| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 13:36:09 -0400 (Tue, 09 Apr 2019).
| Package 115/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bcSeq 1.5.1 Jiaxing Lin
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | ERROR | skipped | |||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | ERROR | skipped | skipped | |||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] |
| Package: bcSeq |
| Version: 1.5.1 |
| Command: rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bcSeq_1.5.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bcSeq.buildbin-libdir |
| StartedAt: 2019-04-09 04:46:40 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 04:47:53 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 72.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: bcSeq_1.5.1.tgz |
| PackageFileSize: 345.2 KiB |
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### Running command:
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### rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bcSeq_1.5.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bcSeq.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bcSeq.buildbin-libdir bcSeq_1.5.1.tar.gz'
>>>>>>>
* installing *source* package ‘bcSeq’ ...
** 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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c CRISPR_matching.cpp -o CRISPR_matching.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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c Trie_edit.cpp -o Trie_edit.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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c Trie_hamming.cpp -o Trie_hamming.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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c Trie_util.cpp -o Trie_util.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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c alignment.cpp -o alignment.o
clang -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/Matrix/include" -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c trimRead.cpp -o trimRead.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/Matrix/include" -I/usr/local/include -pthread -fPIC -Wall -g -O2 -c uniqueBar.cpp -o uniqueBar.o
uniqueBar.cpp:21:9: warning: unused variable 'length' [-Wunused-variable]
int length = 0;
^
1 warning generated.
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 bcSeq.so CRISPR_matching.o RcppExports.o Trie_edit.o Trie_hamming.o Trie_util.o alignment.o init.o trimRead.o uniqueBar.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/bcSeq.buildbin-libdir/bcSeq/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 (bcSeq)
>>>>>>>
>>>>>>> FIXING LINKS FOR bcSeq.buildbin-libdir/bcSeq/libs//bcSeq.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" "bcSeq.buildbin-libdir/bcSeq/libs//bcSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "bcSeq.buildbin-libdir/bcSeq/libs//bcSeq.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" "bcSeq.buildbin-libdir/bcSeq/libs//bcSeq.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "bcSeq.buildbin-libdir/bcSeq/libs//bcSeq.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "bcSeq.buildbin-libdir/bcSeq/libs//bcSeq.so"