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BUILD BIN report for scater on celaya2

This page was generated on 2019-04-09 13:15:37 -0400 (Tue, 09 Apr 2019).

Package 1433/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.11.15
Davis McCarthy
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/scater
Branch: master
Last Commit: 30a42c8
Last Changed Date: 2019-04-07 14:45:06 -0400 (Sun, 07 Apr 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: scater
Version: 1.11.15
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scater_1.11.15.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
StartedAt: 2019-04-09 07:44:01 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 07:46:22 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 141.7 seconds
RetCode: 0
Status:  OK 
PackageFile: scater_1.11.15.tgz
PackageFileSize: 4.622 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_1.11.15.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scater.buildbin-libdir scater_1.11.15.tar.gz'
>>>>>>> 

* installing *source* package ‘scater’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c calc_exprs.cpp -o calc_exprs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c combined_qc.cpp -o combined_qc.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.cpp -o init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c num_exprs.cpp -o num_exprs.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c sum_counts.cpp -o sum_counts.o
sum_counts.cpp:72:18: warning: unused variable 'ncells' [-Wunused-variable]
    const size_t ncells=end_index - start_index;
                 ^
sum_counts.cpp:96:18: warning: unused variable 'ncells' [-Wunused-variable]
    const size_t ncells=mat->get_ncol();
                 ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include  -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
clang++ -std=gnu++11 -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 combined_qc.o init.o num_exprs.o sum_counts.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/scater.buildbin-libdir/00LOCK-scater/00new/scater/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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/3.6/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/3.6/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/3.6/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/3.6/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/3.6/Resources/lib/libquadmath.0.dylib" "scater.buildbin-libdir/scater/libs//scater.so"