BioC 3.5: CHECK report for BitSeq on tokay2
This page was generated on 2017-10-18 14:21:48 -0400 (Wed, 18 Oct 2017).
BitSeq 1.20.0
Antti Honkela , Panagiotis Papastamoulis
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/BitSeq | | Branch: RELEASE_3_5 | | Last Commit: da3cfa6 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
| Package: BitSeq
|
| Version: 1.20.0
|
| Command: rm -rf BitSeq.buildbin-libdir BitSeq.Rcheck && mkdir BitSeq.buildbin-libdir BitSeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.20.0.tar.gz >BitSeq.Rcheck\00install.out 2>&1 && cp BitSeq.Rcheck\00install.out BitSeq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BitSeq.buildbin-libdir --install="check:BitSeq-install.out" --force-multiarch --no-vignettes --timings BitSeq_1.20.0.tar.gz
|
| StartedAt: 2017-10-17 22:23:55 -0400 (Tue, 17 Oct 2017)
|
| EndedAt: 2017-10-17 22:30:25 -0400 (Tue, 17 Oct 2017)
|
| EllapsedTime: 390.6 seconds
|
| RetCode: 0
|
| Status: OK
|
| CheckDir: BitSeq.Rcheck
|
| Warnings: 0
|
Command output
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###
### Running command:
###
### rm -rf BitSeq.buildbin-libdir BitSeq.Rcheck && mkdir BitSeq.buildbin-libdir BitSeq.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.20.0.tar.gz >BitSeq.Rcheck\00install.out 2>&1 && cp BitSeq.Rcheck\00install.out BitSeq-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BitSeq.buildbin-libdir --install="check:BitSeq-install.out" --force-multiarch --no-vignettes --timings BitSeq_1.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BitSeq.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BitSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BitSeq' version '1.20.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BitSeq' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.4Mb
sub-directories of 1Mb or more:
extdata 4.5Mb
libs 2.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License components with restrictions not permitted:
Artistic-2.0 + file LICENSE
Versioned 'LinkingTo' value for 'Rsamtools' is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'Rsamtools'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getExpression: no visible global function definition for 'read.table'
loadSamples: no visible global function definition for 'read.table'
tri.load: no visible global function definition for 'read.table'
tri.save: no visible global function definition for 'is'
tri.save: no visible global function definition for 'write.table'
tri.setGeneNames: no visible global function definition for 'is'
writeSamples: no visible global function definition for 'is'
writeSamples: no visible global function definition for 'write.table'
Undefined global functions or variables:
is read.table write.table
Consider adding
importFrom("methods", "is")
importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/i386/BitSeq.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'puts', possibly from 'printf' (C), 'puts' (C)
Found 'rand', possibly from 'rand' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/BitSeq.Rcheck/00check.log'
for details.
BitSeq.Rcheck/00install.out:
install for i386
* installing *source* package 'BitSeq' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ArgumentParser.cpp -o ArgumentParser.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c CollapsedSampler.cpp -o CollapsedSampler.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c FileHeader.cpp -o FileHeader.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c GibbsParameters.cpp -o GibbsParameters.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c MyTimer.cpp -o MyTimer.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c PosteriorSamples.cpp -o PosteriorSamples.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c R_init_BitSeq.cpp -o R_init_BitSeq.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
^
ReadDistribution.cpp:923:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
^
ReadDistribution.cpp:928:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c Sampler.cpp -o Sampler.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:count)
^
SimpleSparse.cpp:45:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
^
SimpleSparse.cpp:57:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TagAlignments.cpp -o TagAlignments.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TranscriptExpression.cpp -o TranscriptExpression.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TranscriptInfo.cpp -o TranscriptInfo.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TranscriptSequence.cpp -o TranscriptSequence.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:96:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(err) reduction(+:totalError)
^
VariationalBayes.cpp:103:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:110:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:A,B)
^
VariationalBayes.cpp:119:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:C)
^
VariationalBayes.cpp:172:0: 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:219:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:224:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:238:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c common.cpp -o common.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateDE.cpp -o estimateDE.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
^
estimateExpression.cpp:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateHyperPar.cpp -o estimateHyperPar.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateVBExpression.cpp -o estimateVBExpression.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getGeneExpression.cpp -o getGeneExpression.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getVariance.cpp -o getVariance.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c lowess.cpp -o lowess.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c misc.cpp -o misc.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c parseAlignment.cpp -o parseAlignment.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c transposeFiles.cpp -o transposeFiles.o
C:/Rtools/mingw_32/bin/g++ -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 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-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'BitSeq' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ArgumentParser.cpp -o ArgumentParser.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c CollapsedSampler.cpp -o CollapsedSampler.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c FileHeader.cpp -o FileHeader.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c GibbsParameters.cpp -o GibbsParameters.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c MyTimer.cpp -o MyTimer.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c PosteriorSamples.cpp -o PosteriorSamples.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c R_init_BitSeq.cpp -o R_init_BitSeq.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
^
ReadDistribution.cpp:923:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for \
^
ReadDistribution.cpp:928:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c Sampler.cpp -o Sampler.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:count)
^
SimpleSparse.cpp:45:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
^
SimpleSparse.cpp:57:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(i,logRowSum)
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TagAlignments.cpp -o TagAlignments.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TranscriptExpression.cpp -o TranscriptExpression.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TranscriptInfo.cpp -o TranscriptInfo.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c TranscriptSequence.cpp -o TranscriptSequence.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:96:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(err) reduction(+:totalError)
^
VariationalBayes.cpp:103:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:110:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:A,B)
^
VariationalBayes.cpp:119:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for reduction(+:C)
^
VariationalBayes.cpp:172:0: 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:219:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:224:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
VariationalBayes.cpp:238:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c common.cpp -o common.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateDE.cpp -o estimateDE.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
^
estimateExpression.cpp:244:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for private(subCounter)
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateHyperPar.cpp -o estimateHyperPar.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c estimateVBExpression.cpp -o estimateVBExpression.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getGeneExpression.cpp -o getGeneExpression.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getVariance.cpp -o getVariance.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c lowess.cpp -o lowess.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c misc.cpp -o misc.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c parseAlignment.cpp -o parseAlignment.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD -I. -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c transposeFiles.cpp -o transposeFiles.o
C:/Rtools/mingw_64/bin/g++ -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 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-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BitSeq' as BitSeq_1.20.0.zip
* DONE (BitSeq)
BitSeq.Rcheck/examples_i386/BitSeq-Ex.timings:
| name | user | system | elapsed
|
| BitSeq-package | 0 | 0 | 0 |
|
| estimateDE | 0 | 0 | 0 |
|
| estimateExpression | 0 | 0 | 0 |
|
| estimateHyperPar | 0 | 0 | 0 |
|
| estimateVBExpression | 0 | 0 | 0 |
|
| getDE | 0 | 0 | 0 |
|
| getExpression | 0 | 0 | 0 |
|
BitSeq.Rcheck/examples_x64/BitSeq-Ex.timings:
| name | user | system | elapsed
|
| BitSeq-package | 0 | 0 | 0 |
|
| estimateDE | 0 | 0 | 0 |
|
| estimateExpression | 0 | 0 | 0 |
|
| estimateHyperPar | 0 | 0 | 0 |
|
| estimateVBExpression | 0 | 0 | 0 |
|
| getDE | 0 | 0 | 0 |
|
| getExpression | 0 | 0 | 0 |
|