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BioC 3.0: INSTALL report for deepSNV on moscato1

This page was generated on 2015-04-10 09:47:42 -0700 (Fri, 10 Apr 2015).

Package 229/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.12.0
Moritz Gerstung
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/deepSNV
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: deepSNV
Version: 1.12.0
Command: C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.0/bioc/src/contrib/deepSNV_1.12.0.tar.gz && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch deepSNV_1.12.0.tar.gz && rm deepSNV_1.12.0.tar.gz
StartedAt: 2015-04-09 18:33:10 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 18:34:53 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 102.6 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin1/BBS/3.0/bioc/src/contrib/deepSNV_1.12.0.tar.gz && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch deepSNV_1.12.0.tar.gz && rm deepSNV_1.12.0.tar.gz
###
##############################################################################
##############################################################################


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100 1268k  100 1268k    0     0  41.3M      0 --:--:-- --:--:-- --:--:-- 56.3M

install for i386

* installing to library 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'deepSNV' ...

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


** libs
g++ -m32 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:85:6: warning: unused variable 'c' [-Wunused-variable]
g++ -m32 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libbcf.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/i386/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/i386 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/deepSNV/libs/i386
** R
** data
** 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 'D:/biocbld/bbs-3.0-bioc/R/library'
* installing *source* package 'deepSNV' ...

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


** libs
g++ -m64 -I"D:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/include" -I"D:/biocbld/BBS-3˜1.0-B/R/include" -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE   -I"D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c bam2R.cpp -o bam2R.o
bam2R.cpp: In function 'int bam2R(char**, char**, int*, int*, int*, int*, int*, int*, int*, int*)':
bam2R.cpp:85:6: warning: unused variable 'c' [-Wunused-variable]
g++ -m64 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbam.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libbcf.a D:/biocbld/bbs-3.0-bioc/R/library/Rsamtools/usrlib/x64/libtabix.a -lws2_32 -pthread -LD:/biocbld/bbs-3.0-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-3˜1.0-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-3.0-bioc/R/library/deepSNV/libs/x64
** testing if installed package can be loaded
* DONE (deepSNV)