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BioC 3.5: BUILD BIN report for scater on oaxaca

This page was generated on 2017-03-04 16:51:43 -0500 (Sat, 04 Mar 2017).

Package 1147/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.3.35
Davis McCarthy
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/scater
Last Changed Rev: 125348 / Revision: 127142
Last Changed Date: 2016-12-20 12:52:55 -0500 (Tue, 20 Dec 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  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 ]

Summary

Package: scater
Version: 1.3.35
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scater_1.3.35.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
StartedAt: 2017-03-04 12:21:12 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 12:21:36 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 23.2 seconds
RetCode: 0
Status:  OK 
PackageFile: scater_1.3.35.tgz
PackageFileSize: 7.005 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scater_1.3.35.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scater.buildbin-libdir scater_1.3.35.tar.gz'
>>>>>>> 

* installing *source* package ‘scater’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c calc_exprs.cpp -o calc_exprs.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c init.cpp -o init.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c matrix_info.cpp -o matrix_info.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c utils.cpp -o utils.o
utils.cpp:86:13: warning: unused variable 's' [-Wunused-variable]
        int s;
            ^
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 scater.so calc_exprs.o init.o matrix_info.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/scater.buildbin-libdir/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a new generic function for ‘mutate’ in package ‘scater’
Creating a new generic function for ‘filter’ in package ‘scater’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (scater)


>>>>>>> 
>>>>>>> FIXING LINKS FOR scater.buildbin-libdir/scater/libs//scater.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" "scater.buildbin-libdir/scater/libs//scater.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libgfortran.3.dylib" "scater.buildbin-libdir/scater/libs//scater.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" "scater.buildbin-libdir/scater/libs//scater.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libreadline.dylib" "scater.buildbin-libdir/scater/libs//scater.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libquadmath.0.dylib" "scater.buildbin-libdir/scater/libs//scater.so"