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BioC 3.2: BUILD BIN report for R3CPET on oaxaca

This page was generated on 2016-04-23 10:29:12 -0700 (Sat, 23 Apr 2016).

Package 831/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
R3CPET 1.2.0
Mohamed Nadhir Djekidel
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/R3CPET
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: R3CPET
Version: 1.2.0
Command: rm -rf R3CPET.buildbin-libdir && mkdir R3CPET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh R3CPET_1.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R R3CPET.buildbin-libdir
StartedAt: 2016-04-23 05:59:37 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 06:00:30 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 53.4 seconds
RetCode: 0
Status:  OK 
PackageFile: R3CPET_1.2.0.tgz
PackageFileSize: 4.943 MiB

Command output

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###
### Running command:
###
###   rm -rf R3CPET.buildbin-libdir && mkdir R3CPET.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh R3CPET_1.2.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R R3CPET.buildbin-libdir
###
##############################################################################
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=R3CPET.buildbin-libdir R3CPET_1.2.0.tar.gz'
>>>>>>> 

* installing *source* package ‘R3CPET’ ...
** 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/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R3CPET_init.c -o R3CPET_init.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/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.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/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c corpus.cpp -o corpus.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/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c main.cpp -o main.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/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c state.cpp -o state.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/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c stirln.cpp -o stirln.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/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.cpp -o utils.o
utils.cpp:5:14: warning: unused variable 'half_ln_2pi' [-Wunused-const-variable]
const double half_ln_2pi = 0.91893853320467267;
             ^
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 R3CPET.so R3CPET_init.o RcppExports.o corpus.o main.o state.o stirln.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/R3CPET.buildbin-libdir/R3CPET/libs
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
No methods found in "GenomicRanges" for requests: seqlengths
No methods found in "GenomicRanges" for requests: keepSeqlevels
No methods found in "GenomicRanges" for requests: seqlevels
No methods found in "GenomicRanges" for requests: seqlengths<-
NOTE: arguments in definition for validity method for class 'ChromMaintainers' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'HLDAResult' changed from (x) to (object)
NOTE: arguments in definition for validity method for class 'NetworkCollection' changed from (x) to (object)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘ggbio’
No methods found in "GenomicRanges" for requests: seqlengths
No methods found in "GenomicRanges" for requests: keepSeqlevels
No methods found in "GenomicRanges" for requests: seqlevels
No methods found in "GenomicRanges" for requests: seqlengths<-
* DONE (R3CPET)


>>>>>>> 
>>>>>>> FIXING LINKS FOR R3CPET.buildbin-libdir/R3CPET/libs//R3CPET.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" "R3CPET.buildbin-libdir/R3CPET/libs//R3CPET.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.3.dylib" "R3CPET.buildbin-libdir/R3CPET/libs//R3CPET.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" "R3CPET.buildbin-libdir/R3CPET/libs//R3CPET.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "R3CPET.buildbin-libdir/R3CPET/libs//R3CPET.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libquadmath.0.dylib" "R3CPET.buildbin-libdir/R3CPET/libs//R3CPET.so"