ShortRead 1.34.0
Bioconductor Package Maintainer
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ShortRead | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf ShortRead.buildbin-libdir && mkdir ShortRead.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.5/bioc/src/contrib/ShortRead_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --library=ShortRead.buildbin-libdir --merge-multiarch ShortRead_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL ShortRead_1.34.0.zip && rm ShortRead_1.34.0.tar.gz ShortRead_1.34.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 4895k 100 4895k 0 0 31.5M 0 --:--:-- --:--:-- --:--:-- 31.8M
install for i386
* installing *source* package 'ShortRead' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/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]
int name_len, seq_ori_len, seq_len, status;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c trim.c -o trim.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c util.c -o util.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ShortRead.buildbin-libdir/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 *source* package 'ShortRead' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/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-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io.c -o io.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/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]
int name_len, seq_ori_len, seq_len, status;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c trim.c -o trim.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/include" -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -LC:/Users/biocbuild/bbs-3.5-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ShortRead' as ShortRead_1.34.0.zip
* DONE (ShortRead)
* installing to library 'C:/Users/biocbuild/bbs-3.5-bioc/R/library'
package 'ShortRead' successfully unpacked and MD5 sums checked