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BioC 3.3: INSTALL report for VariantAnnotation on moscato2

This page was generated on 2016-10-13 12:50:03 -0700 (Thu, 13 Oct 2016).

Package 1188/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.18.7
Valerie Obenchain
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/VariantAnnotation
Last Changed Rev: 120246 / Revision: 122332
Last Changed Date: 2016-08-18 07:21:57 -0700 (Thu, 18 Aug 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.18.7
Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/VariantAnnotation_1.18.7.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantAnnotation.buildbin-libdir --merge-multiarch VariantAnnotation_1.18.7.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.18.7.zip && rm VariantAnnotation_1.18.7.tar.gz VariantAnnotation_1.18.7.zip
StartedAt: 2016-10-12 19:11:13 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 19:16:16 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 302.8 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/VariantAnnotation_1.18.7.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantAnnotation.buildbin-libdir --merge-multiarch VariantAnnotation_1.18.7.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.18.7.zip  && rm VariantAnnotation_1.18.7.tar.gz VariantAnnotation_1.18.7.zip
###
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install for i386

* installing *source* package 'VariantAnnotation' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rle.c -o rle.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c strhash.c -o strhash.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c vcffile.c -o vcffile.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c vcftype.c -o vcftype.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c writevcf.c -o writevcf.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'tabulate' in package 'VariantAnnotation'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'VariantAnnotation' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c dna_hash.c -o dna_hash.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rle.c -o rle.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c strhash.c -o strhash.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c vcffile.c -o vcffile.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c vcftype.c -o vcftype.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c writevcf.c -o writevcf.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o VariantAnnotation.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a E:/biocbld/bbs-3.3-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.18.7.zip
* DONE (VariantAnnotation)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'VariantAnnotation' successfully unpacked and MD5 sums checked