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CHECK report for BitSeq on tokay1

This page was generated on 2020-08-12 11:40:01 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BitSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 184/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BitSeq 1.33.1
Antti Honkela , Panagiotis Papastamoulis
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/BitSeq
Branch: master
Last Commit: a27c864
Last Changed Date: 2020-07-14 16:10:37 -0400 (Tue, 14 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: BitSeq
Version: 1.33.1
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BitSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BitSeq_1.33.1.tar.gz
StartedAt: 2020-08-12 00:48:21 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 00:51:15 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 174.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BitSeq.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BitSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings BitSeq_1.33.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/BitSeq.Rcheck'
* using R version 4.0.2 (2020-06-22)
* 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 '1.33.1'
* 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 12.7Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      7.9Mb
* 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 'Rhtslib' 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
* 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 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 ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... 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-3.12-bioc/R/library/BitSeq/libs/i386/BitSeq.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/libs/x64/BitSeq.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
  Warning: working directory was changed to 'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BitSeq/extdata', resetting
* 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: 2 WARNINGs, 6 NOTEs
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/BitSeq.Rcheck/00check.log'
for details.



Installation output

BitSeq.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/BitSeq_1.33.1.tar.gz && rm -rf BitSeq.buildbin-libdir && mkdir BitSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BitSeq.buildbin-libdir BitSeq_1.33.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL BitSeq_1.33.1.zip && rm BitSeq_1.33.1.tar.gz BitSeq_1.33.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1018k  100 1018k    0     0  3317k      0 --:--:-- --:--:-- --:--:-- 3362k

install for i386

* installing *source* package 'BitSeq' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ArgumentParser.cpp -o ArgumentParser.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CollapsedSampler.cpp -o CollapsedSampler.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c FileHeader.cpp -o FileHeader.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GibbsParameters.cpp -o GibbsParameters.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GibbsSampler.cpp -o GibbsSampler.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MyTimer.cpp -o MyTimer.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PosteriorSamples.cpp -o PosteriorSamples.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_init_BitSeq.cpp -o R_init_BitSeq.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for \
 
ReadDistribution.cpp:923: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for \
 
ReadDistribution.cpp:928: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
          #pragma omp critical
 
ReadDistribution.cpp: In function 'long int ns_rD::countDeletions(const bam1_t*)':
ReadDistribution.cpp:66:18: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
    for(long i=0;i<samA->core.n_cigar;i++){
                 ~^~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In function 'bool ns_rD::getCigarOp(const bam1_t*, long int, long int*, long int*)':
ReadDistribution.cpp:79:29: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
    if((cigarI<0) || (cigarI >= samA->core.n_cigar)) return false;
                      ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
        (! frag->second->core.flag & BAM_FREVERSE))){
         ^~~~~~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)':
ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
             (! frag->second->core.flag & BAM_FREVERSE))){
              ^~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_sam.c -o Rhtslib_sam.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Sampler.cpp -o Sampler.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:count)
 
SimpleSparse.cpp:45: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 
SimpleSparse.cpp:57: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TagAlignments.cpp -o TagAlignments.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TranscriptExpression.cpp -o TranscriptExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TranscriptInfo.cpp -o TranscriptInfo.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TranscriptSequence.cpp -o TranscriptSequence.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for
 
VariationalBayes.cpp:96: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(err) reduction(+:totalError)
 
VariationalBayes.cpp:103: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for
 
VariationalBayes.cpp:110: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:A,B)
 
VariationalBayes.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:C)
 
VariationalBayes.cpp:172: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(i,phiGradPhiSum_r,natGrad_i,gradGamma_i) reduction(+:squareNorm,valBeta,valBetaDiv)
 
VariationalBayes.cpp:219: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 
VariationalBayes.cpp:224: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 
VariationalBayes.cpp:238: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c common.cpp -o common.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateDE.cpp -o estimateDE.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(subCounter)
 
estimateExpression.cpp:244: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for private(subCounter)
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateHyperPar.cpp -o estimateHyperPar.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateVBExpression.cpp -o estimateVBExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c getGeneExpression.cpp -o getGeneExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c getVariance.cpp -o getVariance.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c lowess.cpp -o lowess.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c parseAlignment.cpp -o parseAlignment.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c transposeFiles.cpp -o transposeFiles.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Rhtslib_bam_plbuf.o Rhtslib_sam.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BitSeq.buildbin-libdir/00LOCK-BitSeq/00new/BitSeq/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BitSeq'
    finding HTML links ... done
    BitSeq-package                          html  
    estimateDE                              html  
    estimateExpression                      html  
    estimateHyperPar                        html  
    estimateVBExpression                    html  
    getDE                                   html  
    getExpression                           html  
    getGeneExpression                       html  
    getMeanVariance                         html  
    loadSamples                             html  
    parseAlignment                          html  
    transcriptInfo                          html  
    transcriptInfoFile                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BitSeq' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ArgumentParser.cpp -o ArgumentParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c CollapsedSampler.cpp -o CollapsedSampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c FileHeader.cpp -o FileHeader.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GibbsParameters.cpp -o GibbsParameters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c GibbsSampler.cpp -o GibbsSampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c MyTimer.cpp -o MyTimer.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c PosteriorSamples.cpp -o PosteriorSamples.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_init_BitSeq.cpp -o R_init_BitSeq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c ReadDistribution.cpp -o ReadDistribution.o
ReadDistribution.cpp:838: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for \
 
ReadDistribution.cpp:923: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for \
 
ReadDistribution.cpp:928: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
          #pragma omp critical
 
ReadDistribution.cpp: In function 'long int ns_rD::countDeletions(const bam1_t*)':
ReadDistribution.cpp:66:18: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
    for(long i=0;i<samA->core.n_cigar;i++){
                 ~^~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In function 'bool ns_rD::getCigarOp(const bam1_t*, long int, long int*, long int*)':
ReadDistribution.cpp:79:29: warning: comparison of integer expressions of different signedness: 'long int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare]
    if((cigarI<0) || (cigarI >= samA->core.n_cigar)) return false;
                      ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::observed(ns_rD::fragmentP)':
ReadDistribution.cpp:265:9: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
        (! frag->second->core.flag & BAM_FREVERSE))){
         ^~~~~~~~~~~~~~~~~~~~~~~~~
ReadDistribution.cpp: In member function 'bool ReadDistribution::getP(ns_rD::fragmentP, double&, double&)':
ReadDistribution.cpp:687:14: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
             (! frag->second->core.flag & BAM_FREVERSE))){
              ^~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_bam_plbuf.c -o Rhtslib_bam_plbuf.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rhtslib_sam.c -o Rhtslib_sam.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c Sampler.cpp -o Sampler.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c SimpleSparse.cpp -o SimpleSparse.o
SimpleSparse.cpp:35: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:count)
 
SimpleSparse.cpp:45: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 
SimpleSparse.cpp:57: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(i,logRowSum)
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TagAlignments.cpp -o TagAlignments.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TranscriptExpression.cpp -o TranscriptExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TranscriptInfo.cpp -o TranscriptInfo.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c TranscriptSequence.cpp -o TranscriptSequence.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c VariationalBayes.cpp -o VariationalBayes.o
VariationalBayes.cpp:86: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for
 
VariationalBayes.cpp:96: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for private(err) reduction(+:totalError)
 
VariationalBayes.cpp:103: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for
 
VariationalBayes.cpp:110: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:A,B)
 
VariationalBayes.cpp:119: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
    #pragma omp parallel for reduction(+:C)
 
VariationalBayes.cpp:172: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(i,phiGradPhiSum_r,natGrad_i,gradGamma_i) reduction(+:squareNorm,valBeta,valBetaDiv)
 
VariationalBayes.cpp:219: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 
VariationalBayes.cpp:224: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 
VariationalBayes.cpp:238: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c common.cpp -o common.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateDE.cpp -o estimateDE.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateExpression.cpp -o estimateExpression.o
estimateExpression.cpp:208: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
       #pragma omp parallel for private(subCounter)
 
estimateExpression.cpp:244: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
          #pragma omp parallel for private(subCounter)
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateHyperPar.cpp -o estimateHyperPar.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c estimateVBExpression.cpp -o estimateVBExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c getGeneExpression.cpp -o getGeneExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c getVariance.cpp -o getVariance.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c getWithinGeneExpression.cpp -o getWithinGeneExpression.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c lowess.cpp -o lowess.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c misc.cpp -o misc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c parseAlignment.cpp -o parseAlignment.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -DBS_VERSION=\"1.27.2\" -DBIOC_BUILD  -I. -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c transposeFiles.cpp -o transposeFiles.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o BitSeq.dll tmp.def ArgumentParser.o CollapsedSampler.o FileHeader.o GibbsParameters.o GibbsSampler.o MyTimer.o PosteriorSamples.o R_init_BitSeq.o ReadDistribution.o Rhtslib_bam_plbuf.o Rhtslib_sam.o Sampler.o SimpleSparse.o TagAlignments.o TranscriptExpression.o TranscriptInfo.o TranscriptSequence.o VariationalBayes.o common.o estimateDE.o estimateExpression.o estimateHyperPar.o estimateVBExpression.o getGeneExpression.o getVariance.o getWithinGeneExpression.o lowess.o misc.o parseAlignment.o transposeFiles.o C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/BitSeq.buildbin-libdir/BitSeq/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BitSeq' as BitSeq_1.33.1.zip
* DONE (BitSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'BitSeq' successfully unpacked and MD5 sums checked

Tests output


Example timings

BitSeq.Rcheck/examples_i386/BitSeq-Ex.timings

nameusersystemelapsed
BitSeq-package000
estimateDE000
estimateExpression000
estimateHyperPar000
estimateVBExpression000
getDE000
getExpression000
loadSamples000
parseAlignment000

BitSeq.Rcheck/examples_x64/BitSeq-Ex.timings

nameusersystemelapsed
BitSeq-package000
estimateDE000
estimateExpression000
estimateHyperPar000
estimateVBExpression000
getDE000
getExpression000
loadSamples000
parseAlignment000