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INSTALL report for chromVAR on tokay2

This page was generated on 2019-10-16 12:39:35 -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:\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
StartedAt: 2019-10-15 20:33:13 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:35:19 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 125.4 seconds
RetCode: 0
Status:  OK  

Command output

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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
###
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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