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BioC 3.1: INSTALL report for VariantAnnotation on moscato2

This page was generated on 2015-10-09 09:29:21 -0700 (Fri, 09 Oct 2015).

Package 1003/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantAnnotation 1.14.13
Valerie Obenchain
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/VariantAnnotation
Last Changed Rev: 107909 / Revision: 109384
Last Changed Date: 2015-08-28 13:56:52 -0700 (Fri, 28 Aug 2015)
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
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantAnnotation
Version: 1.14.13
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/VariantAnnotation_1.14.13.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch VariantAnnotation_1.14.13.tar.gz && rm VariantAnnotation_1.14.13.tar.gz
StartedAt: 2015-10-08 18:57:59 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 19:00:22 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 142.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/VariantAnnotation_1.14.13.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch VariantAnnotation_1.14.13.tar.gz && rm VariantAnnotation_1.14.13.tar.gz
###
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install for i386

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'VariantAnnotation' ...
** libs
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c dna_hash.c -o dna_hash.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c rle.c -o rle.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c strhash.c -o strhash.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c vcffile.c -o vcffile.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c vcftype.c -o vcftype.o
gcc -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c writevcf.c -o writevcf.o
gcc -m32 -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-3.1-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/usrlib/i386/libbam.a E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/VariantAnnotation/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'VariantAnnotation' ...
** libs
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c dna_hash.c -o dna_hash.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c rle.c -o rle.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c strhash.c -o strhash.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c utilities.c -o utilities.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c vcffile.c -o vcffile.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c vcftype.c -o vcftype.o
gcc -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include"   -I"E:/biocbld/bbs-3.1-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Biostrings/include" -I"E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c writevcf.c -o writevcf.o
gcc -m64 -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-3.1-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/usrlib/x64/libbam.a E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a E:/biocbld/bbs-3.1-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LE:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/VariantAnnotation/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (VariantAnnotation)