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BioC 3.3: INSTALL report for VariantFiltering on moscato2

This page was generated on 2016-10-13 12:52:30 -0700 (Thu, 13 Oct 2016).

Package 1189/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.8.6
Robert Castelo
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/VariantFiltering
Last Changed Rev: 119277 / Revision: 122332
Last Changed Date: 2016-07-11 08:47:52 -0700 (Mon, 11 Jul 2016)
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
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: VariantFiltering
Version: 1.8.6
Command: rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/VariantFiltering_1.8.6.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantFiltering.buildbin-libdir --merge-multiarch VariantFiltering_1.8.6.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.8.6.zip && rm VariantFiltering_1.8.6.tar.gz VariantFiltering_1.8.6.zip
StartedAt: 2016-10-12 19:29:19 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 19:31:13 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 114.1 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.3/bioc/src/contrib/VariantFiltering_1.8.6.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --library=VariantFiltering.buildbin-libdir --merge-multiarch VariantFiltering_1.8.6.tar.gz && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL VariantFiltering_1.8.6.zip  && rm VariantFiltering_1.8.6.tar.gz VariantFiltering_1.8.6.zip
###
##############################################################################
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install for i386

* installing *source* package 'VariantFiltering' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
C:/Rtools/mingw_32/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c: In function 'scoss_wm_score':
methods-WeightMatrix.c:100:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:99:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
methods-WeightMatrix.c:96:13: warning: variable 'k' set but not used [-Wunused-but-set-variable]
   int i, j, k;
             ^
methods-WeightMatrix.c: In function 'scoss_wm_score_DNAStringSet':
methods-WeightMatrix.c:131:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:129:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -Lc:/local323/lib/i386 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs/i386
** R
** 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 *source* package 'VariantFiltering' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Biostrings_stubs.c -o Biostrings_stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
C:/Rtools/mingw_64/bin/gcc  -I"E:/biocbld/BBS-3˜1.3-B/R/include" -DNDEBUG    -I"E:/biocbld/bbs-3.3-bioc/R/library/S4Vectors/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/IRanges/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/XVector/include" -I"E:/biocbld/bbs-3.3-bioc/R/library/Biostrings/include" -I"c:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c: In function 'scoss_wm_score':
methods-WeightMatrix.c:100:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:99:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
methods-WeightMatrix.c:96:13: warning: variable 'k' set but not used [-Wunused-but-set-variable]
   int i, j, k;
             ^
methods-WeightMatrix.c: In function 'scoss_wm_score_DNAStringSet':
methods-WeightMatrix.c:131:11: warning: unused variable 'scores' [-Wunused-variable]
   double* scores;
           ^
methods-WeightMatrix.c:129:7: warning: unused variable 'nsco' [-Wunused-variable]
   int nsco = INTEGER(nscoR)[0];
       ^
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o VariantFiltering.dll tmp.def Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -Lc:/local323/lib/x64 -Lc:/local323/lib -LE:/biocbld/BBS-3˜1.3-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.3-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'VariantFiltering' as VariantFiltering_1.8.6.zip
* DONE (VariantFiltering)
* installing to library 'E:/biocbld/bbs-3.3-bioc/R/library'
package 'VariantFiltering' successfully unpacked and MD5 sums checked