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INSTALL report for podkat on tokay2

This page was generated on 2018-10-17 08:40:14 -0400 (Wed, 17 Oct 2018).

Package 1110/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
podkat 1.12.0
Ulrich Bodenhofer
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/podkat
Branch: RELEASE_3_7
Last Commit: 950564c
Last Changed Date: 2018-04-30 10:35:36 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: podkat
Version: 1.12.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/podkat_1.12.0.tar.gz && rm -rf podkat.buildbin-libdir && mkdir podkat.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=podkat.buildbin-libdir podkat_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL podkat_1.12.0.zip && rm podkat_1.12.0.tar.gz podkat_1.12.0.zip
StartedAt: 2018-10-16 20:01:16 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:06:06 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 290.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/podkat_1.12.0.tar.gz && rm -rf podkat.buildbin-libdir && mkdir podkat.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=podkat.buildbin-libdir podkat_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL podkat_1.12.0.zip && rm podkat_1.12.0.tar.gz podkat_1.12.0.zip
###
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install for i386

* installing *source* package 'podkat' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_podkat.cpp -o R_init_podkat.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bernoulliExact.cpp -o bernoulliExact.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cumMax.cpp -o cumMax.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c doubleMale.cpp -o doubleMale.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kernels.cpp -o kernels.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pValues.cpp -o pValues.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c partitionRegions.cpp -o partitionRegions.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c qfc.cpp -o qfc.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readVariantInfo.cpp -o readVariantInfo.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o podkat.dll tmp.def R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/podkat.buildbin-libdir/podkat/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'p.adjust' from package 'stats' in package 'podkat'
Creating a generic function for 'qqplot' from package 'stats' in package 'podkat'
** help
*** installing help indices
  converting help for package 'podkat'
    finding HTML links ... done
    AssocTestResult-class                   html  
    AssocTestResultRanges-class             html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/AssocTestResultRanges-class.Rd:40: file link 'mcols' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/AssocTestResultRanges-class.Rd:40: file link 'elementMetadata' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/AssocTestResultRanges-class.Rd:106: file link 'print' in package 'podkat' does not exist and so has been treated as a topic
    GenotypeMatrix-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/GenotypeMatrix-class.Rd:56: file link 'rownames' in package 'base' does not exist and so has been treated as a topic
    NullModel-class                         html  
    VariantInfo-class                       html  
    assocTest-methods                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/assocTest-methods.Rd:41: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/assocTest-methods.Rd:103: file link 'makePSOCKcluster' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/assocTest-methods.Rd:246: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/assocTest-methods.Rd:253: file link 'makePSOCKcluster' in package 'parallel' does not exist and so has been treated as a topic
    computeKernel                           html  
    filterResult-methods                    html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/filterResult-methods.Rd:62: file link 'p.adjust' in package 'podkat' does not exist and so has been treated as a topic
    genotypeMatrix-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/genotypeMatrix-methods.Rd:33: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/genotypeMatrix-methods.Rd:149: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/genotypeMatrix-methods.Rd:150: file link 'SnpSet' in package 'Biobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/genotypeMatrix-methods.Rd:152: file link 'eSet' in package 'Biobase' does not exist and so has been treated as a topic
    hgA                                     html  
    nullModel-methods                       html  
    p.adjust-methods                        html  
    partitionRegions-methods                html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/partitionRegions-methods.Rd:20: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/partitionRegions-methods.Rd:55: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
    plot-methods                            html  
    podkat-package                          html  
    print-methods                           html  
    qqplot-methods                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/qqplot-methods.Rd:76: file link 'qqplot' in package 'stats' does not exist and so has been treated as a topic
    readGenotypeMatrix-methods              html  
    readRegionsFromBedFile                  html  
    readSampleNamesFromVcfHeader            html  
    readVariantInfo-methods                 html  
    sort-methods                            html  
    split-methods                           html  
    unmasked-datasets                       html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmasked-datasets.Rd:30: file link 'pseudoautosomal.hg18' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmasked-datasets.Rd:31: file link 'pseudoautosomal.hg19' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmasked-datasets.Rd:32: file link 'pseudoautosomal.hg38' in package 'GWASTools' does not exist and so has been treated as a topic
    unmaskedRegions                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:6: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:13: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:19: file link 'pseudoautosomal.hg18' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:20: file link 'pseudoautosomal.hg19' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:21: file link 'pseudoautosomal.hg38' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:29: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:34: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:47: file link 'BSgenome' in package 'BSgenome' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:51: file link 'pseudoautosomal.hg18' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:52: file link 'pseudoautosomal.hg19' in package 'GWASTools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/unmaskedRegions.Rd:53: file link 'pseudoautosomal.hg38' in package 'GWASTools' does not exist and so has been treated as a topic
    weightFuncs                             html  
    weights-methods                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/weights-methods.Rd:20: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/weights-methods.Rd:65: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpAXyWgd/R.INSTALL1dd848ac1cdc/podkat/man/weights-methods.Rd:92: file link 'TabixFile' in package 'Rsamtools' does not exist and so has been treated as a topic
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'podkat' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c R_init_podkat.cpp -o R_init_podkat.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bernoulliExact.cpp -o bernoulliExact.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c checkAndFixGenotype.cpp -o checkAndFixGenotype.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cumMax.cpp -o cumMax.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c doubleMale.cpp -o doubleMale.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c kernels.cpp -o kernels.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pValues.cpp -o pValues.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c partitionRegions.cpp -o partitionRegions.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c qfc.cpp -o qfc.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readGenotypeMatrix.cpp -o readGenotypeMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c readVariantInfo.cpp -o readVariantInfo.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o podkat.dll tmp.def R_init_podkat.o bernoulliExact.o checkAndFixGenotype.o cumMax.o doubleMale.o kernels.o pValues.o partitionRegions.o qfc.o readGenotypeMatrix.o readVariantInfo.o C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.7-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/podkat.buildbin-libdir/podkat/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'podkat' as podkat_1.12.0.zip
* DONE (podkat)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'podkat' successfully unpacked and MD5 sums checked
In R CMD INSTALL