Package: bamsignals

Version: 1.19.0

Command: rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bamsignals_1.19.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bamsignals.buildbin-libdir

StartedAt: 2020-01-16 10:28:23 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 10:29:15 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 52.2 seconds

RetCode: 0

Status:  OK

PackageFile: bamsignals_1.19.0.tgz

PackageFileSize: 3.046 MiB

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### Running command:
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###   rm -rf bamsignals.buildbin-libdir && mkdir bamsignals.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bamsignals_1.19.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bamsignals.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bamsignals.buildbin-libdir bamsignals_1.19.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bamsignals’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c CountSignals.cpp -o CountSignals.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/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 -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bamsignals.cpp -o bamsignals.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/zlibbioc/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bamsignals_init.c -o bamsignals_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 bamsignals.so CountSignals.o RcppExports.o bamsignals.o bamsignals_init.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/bamsignals.buildbin-libdir/00LOCK-bamsignals/00new/bamsignals/libs
** R
** 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 (bamsignals)


>>>>>>> 
>>>>>>> FIXING LINKS FOR bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.5.2.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "bamsignals.buildbin-libdir/bamsignals/libs//bamsignals.so"