Alicia Schep
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/chromVAR |
| Branch: RELEASE_3_11 |
| Last Commit: 08e915a |
| Last Changed Date: 2020-04-27 15:11:06 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:16 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE chromVAR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 297/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromVAR 1.10.0 Alicia Schep
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
| Package: chromVAR |
| Version: 1.10.0 |
| Command: rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromVAR.buildbin-libdir chromVAR_1.10.0.tar.gz |
| StartedAt: 2020-10-17 10:06:35 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 10:09:16 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 160.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: chromVAR_1.10.0.zip |
| PackageFileSize: 2.474 MiB |
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### Running command:
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### rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromVAR.buildbin-libdir chromVAR_1.10.0.tar.gz
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install for i386
* installing *source* package 'chromVAR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwm_similarity.cpp -o pwm_similarity.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for( int j=0; j < X.n_rows; j++ ) {
~~^~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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-3.11-bioc/tmpdir/RtmpEj0Kh0/R.INSTALL302c63f65a9f/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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwm_similarity.cpp -o pwm_similarity.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c utils.cpp -o utils.o
utils.cpp: In function 'Rcpp::NumericVector row_sds(arma::mat&, bool)':
utils.cpp:12:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
for( int j=0; j < X.n_rows; j++ ) {
~~^~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o chromVAR.dll tmp.def RcppExports.o pwm_similarity.o utils.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/chromVAR.buildbin-libdir/chromVAR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'chromVAR' as chromVAR_1.10.0.zip
* DONE (chromVAR)