VariantAnnotation 1.20.3
Valerie Obenchain
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/VariantAnnotation | | Last Changed Rev: 127452 / Revision: 128728 | | Last Changed Date: 2017-03-15 22:03:50 -0400 (Wed, 15 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.4/bioc/src/contrib/VariantAnnotation_1.20.3.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantAnnotation.buildbin-libdir --merge-multiarch VariantAnnotation_1.20.3.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL VariantAnnotation_1.20.3.zip && rm VariantAnnotation_1.20.3.tar.gz VariantAnnotation_1.20.3.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
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0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1297k 100 1297k 0 0 47.4M 0 --:--:-- --:--:-- --:--:-- 48.7M
install for i386
* installing *source* package 'VariantAnnotation' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libbam.a C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/Biostrings/include" -I"C:/Users/biocbuild/bbs-3.4-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 C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbam.a C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a C:/Users/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LC:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantAnnotation' as VariantAnnotation_1.20.3.zip
* DONE (VariantAnnotation)
* installing to library 'C:/Users/biocbuild/bbs-3.4-bioc/R/library'
package 'VariantAnnotation' successfully unpacked and MD5 sums checked