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BioC 3.3: INSTALL report for deepSNV on windows2.bioconductor.org

This page was generated on 2015-10-27 12:14:58 -0400 (Tue, 27 Oct 2015).

Package 259/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
deepSNV 1.17.0
Moritz Gerstung
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/deepSNV
Last Changed Rev: 109592 / Revision: 109948
Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015)
linux2.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
windows2.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: deepSNV
Version: 1.17.0
Command: C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/deepSNV_1.17.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch deepSNV_1.17.0.tar.gz && rm deepSNV_1.17.0.tar.gz
StartedAt: 2015-10-26 21:13:03 -0400 (Mon, 26 Oct 2015)
EndedAt: 2015-10-26 21:13:29 -0400 (Mon, 26 Oct 2015)
EllapsedTime: 25.9 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin64\bin\curl.exe -O http://linux2.bioconductor.org/BBS/3.3/bioc/src/contrib/deepSNV_1.17.0.tar.gz && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch deepSNV_1.17.0.tar.gz && rm deepSNV_1.17.0.tar.gz
###
##############################################################################
##############################################################################


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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1273k  100 1273k    0     0  74.9M      0 --:--:-- --:--:-- --:--:--  103M

install for i386

* installing to library 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'deepSNV' ...

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


** libs
g++ -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"d:/RCompile/r-compiling/local/local320/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:43:13: warning: unused variable 'iter' [-Wunused-variable]
bam2R.cpp:46:6: warning: unused variable 'c' [-Wunused-variable]
gcc -m32 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
g++ -m32 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/lib/i386 -lhts -pthread -lws2_32 C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/i386/libzbioc.a -Ld:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to c:/biocbld/bbs-3.3-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 'c:/biocbld/bbs-3.3-bioc/R/library'
* installing *source* package 'deepSNV' ...

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


** libs
g++ -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"d:/RCompile/r-compiling/local/local320/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:43:13: warning: unused variable 'iter' [-Wunused-variable]
bam2R.cpp:46:6: warning: unused variable 'c' [-Wunused-variable]
gcc -m64 -I"c:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"c:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/include" -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c betabinom.c -o betabinom.o
betabinom.c: In function 'pbb':
betabinom.c:27:9: warning: unused variable 'log' [-Wunused-variable]
g++ -m64 -shared -s -static-libgcc -o deepSNV.dll tmp.def bam2R.o betabinom.o -LC:/biocbld/bbs-3.3-bioc/R/library/Rhtslib/lib/x64 -lhts -pthread -lws2_32 C:/biocbld/bbs-3.3-bioc/R/library/zlibbioc/libs/x64/libzbioc.a -Ld:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -Lc:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to c:/biocbld/bbs-3.3-bioc/R/library/deepSNV/libs/x64
** testing if installed package can be loaded
* DONE (deepSNV)