumplex’

citr

Version: 0.3.0

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

CTRE

Version: 0.1.0

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

DChIPRep

Version: 1.12.0

checking whether package ‘DChIPRep’ can be installed ... ERROR Installation failed. See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/DChIPRep/new/DChIPRep.Rcheck/00install.out’ for details.

* installing *source* package ‘DChIPRep’ ...
** R
** data
*** moving datasets to lazyload DB
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
** exec
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GO.db’
ERROR: lazy loading failed for package ‘DChIPRep’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/DChIPRep/new/DChIPRep.Rcheck/DChIPRep’

* installing *source* package ‘DChIPRep’ ...
** R
** data
*** moving datasets to lazyload DB
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
Warning: namespace ‘DChIPRep’ is not available and has been replaced
by .GlobalEnv when processing object ‘testData’
** exec
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GO.db’
ERROR: lazy loading failed for package ‘DChIPRep’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/DChIPRep/old/DChIPRep.Rcheck/DChIPRep’

DEP

Version: 1.4.1

checking installed package size ... NOTE installed size is 6.0Mb sub-directories of 1Mb or more: R 1.2Mb data 1.4Mb doc 3.1Mb

detrendr

Version: 0.6.0

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

disto

Version: 0.2.0

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

dplyr

Version: 0.8.0.1

checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: R 2.1Mb libs 3.0Mb
checking data for non-ASCII characters ... NOTE Note: found 4 marked UTF-8 strings

ecoengine

Version: 1.11.0

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

gastempt

Version: 0.4.4

checking installed package size ... NOTE installed size is 7.7Mb sub-directories of 1Mb or more: libs 7.2Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘methods’ ‘rstantools’ All declared Imports should be used.
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

GeneAccord

Version: 1.0.0

checking installed package size ... NOTE installed size is 11.2Mb sub-directories of 1Mb or more: data 3.0Mb doc 1.0Mb extdata 6.5Mb

GerminaR

Version: 1.2

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

glmmfields

Version: 0.1.2

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

googleAuthR

Version: 0.7.0

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

grattan

Version: 1.7.0.0

checking package dependencies ... NOTE Packages suggested but not available for checking: ‘taxstats’ ‘taxstats1516’

heatmaply

Version: 0.15.2

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: doc 4.6Mb
checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘d3heatmap’

highcharter

Version: 0.7.0

checking installed package size ... NOTE installed size is 9.2Mb sub-directories of 1Mb or more: doc 3.7Mb htmlwidgets 4.0Mb

HMP16SData

Version: 1.2.1

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

The following object is masked from 'package:stats':
```
cutree
```
======================================== circlize version 0.4.5 CRAN page: https://cran.r-project.org/package=circlize Github page: https://github.com/jokergoo/circlize Documentation: http://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite: Gu, Z. circlize implements and enhances circular visualization in R. Bioinformatics 2014. ========================================

Quitting from lines 58-71 (HMP16SData.Rmd) Error: processing vignette 'HMP16SData.Rmd' failed with diagnostics: there is no package called 'curatedMetagenomicData' Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘curatedMetagenomicData’
checking installed package size ... NOTE installed size is 19.1Mb sub-directories of 1Mb or more: doc 1.5Mb extdata 17.4Mb

huxtable

Version: 4.4.0

checking tests ... `` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Fontconfig error: "/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/huxtable/magick/etc/fonts/conf.d/90-synthetic.conf", line 6: invalid attribute 'version' Fontconfig error: Cannot load default config file [31m──[39m [31m1. Failure: huxreg copes with different models (@test-huxreg.R#31) [39m [31m───────────[39mhr <- huxreg(lm1, lm2, glm1)` produced warnings.

[31m──[39m [31m2. Failure: Data written in appropriate format (@test-openxlsx.R#101) [39m [31m────────[39m openxlsx::saveWorkbook(wb, file = "test-xlsx.xlsx", overwrite = TRUE) produced messages.

══ testthat results ═════════════════════════════════════════════════════════════ OK: 888 SKIPPED: 57 FAILED: 2 1. Failure: huxreg copes with different models (@test-huxreg.R#31) 2. Failure: Data written in appropriate format (@test-openxlsx.R#101)

Error: testthat unit tests failed Execution halted ```
checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: R 2.1Mb doc 2.9Mb

kdensity

Version: 1.0.0

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

MonetDBLite

Version: 0.6.0

R CMD check timed out

checking installed package size ... NOTE installed size is 6.1Mb sub-directories of 1Mb or more: libs 5.4Mb

nandb

Version: 2.0.0

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

nima

Version: 0.5.0

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

paramlink

Version: 1.1-2

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

perturbatr

Version: 1.2.1

checking installed package size ... NOTE installed size is 5.9Mb sub-directories of 1Mb or more: data 3.8Mb

phantasus

Version: 1.2.1

checking installed package size ... NOTE installed size is 14.9Mb sub-directories of 1Mb or more: doc 2.6Mb www 11.5Mb
checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'GEOquery:::getDirListing' 'opencpu:::rookhandler' 'opencpu:::tmp_root' 'opencpu:::win_or_mac' See the note in ?`:::` about the use of this operator.

pivot

Version: 18.4.17

checking package dependencies ... NOTE Package which this enhances but not available for checking: ‘odbc’
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘colorspace’ ‘lubridate’ All declared Imports should be used.

pkgcache

Version: 1.0.3

checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 1: read_packages_file(pf[1], mirror = "m1", repodir = "r1", platform = "source", rversion = "*") at testthat/test-packages-gz.R:88 2: as_tibble(read.dcf.gz(path)) at /Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/pkgcache/new/pkgcache.Rcheck/00_pkg_src/pkgcache/R/packages-gz.R:19 3: read.dcf.gz(path) at /Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/pkgcache/new/pkgcache.Rcheck/00_pkg_src/pkgcache/R/packages-gz.R:19 4: gzfile(x, open = "r") at /Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/pkgcache/new/pkgcache.Rcheck/00_pkg_src/pkgcache/R/utils.R:32

══ testthat results ═════════════════════════════════════════════════════════════ OK: 282 SKIPPED: 25 FAILED: 5 1. Error: load_primary_pkgs (@test-metadata-cache.R#177) 2. Error: update_replica_rds (@test-metadata-cache.R#236) 3. Error: read_packages_file (@test-packages-gz.R#63) 4. Error: packages_parse_deps (@test-packages-gz.R#71) 5. Error: merge_packages_data (@test-packages-gz.R#88)

Error: testthat unit tests failed Execution halted ```

prioritizr

Version: 4.0.2

checking package dependencies ... NOTE Packages suggested but not available for checking: ‘gurobi’ ‘Rsymphony’

qPLEXanalyzer

Version: 1.0.3

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

Loading required package: ProtGenerics

This is MSnbase version 2.8.3 Visit https://lgatto.github.io/MSnbase/ to get started.

Attaching package: 'MSnbase'

The following object is masked from 'package:stats':
```
smooth
```
The following object is masked from 'package:base':
```
trimws
```
Quitting from lines 67-71 (qPLEXanalyzer.rnw) Error: processing vignette 'qPLEXanalyzer.rnw' failed with diagnostics: there is no package called 'gridExtra' Execution halted ```
checking package dependencies ... NOTE Package suggested but not available for checking: ‘qPLEXdata’
checking R code for possible problems ... NOTE ... rliPlot: no visible binding for global variable ‘logInt’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/plots.R:599-621) rliPlot: no visible binding for global variable ‘medianLogInt’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/plots.R:599-621) summarizeIntensities: no visible binding for global variable ‘Accessions’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:55-60) summarizeIntensities: no visible binding for global variable ‘Sequences’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:55-60) summarizeIntensities: no visible binding for global variable ‘Accessions’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:62-68) summarizeIntensities: no visible binding for global variable ‘Count’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/qPLEXanalyzer/new/qPLEXanalyzer.Rcheck/00_pkg_src/qPLEXanalyzer/R/Allfunctions.R:62-68) Undefined global functions or variables: . Accessions AveExpr B Cor CorTxt Count GeneSymbol Grouping_column Intensity Mean Modifications PeptideID RawIntensity RowID SampleName Sequence Sequences Variance X Y adj.P.Val controlLogFoldChange group logFC logInt logIntensity meanscaledIntensity medianLogInt normalizedIntensities scaledIntensity scalingFactors x xend y yend
checking for unstated dependencies in vignettes ... NOTE 'library' or 'require' call not declared from: ‘gridExtra’

qualpalr

Version: 0.4.3

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

r511

Version: 0.1.1

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

raptr

Version: 0.1.3

checking package dependencies ... NOTE Package suggested but not available for checking: ‘gurobi’
checking installed package size ... NOTE installed size is 6.7Mb sub-directories of 1Mb or more: data 3.6Mb doc 1.4Mb

RBesT

Version: 1.3-7

checking installed package size ... NOTE installed size is 5.6Mb sub-directories of 1Mb or more: R 1.1Mb doc 1.9Mb libs 2.2Mb
checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements.

rmapzen

Version: 0.4.1

checking data for non-ASCII characters ... NOTE Note: found 31 marked UTF-8 strings

routr

Version: 0.3.0

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

rprime

Version: 0.1.0

checking R code for possible problems ... NOTE but_last: no visible global function definition for ‘head’ first: no visible global function definition for ‘head’ last: no visible global function definition for ‘tail’ preview_frames: no visible global function definition for ‘str’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rprime/new/rprime.Rcheck/00_pkg_src/rprime/R/preview.R:37) print.EprimeFrame: no visible global function definition for ‘str’ print.FrameList: no visible global function definition for ‘str’ Undefined global functions or variables: head str tail Consider adding importFrom("utils", "head", "str", "tail") to your NAMESPACE file.

rrd

Version: 0.2.1

checking whether package ‘rrd’ can be installed ... ERROR Installation failed. See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rrd/new/rrd.Rcheck/00install.out’ for details.

* installing *source* package ‘rrd’ ...
** package ‘rrd’ successfully unpacked and MD5 sums checked
** libs
ccache clang -Qunused-arguments  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
ccache clang -Qunused-arguments  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rrd.c -o rrd.o
rrd.c:1:10: fatal error: 'rrd.h' file not found
#include <rrd.h>
         ^~~~~~~
1 error generated.
make: *** [rrd.o] Error 1
ERROR: compilation failed for package ‘rrd’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rrd/new/rrd.Rcheck/rrd’

* installing *source* package ‘rrd’ ...
** package ‘rrd’ successfully unpacked and MD5 sums checked
** libs
ccache clang -Qunused-arguments  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
ccache clang -Qunused-arguments  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rrd.c -o rrd.o
rrd.c:1:10: fatal error: 'rrd.h' file not found
#include <rrd.h>
         ^~~~~~~
1 error generated.
make: *** [rrd.o] Error 1
ERROR: compilation failed for package ‘rrd’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/rrd/old/rrd.Rcheck/rrd’

RTCGA

Version: 1.12.1

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

Name: boxplotTCGA

Title: Create Boxplots for TCGA Datasets

Aliases: boxplotTCGA

** Examples

library(RTCGA.rnaseq) Error in library(RTCGA.rnaseq) : there is no package called ‘RTCGA.rnaseq’ Execution halted ```
checking tests ... ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(RTCGA) Welcome to the RTCGA (version: 1.12.1). > library(RTCGA.rnaseq) Error in library(RTCGA.rnaseq) : there is no package called 'RTCGA.rnaseq' Execution halted
checking package dependencies ... NOTE Packages suggested but not available for checking: ‘RTCGA.rnaseq’ ‘RTCGA.clinical’ ‘RTCGA.mutations’ ‘RTCGA.RPPA’ ‘RTCGA.mRNA’ ‘RTCGA.miRNASeq’ ‘RTCGA.methylation’ ‘RTCGA.CNV’ ‘RTCGA.PANCAN12’
checking R code for possible problems ... NOTE ... (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) ggbiplot: no visible binding for global variable ‘xvar’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) ggbiplot: no visible binding for global variable ‘yvar’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) ggbiplot: no visible binding for global variable ‘angle’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) ggbiplot: no visible binding for global variable ‘hjust’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) read.mutations: no visible binding for global variable ‘.’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:383) read.mutations: no visible binding for global variable ‘.’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:386) read.rnaseq: no visible binding for global variable ‘.’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:372-375) survivalTCGA: no visible binding for global variable ‘times’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/survivalTCGA.R:101-137) whichDateToUse: no visible binding for global variable ‘.’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/downloadTCGA.R:167-168) Undefined global functions or variables: . angle hjust muted times varname xvar yvar
checking Rd cross-references ... NOTE Packages unavailable to check Rd xrefs: ‘RTCGA.rnaseq’, ‘RTCGA.clinical’, ‘RTCGA.mutations’, ‘RTCGA.CNV’, ‘RTCGA.RPPA’, ‘RTCGA.mRNA’, ‘RTCGA.miRNASeq’, ‘RTCGA.methylation’

rvinecopulib

Version: 0.3.0.1.1

checking installed package size ... NOTE installed size is 8.1Mb sub-directories of 1Mb or more: include 2.5Mb libs 4.9Mb

sourceR

Version: 1.0.1

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

sparklyr

Version: 1.0.0

checking installed package size ... NOTE installed size is 6.8Mb sub-directories of 1Mb or more: R 4.1Mb java 1.5Mb

sss

Version: 0.1-0

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

testextra

Version: 0.1.0

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

textreuse

Version: 0.1.4

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

tidytransit

Version: 0.3.8

checking installed package size ... NOTE installed size is 5.3Mb sub-directories of 1Mb or more: extdata 4.4Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘here’ ‘htmltools’ ‘scales’ ‘stringr’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 41 marked UTF-8 strings

tricolore

Version: 1.2.0

checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘dplyr’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 88 marked UTF-8 strings

trread

Version: 0.2.7

checking installed package size ... NOTE installed size is 5.2Mb sub-directories of 1Mb or more: extdata 4.4Mb
checking dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘here’ ‘htmltools’ ‘scales’ ‘stringr’ All declared Imports should be used.
checking data for non-ASCII characters ... NOTE Note: found 41 marked UTF-8 strings

updog

Version: 1.0.1

checking whether package ‘updog’ can be installed ... ERROR Installation failed. See ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/updog/new/updog.Rcheck/00install.out’ for details.

* installing *source* package ‘updog’ ...
** package ‘updog’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/RcppArmadillo/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘updog’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/updog/new/updog.Rcheck/updog’

* installing *source* package ‘updog’ ...
** package ‘updog’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/Rcpp/include" -I"/Users/hadley/Documents/devtools/assertthat/revdep/library.noindex/updog/RcppArmadillo/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang: error: unsupported option '-fopenmp'
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘updog’
* removing ‘/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/updog/old/updog.Rcheck/updog’

wiggleplotr

Version: 1.6.1

checking examples ... ERROR ``` ... Loading required package: TxDb.Hsapiens.UCSC.hg38.knownGene 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")'.
```
Attaching package: ‘AnnotationDbi’

The following object is masked from ‘package:dplyr’:
```
select
```
orgdb = org.Hs.eg.db Error: object 'org.Hs.eg.db' not found Execution halted ```
checking for code/documentation mismatches ... WARNING Codoc mismatches from documentation object 'getGenotypePalette': getGenotypePalette Code: function(old = FALSE) Docs: function() Argument names in code not in docs: old
checking re-building of vignette outputs ... WARNING Error in re-building vignettes: ... Quitting from lines 18-28 (wiggleplotr.Rmd) Error: processing vignette 'wiggleplotr.Rmd' failed with diagnostics: there is no package called 'EnsDb.Hsapiens.v86' Execution halted
checking package dependencies ... NOTE Packages suggested but not available for checking: ‘EnsDb.Hsapiens.v86’ ‘org.Hs.eg.db’
checking R code for possible problems ... NOTE plotCoverage: no visible global function definition for ‘is’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:184) plotCoverage: no visible global function definition for ‘is’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:185) plotTranscripts: no visible global function definition for ‘is’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:33) plotTranscripts: no visible global function definition for ‘is’ (/Users/hadley/Documents/devtools/assertthat/revdep/checks.noindex/wiggleplotr/new/wiggleplotr.Rcheck/00_pkg_src/wiggleplotr/R/wiggleplotr.R:34) Undefined global functions or variables: is Consider adding importFrom("methods", "is") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods').

wordbankr

Version: 0.3.0

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

XKCDdata

Version: 0.1.0

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

ztype

Version: 0.1.0

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

hadley/assertthat documentation built on June 5, 2019, 2:02 p.m.

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Easy Pre and Post Assertions

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