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CHECK report for chromVAR on tokay2

This page was generated on 2019-10-16 12:39:36 -0400 (Wed, 16 Oct 2019).

Package 275/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chromVAR 1.6.0
Alicia Schep
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/chromVAR
Branch: RELEASE_3_9
Last Commit: 6305c5e
Last Changed Date: 2019-05-02 11:54:09 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chromVAR
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromVAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chromVAR_1.6.0.tar.gz
StartedAt: 2019-10-16 02:40:12 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:50:10 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 598.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: chromVAR.Rcheck
Warnings: 1

Command output

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##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:chromVAR.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings chromVAR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/chromVAR.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chromVAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chromVAR' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'chromVAR' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/chromVARDeviations-class.Rd:12: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/example_counts.Rd:11: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:16: file link 'getMatrixSet' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:25: file link 'getMatrixSet' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:26: file link 'JASPAR2016' in package 'JASPAR2016' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:19: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getPeaks.Rd:17: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:41: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:42: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:42: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:53: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/mini_counts.Rd:11: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/mini_ix.Rd:11: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/pwmDistance.Rd:27: file link 'PWMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/pwmDistance.Rd:28: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/chromVAR.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/chromVAR/libs/i386/chromVAR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.9-bioc/R/library/chromVAR/libs/x64/chromVAR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
deviationsCovariability 23.95   1.97   26.97
getJasparMotifs          7.94   0.30    8.24
pwmDistance              5.92   0.22    6.14
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
deviationsCovariability 25.20   1.36   26.66
getJasparMotifs          8.11   0.32    8.42
pwmDistance              5.50   0.19    5.69
computeVariability       5.19   0.10    5.32
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/chromVAR.Rcheck/00check.log'
for details.



Installation output

chromVAR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/chromVAR_1.6.0.tar.gz && rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromVAR.buildbin-libdir chromVAR_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL chromVAR_1.6.0.zip && rm chromVAR_1.6.0.tar.gz chromVAR_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  531k  100  531k    0     0  9396k      0 --:--:-- --:--:-- --:--:--  9.9M

install for i386

* installing *source* package 'chromVAR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pwm_similarity.cpp -o pwm_similarity.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int j=0; j < X.n_rows; j++ ) {
                     ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/chromVAR.buildbin-libdir/00LOCK-chromVAR/00new/chromVAR/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chromVAR'
    finding HTML links ... done
    addGCBias                               html  
    annotationMatches                       html  
    assembleKmers                           html  
    cbind-chromVARDeviations-method         html  
    chromVAR                                html  
    chromVARDeviations-class                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/chromVARDeviations-class.Rd:12: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    chromVAR_theme                          html  
    computeDeviations                       html  
    computeExpectations                     html  
    computeVariability                      html  
    counts                                  html  
    deviationScores                         html  
    deviations                              html  
    deviationsCovariability                 html  
    deviationsTsne                          html  
    differentialDeviations                  html  
    differentialVariability                 html  
    example_counts                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/example_counts.Rd:11: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    filterPeaks                             html  
    filterSamples                           html  
    filterSamplesPlot                       html  
    getAnnotationCorrelation                html  
    getAnnotationSynergy                    html  
    getAnnotations                          html  
    getBackgroundPeaks                      html  
    getCisGroups                            html  
    getCounts                               html  
    getFragmentsPerPeak                     html  
    getFragmentsPerSample                   html  
    getJasparMotifs                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:16: file link 'getMatrixSet' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:25: file link 'getMatrixSet' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:26: file link 'JASPAR2016' in package 'JASPAR2016' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getJasparMotifs.Rd:19: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
    getPeaks                                html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/getPeaks.Rd:17: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    getPermutedData                         html  
    getSampleCorrelation                    html  
    getSampleDepths                         html  
    getSampleDistance                       html  
    getTotalFragments                       html  
    makeBiasBins                            html  
    makePermutedSets                        html  
    matchKmers                              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:41: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:42: file link 'DNAStringSet' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:42: file link 'DNAString' in package 'Biostrings' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/matchKmers.Rd:53: file link 'GenomicRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    mini_counts                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/mini_counts.Rd:11: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    mini_dev                                html  
    mini_ix                                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/mini_ix.Rd:11: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    plotDeviationsTsne                      html  
    plotKmerMismatch                        html  
    plotVariability                         html  
    pwmDistance                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/pwmDistance.Rd:27: file link 'PWMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpUZt83i/R.INSTALL13a4f743afe/chromVAR/man/pwmDistance.Rd:28: file link 'PFMatrixList' in package 'TFBSTools' does not exist and so has been treated as a topic
    rbind-chromVARDeviations-method         html  
    readNarrowpeaks                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'chromVAR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pwm_similarity.cpp -o pwm_similarity.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for( int j=0; j < X.n_rows; j++ ) {
                     ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/chromVAR.buildbin-libdir/chromVAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromVAR' as chromVAR_1.6.0.zip
* DONE (chromVAR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'chromVAR' successfully unpacked and MD5 sums checked

Tests output

chromVAR.Rcheck/tests_i386/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(chromVAR)

> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
== testthat results  ===========================================================
[ OK: 65 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  20.59    3.84   24.43 

chromVAR.Rcheck/tests_x64/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(chromVAR)

> BiocParallel::register(BiocParallel::SerialParam())
> test_check("chromVAR")
== testthat results  ===========================================================
[ OK: 65 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  21.06    1.65   22.71 

Example timings

chromVAR.Rcheck/examples_i386/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias1.000.091.10
annotationMatches0.020.000.02
chromVAR_theme0.030.000.03
computeDeviations4.610.154.99
computeExpectations0.030.020.04
computeVariability3.390.513.91
counts000
deviationScores000
deviations0.020.000.01
deviationsCovariability23.95 1.9726.97
deviationsTsne0.160.030.19
differentialDeviations0.010.000.02
differentialVariability0.040.000.03
example_counts000
filterPeaks0.260.000.27
filterSamples0.090.000.09
filterSamplesPlot0.150.000.15
getAnnotations0.480.000.48
getBackgroundPeaks3.000.123.12
getCisGroups0.060.000.06
getCounts3.630.844.67
getFragmentsPerPeak0.010.000.02
getFragmentsPerSample0.020.000.01
getJasparMotifs7.940.308.24
getPeaks0.080.020.09
getPermutedData4.100.234.34
getSampleCorrelation0.020.000.02
getSampleDepths0.140.020.16
getSampleDistance0.020.000.01
getTotalFragments0.010.000.02
makeBiasBins0.060.000.06
makePermutedSets1.070.071.16
matchKmers1.430.101.53
mini_counts0.000.010.01
mini_dev000
mini_ix0.020.000.02
plotVariability4.810.024.83
pwmDistance5.920.226.14
rbind-chromVARDeviations-method0.070.000.06

chromVAR.Rcheck/examples_x64/chromVAR-Ex.timings

nameusersystemelapsed
addGCBias0.940.030.97
annotationMatches0.100.000.11
chromVAR_theme0.030.000.03
computeDeviations4.360.294.65
computeExpectations0.030.000.03
computeVariability5.190.105.32
counts0.020.000.02
deviationScores0.010.000.02
deviations000
deviationsCovariability25.20 1.3626.66
deviationsTsne0.140.030.17
differentialDeviations0.020.000.02
differentialVariability0.050.000.04
example_counts000
filterPeaks0.280.000.28
filterSamples0.080.000.08
filterSamplesPlot0.140.020.16
getAnnotations0.560.010.58
getBackgroundPeaks1.710.101.81
getCisGroups0.070.010.08
getCounts3.370.814.19
getFragmentsPerPeak0.020.000.02
getFragmentsPerSample0.010.000.01
getJasparMotifs8.110.328.42
getPeaks0.110.000.11
getPermutedData4.690.234.94
getSampleCorrelation0.010.000.02
getSampleDepths0.110.000.10
getSampleDistance0.020.000.02
getTotalFragments0.020.000.02
makeBiasBins0.040.000.04
makePermutedSets0.770.080.85
matchKmers1.290.091.39
mini_counts0.000.020.01
mini_dev000
mini_ix000
plotVariability4.660.004.66
pwmDistance5.500.195.69
rbind-chromVARDeviations-method0.080.000.07