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BUILD BIN report for girafe on celaya2

This page was generated on 2019-10-16 12:48:01 -0400 (Wed, 16 Oct 2019).

Package 680/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
girafe 1.36.0
J. Toedling
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/girafe
Branch: RELEASE_3_9
Last Commit: 6696c01
Last Changed Date: 2019-05-02 11:53:13 -0400 (Thu, 02 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  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

Summary

Package: girafe
Version: 1.36.0
Command: rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh girafe_1.36.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R girafe.buildbin-libdir
StartedAt: 2019-10-16 08:41:36 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:42:28 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 52.2 seconds
RetCode: 0
Status:  OK 
PackageFile: girafe_1.36.0.tgz
PackageFileSize: 2.098 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf girafe.buildbin-libdir && mkdir girafe.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh girafe_1.36.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R girafe.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=girafe.buildbin-libdir girafe_1.36.0.tar.gz'
>>>>>>> 

* installing *source* package ‘girafe’ ...
** 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 coverage.cpp -o coverage.o
coverage.cpp:2:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c girafe_init.c -o girafe_init.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 girafe.so coverage.o girafe_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/girafe.buildbin-libdir/00LOCK-girafe/00new/girafe/libs
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘girafe’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
No methods found in package ‘IRanges’ for request: ‘sort’ when loading ‘girafe’
** testing if installed package keeps a record of temporary installation path
* DONE (girafe)


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