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BUILD BIN report for Cardinal on celaya2

This page was generated on 2019-10-16 12:54:55 -0400 (Wed, 16 Oct 2019).

Package 212/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Cardinal 2.2.6
Kylie A. Bemis
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Cardinal
Branch: RELEASE_3_9
Last Commit: 66fed1d
Last Changed Date: 2019-05-22 16:53:28 -0400 (Wed, 22 May 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  OK  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

Summary

Package: Cardinal
Version: 2.2.6
Command: rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Cardinal_2.2.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Cardinal.buildbin-libdir
StartedAt: 2019-10-16 08:17:00 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:18:08 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 68.0 seconds
RetCode: 0
Status:  OK 
PackageFile: Cardinal_2.2.6.tgz
PackageFileSize: 7.139 MiB

Command output

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###
### Running command:
###
###   rm -rf Cardinal.buildbin-libdir && mkdir Cardinal.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Cardinal_2.2.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Cardinal.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Cardinal.buildbin-libdir Cardinal_2.2.6.tar.gz'
>>>>>>> 

* installing *source* package ‘Cardinal’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c DIP.cpp -o DIP.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c dynAlign.cpp -o dynAlign.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c imzML.cpp -o imzML.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c localMaxima.cpp -o localMaxima.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pugixml.cpp -o pugixml.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c spatial.cpp -o spatial.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 Cardinal.so DIP.o dynAlign.o imzML.o init.o localMaxima.o pugixml.o spatial.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/Cardinal.buildbin-libdir/00LOCK-Cardinal/00new/Cardinal/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘filter’ in package ‘Cardinal’
Creating a new generic function for ‘group_by’ in package ‘Cardinal’
Creating a new generic function for ‘slice’ in package ‘Cardinal’
** 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 (Cardinal)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.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" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.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" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "Cardinal.buildbin-libdir/Cardinal/libs//Cardinal.so"