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Package 424/479HostnameOS / ArchBUILDCHECKBUILD BIN
ShortRead 1.11.23
Biocore Team c/o BioC user list
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ShortRead
Last Changed Rev: 56598 / Revision: 56603
Last Changed Date: 2011-07-06 15:55:59 -0700 (Wed, 06 Jul 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS [ OK ]
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: ShortRead
Version: 1.11.23
Command: mkdir ShortRead.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ShortRead.buildbin-libdir ShortRead_1.11.23.tar.gz
StartedAt: 2011-07-07 07:14:10 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 07:16:14 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 124.1 seconds
RetCode: 0
Status:  OK  
PackageFile: ShortRead_1.11.23.zip
PackageFileSize: 2.707 MiB

Command output


install for i386

* installing *source* package 'ShortRead' ...

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


** libs
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c pileup.c -o pileup.o
g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c readBfaToc.cc -o readBfaToc.o
g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c trim.c -o trim.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.o
gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O3 -Wall  -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.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 -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/i386
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: RColorBrewer
Warning: Class "AssayData" is defined (with package slot 'Biobase') but no metadata object found to revise subclass information---not exported?  Making a copy in package 'ShortRead'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'Overview.Rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'ShortRead' ...

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


** libs
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c IRanges_stubs.c -o IRanges_stubs.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_ShortRead.c -o R_init_ShortRead.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c alphabet.c -o alphabet.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c io.c -o io.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c io_bowtie.c -o io_bowtie.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c io_soap.c -o io_soap.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c pileup.c -o pileup.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c readBfaToc.cc -o readBfaToc.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -mtune=core2 -c read_maq_map.cc -o read_maq_map.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c sampler.c -o sampler.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c trim.c -o trim.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c util.c -o util.o
x86_64-w64-mingw32-gcc  -I"D:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/IRanges/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/Biostrings/include"      -O2 -Wall  -std=gnu99 -mtune=core2 -c xsnap.c -o xsnap.o
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o ShortRead.dll tmp.def Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.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 -LD:/biocbld/bbs-2.9-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/ShortRead.buildbin-libdir/ShortRead/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ShortRead' as ShortRead_1.11.23.zip

* DONE (ShortRead)