Aaron Lun
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/beachmat |
| Branch: RELEASE_3_8 |
| Last Commit: e3b7a21 |
| Last Changed Date: 2018-10-30 11:42:05 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 12:00:48 -0400 (Tue, 16 Apr 2019).
| Package 112/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| beachmat 1.4.0 Aaron Lun
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: beachmat |
| Version: 1.4.0 |
| Command: rm -rf beachmat.buildbin-libdir && mkdir beachmat.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beachmat_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R beachmat.buildbin-libdir |
| StartedAt: 2019-04-16 03:43:20 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:45:03 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 102.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: beachmat_1.4.0.tgz |
| PackageFileSize: 7.449 MiB |
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### Running command:
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### rm -rf beachmat.buildbin-libdir && mkdir beachmat.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beachmat_1.4.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R beachmat.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=beachmat.buildbin-libdir beachmat_1.4.0.tar.gz'
>>>>>>>
* installing *source* package ‘beachmat’ ...
** libs
rm -f libbeachmat.*
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c HDF5_utils.cpp -o HDF5_utils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c character_matrix.cpp -o character_matrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c character_output.cpp -o character_output.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c dim_checker.cpp -o dim_checker.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c find_chunks.cpp -o find_chunks.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c functions.cpp -o functions.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c integer_matrix.cpp -o integer_matrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c logical_matrix.cpp -o logical_matrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c numeric_matrix.cpp -o numeric_matrix.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c output_param.cpp -o output_param.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c repacker.cpp -o repacker.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c utils.cpp -o utils.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 beachmat.so HDF5_utils.o character_matrix.o character_output.o dim_checker.o find_chunks.o functions.o integer_matrix.o logical_matrix.o numeric_matrix.o output_param.o repacker.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ar rc libbeachmat.a dim_checker.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o libbeachmat.so dim_checker.o character_matrix.o character_output.o integer_matrix.o logical_matrix.o numeric_matrix.o utils.o HDF5_utils.o output_param.o `echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "/Library/Frameworks/R.framework/Resources/bin/R" --vanilla --slave`
mkdir -p "/Users/biocbuild/bbs-3.8-bioc/meat/beachmat.buildbin-libdir/beachmat/lib" "/Users/biocbuild/bbs-3.8-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
cp dim_checker.h utils.h beachmat.h HDF5_utils.h output_param.h HDF5_reader.h Csparse_reader.h dense_reader.h simple_reader.h all_readers.h delayed_reader.h unknown_reader.h external_reader.h simple_writer.h Csparse_writer.h HDF5_writer.h all_writers.h LIN_matrix.h LIN_methods_read.h LIN_methods_write.h LIN_output.h logical_matrix.h integer_matrix.h character_matrix.h numeric_matrix.h character_output.h "/Users/biocbuild/bbs-3.8-bioc/meat/beachmat.buildbin-libdir/beachmat/include/beachmat"
mv libbeachmat.* "/Users/biocbuild/bbs-3.8-bioc/meat/beachmat.buildbin-libdir/beachmat/lib"
installing to /Users/biocbuild/bbs-3.8-bioc/meat/beachmat.buildbin-libdir/beachmat/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
* DONE (beachmat)
>>>>>>>
>>>>>>> FIXING LINKS FOR beachmat.buildbin-libdir/beachmat/libs//beachmat.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "beachmat.buildbin-libdir/beachmat/libs//beachmat.so"