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BioC 3.5: BUILD BIN report for SIMLR on veracruz2

This page was generated on 2017-10-18 14:35:01 -0400 (Wed, 18 Oct 2017).

Package 1225/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SIMLR 1.2.3
Daniele Ramazzotti
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/SIMLR
Branch: RELEASE_3_5
Last Commit: adb86f2
Last Changed Date: 2017-09-29 04:47:05 -0400 (Fri, 29 Sep 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  ERROR  OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: SIMLR
Version: 1.2.3
Command: rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SIMLR_1.2.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SIMLR.buildbin-libdir
StartedAt: 2017-10-18 11:33:21 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 11:33:53 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 32.6 seconds
RetCode: 0
Status:  OK 
PackageFile: SIMLR_1.2.3.tgz
PackageFileSize: 4.603 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf SIMLR.buildbin-libdir && mkdir SIMLR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SIMLR_1.2.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SIMLR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SIMLR.buildbin-libdir SIMLR_1.2.3.tar.gz'
>>>>>>> 

* installing *source* package ‘SIMLR’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rtsne.cpp -o Rtsne.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c projsplx_R.c -o projsplx_R.o
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c sptree.cpp -o sptree.o
In file included from sptree.cpp:39:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp.h:27:
In file included from /Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/RcppCommon.h:122:
/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include/Rcpp/exceptions.h:103:53: warning: all paths through this function will call itself [-Winfinite-recursion]
    inline void warning(const std::string& message) {        // #nocov start
                                                    ^
1 warning generated.
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c tsne.cpp -o tsne.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 SIMLR.so RcppExports.o Rtsne.o projsplx_R.o sptree.o tsne.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/SIMLR.buildbin-libdir/SIMLR/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SIMLR)


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