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BioC 3.1: INSTALL report for ShortRead on moscato2

This page was generated on 2015-10-09 09:28:16 -0700 (Fri, 09 Oct 2015).

Package 899/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ShortRead 1.26.0
Bioconductor Package Maintainer
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/ShortRead
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 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: ShortRead
Version: 1.26.0
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/ShortRead_1.26.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch ShortRead_1.26.0.tar.gz && rm ShortRead_1.26.0.tar.gz
StartedAt: 2015-10-08 18:50:22 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:53:12 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 169.8 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/ShortRead_1.26.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch ShortRead_1.26.0.tar.gz && rm ShortRead_1.26.0.tar.gz
###
##############################################################################
##############################################################################




install for i386

* installing to library 'E:/biocbld/bbs-3.1-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-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -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"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    -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"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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_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    -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"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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
g++ -m32 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -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"d:/RCompile/r-compiling/local/local320/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-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c read_maq_map.cc -o read_maq_map.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sampler.c -o sampler.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c trim.c -o trim.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.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    -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"d:/RCompile/r-compiling/local/local320/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 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 -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/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** 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 'ShortRead' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** 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    -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"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    -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"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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c S4Vectors_stubs.c -o S4Vectors_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    -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"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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
g++ -m64 -I"E:/biocbld/bbs-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -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"d:/RCompile/r-compiling/local/local320/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-3.1-bioc/R/library/zlibbioc/include" -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -mtune=core2 -c read_maq_map.cc -o read_maq_map.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sampler.c -o sampler.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c trim.c -o trim.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    -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"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.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    -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"d:/RCompile/r-compiling/local/local320/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 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 -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/ShortRead/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (ShortRead)