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BUILD BIN report for LINC on celaya2

This page was generated on 2019-10-16 12:58:42 -0400 (Wed, 16 Oct 2019).

Package 872/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
LINC 1.12.0
Manuel Goepferich
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/LINC
Branch: RELEASE_3_9
Last Commit: c5e3d58
Last Changed Date: 2019-05-02 11:54:03 -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  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: LINC
Version: 1.12.0
Command: rm -rf LINC.buildbin-libdir && mkdir LINC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh LINC_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R LINC.buildbin-libdir
StartedAt: 2019-10-16 08:51:01 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 08:52:12 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 71.5 seconds
RetCode: 0
Status:  OK 
PackageFile: LINC_1.12.0.tgz
PackageFileSize: 4.93 MiB

Command output

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###
### Running command:
###
###   rm -rf LINC.buildbin-libdir && mkdir LINC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh LINC_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R LINC.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=LINC.buildbin-libdir LINC_1.12.0.tar.gz'
>>>>>>> 

* installing *source* package ‘LINC’ ...
** 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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c Cppspear.cpp -o Cppspear.o
Cppspear.cpp:78:14: warning: unused variable 'qspear' [-Wunused-variable]
      double qspear;double nfraction;
             ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c LINC_init.c -o LINC_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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c docdd.cpp -o docdd.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" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c doesd.cpp -o doesd.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 LINC.so Cppspear.o LINC_init.o RcppExports.o docdd.o doesd.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/LINC.buildbin-libdir/00LOCK-LINC/00new/LINC/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘history’ in package ‘LINC’
** 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 (LINC)


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