ShortRead 1.22.0
Bioconductor Package Maintainer
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/ShortRead | | Last Changed Rev: 88838 / Revision: 95116 | | Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | [ OK ] | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |
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### Running command:
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### C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/ShortRead_1.22.0.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch ShortRead_1.22.0.tar.gz && rm ShortRead_1.22.0.tar.gz
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install for i386
* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'ShortRead' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c: In function 'write_fastq':
io.c:113:16: warning: 'gzbuf_n' may be used uninitialized in this function [-Wuninitialized]
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c pileup.c -o pileup.o
g++ -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)':
readBfaToc.cc:19:40: warning: variable 'status' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c trim.c -o trim.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c util.c -o util.o
gcc -m32 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O3 -Wall -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
g++ -m32 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LE:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'ShortRead' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c XVector_stubs.c -o XVector_stubs.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
io.c: In function 'write_fastq':
io.c:113:16: warning: 'gzbuf_n' may be used uninitialized in this function [-Wuninitialized]
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c pileup.c -o pileup.o
g++ -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)':
readBfaToc.cc:19:40: warning: variable 'status' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c trim.c -o trim.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c util.c -o util.o
gcc -m64 -I"E:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include" -O2 -Wall -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
g++ -m64 -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o pileup.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LE:/biocbld/bbs-2.14-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/ShortRead/libs/x64
** testing if installed package can be loaded
* DONE (ShortRead)