############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/BitSeq_1.36.0.tar.gz && rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BitSeq.buildbin-libdir BitSeq_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BitSeq_1.36.0.zip && rm BitSeq_1.36.0.tar.gz BitSeq_1.36.0.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 46 1021k 46 478k 0 0 950k 0 0:00:01 --:--:-- 0:00:01 949k 100 1021k 100 1021k 0 0 1276k 0 --:--:-- --:--:-- --:--:-- 1276k 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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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;icore.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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3.13-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-3~1.13-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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;icore.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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'C:/Users/biocbuild/bbs-3.13-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-3.13-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-3~1.13-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'BitSeq' as BitSeq_1.36.0.zip * DONE (BitSeq) * installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library' package 'BitSeq' successfully unpacked and MD5 sums checked