Alicia Schep
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/chromVAR |
| Branch: RELEASE_3_10 |
| Last Commit: 7a74fdd |
| Last Changed Date: 2019-10-29 13:10:49 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:29:13 -0400 (Wed, 15 Apr 2020).
| Package 289/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| chromVAR 1.8.0 Alicia Schep
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: chromVAR |
| Version: 1.8.0 |
| Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/chromVAR_1.8.0.tar.gz && rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromVAR.buildbin-libdir chromVAR_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL chromVAR_1.8.0.zip && rm chromVAR_1.8.0.tar.gz chromVAR_1.8.0.zip |
| StartedAt: 2020-04-14 19:57:51 -0400 (Tue, 14 Apr 2020) |
| EndedAt: 2020-04-14 20:00:01 -0400 (Tue, 14 Apr 2020) |
| EllapsedTime: 130.2 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/chromVAR_1.8.0.tar.gz && rm -rf chromVAR.buildbin-libdir && mkdir chromVAR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chromVAR.buildbin-libdir chromVAR_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL chromVAR_1.8.0.zip && rm chromVAR_1.8.0.tar.gz chromVAR_1.8.0.zip
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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-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pwm_similarity.cpp -o pwm_similarity.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
** 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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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-3.10-bioc/tmpdir/RtmpURCj1x/R.INSTALL2170414e5c1d/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
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
** testing if installed package can be loaded from final location
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
** 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-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -c pwm_similarity.cpp -o pwm_similarity.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=core2 -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-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/chromVAR.buildbin-libdir/chromVAR/libs/x64
** testing if installed package can be loaded
No methods found in package 'IRanges' for request: 'score' when loading 'TFBSTools'
* MD5 sums
packaged installation of 'chromVAR' as chromVAR_1.8.0.zip
* DONE (chromVAR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'chromVAR' successfully unpacked and MD5 sums checked