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BioC 3.2: BUILD BIN report for VariantFiltering on oaxaca

This page was generated on 2016-04-23 10:27:45 -0700 (Sat, 23 Apr 2016).

Package 1083/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VariantFiltering 1.6.21
Robert Castelo
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/VariantFiltering
Last Changed Rev: 115617 / Revision: 116712
Last Changed Date: 2016-04-01 06:31:43 -0700 (Fri, 01 Apr 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  TIMEOUT  skipped  skipped 
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: 1.6.21
Command: rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.6.21.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VariantFiltering.buildbin-libdir
StartedAt: 2016-04-23 06:09:41 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:10:14 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 33.8 seconds
RetCode: 0
Status:  OK 
PackageFile: VariantFiltering_1.6.21.tgz
PackageFileSize: 3.325 MiB

Command output

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###
### Running command:
###
###   rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.6.21.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R VariantFiltering.buildbin-libdir
###
##############################################################################
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantFiltering.buildbin-libdir VariantFiltering_1.6.21.tar.gz'
>>>>>>> 

* installing *source* package ‘VariantFiltering’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/XVector/include" -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Biostrings/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c:123:23: warning: unused variable 'k' [-Wunused-variable]
  int S_length, i, j, k;
                      ^
1 warning generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/VariantFiltering.buildbin-libdir/VariantFiltering/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (VariantFiltering)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs//VariantFiltering.so"