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BioC 2.14: INSTALL report for VariantFiltering on moscato2

This page was generated on 2014-10-08 08:56:43 -0700 (Wed, 08 Oct 2014).

Package 804/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.0.4
Robert Castelo
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/VariantFiltering
Last Changed Rev: 91489 / Revision: 95116
Last Changed Date: 2014-06-16 14:56:15 -0700 (Mon, 16 Jun 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: VariantFiltering
Version: 1.0.4
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/VariantFiltering_1.0.4.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch VariantFiltering_1.0.4.tar.gz && rm VariantFiltering_1.0.4.tar.gz
StartedAt: 2014-10-07 18:54:57 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 18:55:52 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 54.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/2.14/bioc/src/contrib/VariantFiltering_1.0.4.tar.gz && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch VariantFiltering_1.0.4.tar.gz && rm VariantFiltering_1.0.4.tar.gz
###
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install for i386

* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'VariantFiltering' ...
** libs
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
gcc -m32 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c: In function 'scoss_wm_score_DNAStringSet':
methods-WeightMatrix.c:122:23: warning: unused variable 'k' [-Wunused-variable]
gcc -m32 -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/VariantFiltering/libs/i386
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

install for x64

* installing to library 'E:/biocbld/bbs-2.14-bioc/R/library'
* installing *source* package 'VariantFiltering' ...
** libs
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
gcc -m64 -I"E:/biocbld/BBS-2˜1.14-/R/include" -DNDEBUG    -I"E:/biocbld/bbs-2.14-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-2.14-bioc/R/library/Biostrings/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c: In function 'scoss_wm_score_DNAStringSet':
methods-WeightMatrix.c:122:23: warning: unused variable 'k' [-Wunused-variable]
gcc -m64 -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2˜1.14-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.14-bioc/R/library/VariantFiltering/libs/x64
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* DONE (VariantFiltering)