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BioC 3.5: BUILD BIN report for oligo on veracruz2

This page was generated on 2017-08-16 13:27:30 -0400 (Wed, 16 Aug 2017).

Package 915/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
oligo 1.40.2
Benilton Carvalho
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/oligo
Last Changed Rev: 131492 / Revision: 131943
Last Changed Date: 2017-07-21 14:08:19 -0400 (Fri, 21 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: oligo
Version: 1.40.2
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.40.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R oligo.buildbin-libdir
StartedAt: 2017-08-16 10:48:12 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 10:48:41 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 29.7 seconds
RetCode: 0
Status:  OK 
PackageFile: oligo_1.40.2.tgz
PackageFileSize: 27.41 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.40.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R oligo.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.40.2.tar.gz'
>>>>>>> 

* installing *source* package ‘oligo’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c DABG.c -o DABG.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ParserGzXYS.c -o ParserGzXYS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c ParserXYS.c -o ParserXYS.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c baseProfile.c -o baseProfile.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c basecontent.c -o basecontent.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma2.c -o rma2.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/preprocessCore/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c trimmed.c -o trimmed.o
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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/oligo.buildbin-libdir/oligo/libs
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
Note: in method for ‘pm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for ‘mm<-’ with signature
‘object="TilingFeatureSet",subset="ANY",target="ANY",value="array"’:
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (oligo)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgcc_s.1.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.5.2.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "oligo.buildbin-libdir/oligo/libs//oligo.so"