Antti Honkela
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/BitSeq |
| Branch: RELEASE_3_11 |
| Last Commit: 73e8dfc |
| Last Changed Date: 2020-04-27 14:29:18 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:10 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE BitSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 191/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BitSeq 1.32.0 Antti Honkela
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: BitSeq |
| Version: 1.32.0 |
| Command: rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BitSeq.buildbin-libdir BitSeq_1.32.0.tar.gz |
| StartedAt: 2020-10-17 09:58:20 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 10:01:39 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 199.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: BitSeq_1.32.0.zip |
| PackageFileSize: 4.191 MiB |
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###
### Running command:
###
### rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BitSeq.buildbin-libdir BitSeq_1.32.0.tar.gz
###
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install for i386
* installing *source* package 'BitSeq' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ArgumentParser.cpp -o ArgumentParser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CollapsedSampler.cpp -o CollapsedSampler.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileHeader.cpp -o FileHeader.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GibbsParameters.cpp -o GibbsParameters.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GibbsSampler.cpp -o GibbsSampler.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MyTimer.cpp -o MyTimer.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PosteriorSamples.cpp -o PosteriorSamples.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_BitSeq.cpp -o R_init_BitSeq.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
ReadDistribution.cpp:923: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
ReadDistribution.cpp:928: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
ReadDistribution.cpp: In function 'long int ns_rD::countDeletions(const bam1_t*)':
ReadDistribution.cpp:66:18: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
for(long i=0;i<samA->core.n_cigar;i++){
~^~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In function 'bool ns_rD::getCigarOp(const bam1_t*, long int, long int*, long int*)':
ReadDistribution.cpp:79:29: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
if((cigarI<0) || (cigarI >= samA->core.n_cigar)) return false;
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^~~~~~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)':
ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_sam.c -o Rhtslib_sam.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Sampler.cpp -o Sampler.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:count)
SimpleSparse.cpp:45: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
SimpleSparse.cpp:57: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TagAlignments.cpp -o TagAlignments.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TranscriptExpression.cpp -o TranscriptExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TranscriptInfo.cpp -o TranscriptInfo.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TranscriptSequence.cpp -o TranscriptSequence.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:96: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(err) reduction(+:totalError)
VariationalBayes.cpp:103: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:110: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:A,B)
VariationalBayes.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:C)
VariationalBayes.cpp:172: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,phiGradPhiSum_r,natGrad_i,gradGamma_i) reduction(+:squareNorm,valBeta,valBetaDiv)
VariationalBayes.cpp:219: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:224: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:238: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c common.cpp -o common.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateDE.cpp -o estimateDE.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
estimateExpression.cpp:244: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateHyperPar.cpp -o estimateHyperPar.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateVBExpression.cpp -o estimateVBExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getGeneExpression.cpp -o getGeneExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getVariance.cpp -o getVariance.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lowess.cpp -o lowess.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parseAlignment.cpp -o parseAlignment.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transposeFiles.cpp -o transposeFiles.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Rhtslib_bam_plbuf.o Rhtslib_sam.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -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/BitSeq.buildbin-libdir/00LOCK-BitSeq/00new/BitSeq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BitSeq'
finding HTML links ... done
BitSeq-package html
estimateDE html
estimateExpression html
estimateHyperPar html
estimateVBExpression html
getDE html
getExpression html
getGeneExpression html
getMeanVariance html
loadSamples html
parseAlignment html
transcriptInfo html
transcriptInfoFile 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 'BitSeq' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ArgumentParser.cpp -o ArgumentParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c CollapsedSampler.cpp -o CollapsedSampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FileHeader.cpp -o FileHeader.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GibbsParameters.cpp -o GibbsParameters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GibbsSampler.cpp -o GibbsSampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c MyTimer.cpp -o MyTimer.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c PosteriorSamples.cpp -o PosteriorSamples.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c R_init_BitSeq.cpp -o R_init_BitSeq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
ReadDistribution.cpp:923: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
ReadDistribution.cpp:928: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
ReadDistribution.cpp: In function 'long int ns_rD::countDeletions(const bam1_t*)':
ReadDistribution.cpp:66:18: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
for(long i=0;i<samA->core.n_cigar;i++){
~^~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In function 'bool ns_rD::getCigarOp(const bam1_t*, long int, long int*, long int*)':
ReadDistribution.cpp:79:29: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
if((cigarI<0) || (cigarI >= samA->core.n_cigar)) return false;
~~~~~~~^~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^~~~~~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)':
ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
(! frag->second->core.flag & BAM_FREVERSE))){
^~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_sam.c -o Rhtslib_sam.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Sampler.cpp -o Sampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:count)
SimpleSparse.cpp:45: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
SimpleSparse.cpp:57: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TagAlignments.cpp -o TagAlignments.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TranscriptExpression.cpp -o TranscriptExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TranscriptInfo.cpp -o TranscriptInfo.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c TranscriptSequence.cpp -o TranscriptSequence.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:96: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(err) reduction(+:totalError)
VariationalBayes.cpp:103: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:110: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:A,B)
VariationalBayes.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:C)
VariationalBayes.cpp:172: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,phiGradPhiSum_r,natGrad_i,gradGamma_i) reduction(+:squareNorm,valBeta,valBetaDiv)
VariationalBayes.cpp:219: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:224: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
VariationalBayes.cpp:238: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c common.cpp -o common.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateDE.cpp -o estimateDE.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
estimateExpression.cpp:244: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateHyperPar.cpp -o estimateHyperPar.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c estimateVBExpression.cpp -o estimateVBExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getGeneExpression.cpp -o getGeneExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getVariance.cpp -o getVariance.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c lowess.cpp -o lowess.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c parseAlignment.cpp -o parseAlignment.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transposeFiles.cpp -o transposeFiles.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Rhtslib_bam_plbuf.o Rhtslib_sam.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -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/BitSeq.buildbin-libdir/BitSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BitSeq' as BitSeq_1.32.0.zip
* DONE (BitSeq)