Package: FastqCleaner

Version: 1.5.0

Command: rm -rf FastqCleaner.buildbin-libdir && mkdir FastqCleaner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FastqCleaner_1.5.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R FastqCleaner.buildbin-libdir

StartedAt: 2020-01-13 10:24:10 -0500 (Mon, 13 Jan 2020)

EndedAt: 2020-01-13 10:25:49 -0500 (Mon, 13 Jan 2020)

EllapsedTime: 98.9 seconds

RetCode: 0

Status:  OK

PackageFile: FastqCleaner_1.5.0.tgz

PackageFileSize: 2.626 MiB

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### Running command:
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###   rm -rf FastqCleaner.buildbin-libdir && mkdir FastqCleaner.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FastqCleaner_1.5.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R FastqCleaner.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=FastqCleaner.buildbin-libdir FastqCleaner_1.5.0.tar.gz'
>>>>>>> 

* installing *source* package ‘FastqCleaner’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.0/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../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp_GC_content.cpp -o cpp_GC_content.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp_base_content.cpp -o cpp_base_content.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp_check_quality_threshold.cpp -o cpp_check_quality_threshold.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp_create_stringvec.cpp -o cpp_create_stringvec.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include/ -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c cpp_which_true.cpp -o cpp_which_true.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 FastqCleaner.so RcppExports.o cpp_GC_content.o cpp_base_content.o cpp_check_quality_threshold.o cpp_create_stringvec.o cpp_which_true.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/FastqCleaner.buildbin-libdir/00LOCK-FastqCleaner/00new/FastqCleaner/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 (FastqCleaner)


>>>>>>> 
>>>>>>> FIXING LINKS FOR FastqCleaner.buildbin-libdir/FastqCleaner/libs//FastqCleaner.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" "FastqCleaner.buildbin-libdir/FastqCleaner/libs//FastqCleaner.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.3.dylib" "FastqCleaner.buildbin-libdir/FastqCleaner/libs//FastqCleaner.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" "FastqCleaner.buildbin-libdir/FastqCleaner/libs//FastqCleaner.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libreadline.dylib" "FastqCleaner.buildbin-libdir/FastqCleaner/libs//FastqCleaner.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "FastqCleaner.buildbin-libdir/FastqCleaner/libs//FastqCleaner.so"