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BioC 3.6: CHECK report for BitSeq on tokay1

This page was generated on 2017-08-16 13:30:25 -0400 (Wed, 16 Aug 2017).

Package 144/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.21.0
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BitSeq
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BitSeq
Version: 1.21.0
Command: rm -rf BitSeq.buildbin-libdir BitSeq.Rcheck && mkdir BitSeq.buildbin-libdir BitSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.21.0.tar.gz >BitSeq.Rcheck\00install.out 2>&1 && cp BitSeq.Rcheck\00install.out BitSeq-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BitSeq.buildbin-libdir --install="check:BitSeq-install.out" --force-multiarch --no-vignettes --timings BitSeq_1.21.0.tar.gz
StartedAt: 2017-08-15 22:04:43 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 22:10:28 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 345.4 seconds
RetCode: 0
Status:  OK  
CheckDir: BitSeq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BitSeq.buildbin-libdir BitSeq.Rcheck && mkdir BitSeq.buildbin-libdir BitSeq.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BitSeq.buildbin-libdir BitSeq_1.21.0.tar.gz >BitSeq.Rcheck\00install.out 2>&1 && cp BitSeq.Rcheck\00install.out BitSeq-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=BitSeq.buildbin-libdir --install="check:BitSeq-install.out" --force-multiarch --no-vignettes --timings BitSeq_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/BitSeq.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '1.21.0'
* 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 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-3.6-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-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -DBS_VERSION=\"1.11.1\" -DBIOC_BUILD  -I. -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/include" -I"C:/Users/biocbuild/bbs-3.6-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-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.6-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BitSeq' as BitSeq_1.21.0.zip
* DONE (BitSeq)

BitSeq.Rcheck/examples_i386/BitSeq-Ex.timings:

nameusersystemelapsed
BitSeq-package000
estimateDE000
estimateExpression000
estimateHyperPar000
estimateVBExpression000
getDE000
getExpression000

BitSeq.Rcheck/examples_x64/BitSeq-Ex.timings:

nameusersystemelapsed
BitSeq-package0.020.000.02
estimateDE000
estimateExpression0.010.000.01
estimateHyperPar000
estimateVBExpression000
getDE000
getExpression000