Antti Honkela
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/BitSeq |
| git_branch: master |
| git_last_commit: ac331d3 |
| git_last_commit_date: 2021-10-26 12:02:43 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:03 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the BitSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BitSeq.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 198/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BitSeq 1.39.0 (landing page) Antti Honkela
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: BitSeq |
| Version: 1.39.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BitSeq |
| StartedAt: 2022-03-17 15:49:15 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 15:50:13 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 58.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL BitSeq
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'BitSeq' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c ArgumentParser.cpp -o ArgumentParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c CollapsedSampler.cpp -o CollapsedSampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c FileHeader.cpp -o FileHeader.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GibbsParameters.cpp -o GibbsParameters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GibbsSampler.cpp -o GibbsSampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c MyTimer.cpp -o MyTimer.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c PosteriorSamples.cpp -o PosteriorSamples.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c R_init_BitSeq.cpp -o R_init_BitSeq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Rhtslib_sam.c -o Rhtslib_sam.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Sampler.cpp -o Sampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c TagAlignments.cpp -o TagAlignments.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c TranscriptExpression.cpp -o TranscriptExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c TranscriptInfo.cpp -o TranscriptInfo.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c TranscriptSequence.cpp -o TranscriptSequence.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c common.cpp -o common.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c estimateDE.cpp -o estimateDE.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c estimateHyperPar.cpp -o estimateHyperPar.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c estimateVBExpression.cpp -o estimateVBExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c getGeneExpression.cpp -o getGeneExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c getVariance.cpp -o getVariance.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c lowess.cpp -o lowess.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c parseAlignment.cpp -o parseAlignment.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD -I. -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 D:/biocbuild/bbs-3.15-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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-BitSeq/00new/BitSeq/libs/x64
** 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
* DONE (BitSeq)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'RCM' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'TCseq' is missing or broken
done