Package: bsseq

Version: 1.19.3

Command: rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bsseq_1.19.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bsseq.buildbin-libdir

StartedAt: 2019-04-09 04:51:57 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:54:47 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 169.3 seconds

RetCode: 0

Status:  OK

PackageFile: bsseq_1.19.3.tgz

PackageFileSize: 8.109 MiB

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### Running command:
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###   rm -rf bsseq.buildbin-libdir && mkdir bsseq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bsseq_1.19.3.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bsseq.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bsseq.buildbin-libdir bsseq_1.19.3.tar.gz'
>>>>>>> 

* installing *source* package ‘bsseq’ ...
** 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" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c check_M_and_Cov.cpp -o check_M_and_Cov.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" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.cpp -o 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" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rhdf5lib/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/beachmat/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.o
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
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 bsseq.so check_M_and_Cov.o init.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
Error: 'pkgconfig' is not an exported object from 'namespace:beachmat'
Execution halted
installing to /Users/biocbuild/bbs-3.9-bioc/meat/bsseq.buildbin-libdir/bsseq/libs
** R
** data
*** moving datasets to lazyload DB
Registered S3 method overwritten by 'R.oo':
  method        from       
  throw.default R.methodsS3
** 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
* DONE (bsseq)


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