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BioC 3.4: BUILD BIN report for scde on morelia

This page was generated on 2016-09-21 03:55:00 -0700 (Wed, 21 Sep 2016).

Package 1086/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scde 2.1.2
Jean Fan
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/scde
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: scde
Version: 2.1.2
Command: rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scde_2.1.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scde.buildbin-libdir
StartedAt: 2016-09-20 15:31:49 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 15:32:23 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 34.7 seconds
RetCode: 0
Status:  OK 
PackageFile: scde_2.1.2.tgz
PackageFileSize: 1.848 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scde_2.1.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scde.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scde.buildbin-libdir scde_2.1.2.tar.gz'
>>>>>>> 

* installing *source* package ‘scde’ ...
** 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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bwpca.cpp -o bwpca.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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
                double maxv=nbp.max(maxij);
                       ^
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
                double maxv=nbp.max(maxij);
                       ^
2 warnings generated.
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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c matSlideMult.cpp -o matSlideMult.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/3.3/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.3/Resources/library/RcppArmadillo/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c pagoda.cpp -o pagoda.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 scde.so bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/scde.buildbin-libdir/scde/libs
** R
** data
*** moving datasets to lazyload DB
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scde)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgcc_s.1.dylib" "scde.buildbin-libdir/scde/libs//scde.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libgfortran.3.dylib" "scde.buildbin-libdir/scde/libs//scde.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.5.2.dylib" "scde.buildbin-libdir/scde/libs//scde.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libreadline.dylib" "scde.buildbin-libdir/scde/libs//scde.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.3/Resources/lib/libquadmath.0.dylib" "scde.buildbin-libdir/scde/libs//scde.so"