Ulrich Bodenhofer
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/podkat |
| Branch: RELEASE_3_12 |
| Last Commit: 64f1344 |
| Last Changed Date: 2020-10-27 11:03:58 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:32:47 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the podkat package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1364/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| podkat 1.22.0 (landing page) Ulrich Bodenhofer
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: podkat |
| Version: 1.22.0 |
| Command: C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/podkat_1.22.0.tar.gz && rm -rf podkat.buildbin-libdir && mkdir podkat.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=podkat.buildbin-libdir podkat_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL podkat_1.22.0.zip && rm podkat_1.22.0.tar.gz podkat_1.22.0.zip |
| StartedAt: 2021-05-05 18:01:26 -0400 (Wed, 05 May 2021) |
| EndedAt: 2021-05-05 18:04:28 -0400 (Wed, 05 May 2021) |
| EllapsedTime: 182.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/podkat_1.22.0.tar.gz && rm -rf podkat.buildbin-libdir && mkdir podkat.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=podkat.buildbin-libdir podkat_1.22.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL podkat_1.22.0.zip && rm podkat_1.22.0.tar.gz podkat_1.22.0.zip
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install for i386
* installing *source* package 'podkat' ...
** using staged installation
** 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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -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_podkat.cpp -o R_init_podkat.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bernoulliExact.cpp -o bernoulliExact.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c checkAndFixGenotype.cpp -o checkAndFixGenotype.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cumMax.cpp -o cumMax.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleMale.cpp -o doubleMale.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernels.cpp -o kernels.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pValues.cpp -o pValues.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c partitionRegions.cpp -o partitionRegions.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qfc.cpp -o qfc.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readGenotypeMatrix.cpp -o readGenotypeMatrix.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readVariantInfo.cpp -o readVariantInfo.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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-3.12-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/podkat.buildbin-libdir/00LOCK-podkat/00new/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/podkat/man/plot-methods.Rd:109: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/podkat/man/plot-methods.Rd:111: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
podkat-package html
print-methods html
qqplot-methods html
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/podkat/man/qqplot-methods.Rd:50: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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-3.12-bioc/tmpdir/RtmpqSvfik/R.INSTALL1be481a2d0b/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 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 'podkat' ...
** 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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -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_podkat.cpp -o R_init_podkat.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c bernoulliExact.cpp -o bernoulliExact.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c checkAndFixGenotype.cpp -o checkAndFixGenotype.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cumMax.cpp -o cumMax.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleMale.cpp -o doubleMale.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kernels.cpp -o kernels.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pValues.cpp -o pValues.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c partitionRegions.cpp -o partitionRegions.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c qfc.cpp -o qfc.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readGenotypeMatrix.cpp -o readGenotypeMatrix.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 -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c readVariantInfo.cpp -o readVariantInfo.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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-3.12-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/podkat.buildbin-libdir/podkat/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'podkat' as podkat_1.22.0.zip
* DONE (podkat)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'podkat' successfully unpacked and MD5 sums checked