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BUILD BIN report for GLAD on merida1

This page was generated on 2019-12-10 13:09:31 -0500 (Tue, 10 Dec 2019).

Package 708/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.50.0
Philippe Hupe
Snapshot Date: 2019-12-09 16:45:09 -0500 (Mon, 09 Dec 2019)
URL: https://git.bioconductor.org/packages/GLAD
Branch: RELEASE_3_10
Last Commit: 34b2862
Last Changed Date: 2019-10-29 13:07:30 -0500 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: GLAD
Version: 2.50.0
Command: rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.50.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GLAD.buildbin-libdir
StartedAt: 2019-12-10 07:46:23 -0500 (Tue, 10 Dec 2019)
EndedAt: 2019-12-10 07:47:13 -0500 (Tue, 10 Dec 2019)
EllapsedTime: 50.1 seconds
RetCode: 0
Status:  OK 
PackageFile: GLAD_2.50.0.tgz
PackageFileSize: 953.1 KiB

Command output

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###
### Running command:
###
###   rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GLAD_2.50.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GLAD.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GLAD.buildbin-libdir GLAD_2.50.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GLAD’ ...
** using staged installation
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm  
PKG_CPPFLAGS = -DIS_MAC_OS

** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c BkpInfo.cpp -o BkpInfo.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c HaarSeg.cpp -o HaarSeg.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c MoveBkp.cpp -o MoveBkp.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c OutliersGNL.cpp -o OutliersGNL.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c chrBreakpoints.cpp -o chrBreakpoints.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c cutree.cpp -o cutree.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c daglad.cpp -o daglad.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c distance.cpp -o distance.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c filterBkp.cpp -o filterBkp.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c findCluster.cpp -o findCluster.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c glad-utils.cpp -o glad-utils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c hclust.cpp -o hclust.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c laws.c -o laws.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DIS_MAC_OS  -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c loopRemove.cpp -o loopRemove.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 GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.10-bioc/meat/GLAD.buildbin-libdir/00LOCK-GLAD/00new/GLAD/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** 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 (GLAD)


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