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BUILD BIN report for pqsfinder on merida1

This page was generated on 2019-04-16 11:59:33 -0400 (Tue, 16 Apr 2019).

Package 1183/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
pqsfinder 1.10.1
Jiri Hon
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/pqsfinder
Branch: RELEASE_3_8
Last Commit: 84e32c7
Last Changed Date: 2019-04-04 04:29:22 -0400 (Thu, 04 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: pqsfinder
Version: 1.10.1
Command: rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pqsfinder_1.10.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R pqsfinder.buildbin-libdir
StartedAt: 2019-04-16 04:33:07 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 04:34:29 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 82.0 seconds
RetCode: 0
Status:  OK 
PackageFile: pqsfinder_1.10.1.tgz
PackageFileSize: 2.799 MiB

Command output

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###
### Running command:
###
###   rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pqsfinder_1.10.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R pqsfinder.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=pqsfinder.buildbin-libdir pqsfinder_1.10.1.tar.gz'
>>>>>>> 

* installing *source* package ‘pqsfinder’ ...
** libs
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/BH/include" -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"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c pqsfinder.cpp -o pqsfinder.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/cregex.cpp -o boost_regex/cregex.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/fileiter.cpp -o boost_regex/fileiter.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/icu.cpp -o boost_regex/icu.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/instances.cpp -o boost_regex/instances.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/usinstances.cpp -o boost_regex/usinstances.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.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/BH/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib"
ar rs "/Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating archive /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(icu.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(instances.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(regex_debug.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(usinstances.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(w32_regex_traits.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a(winstances.o) has no symbols
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 pqsfinder.so RcppExports.o pqsfinder.o /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.8-bioc/meat/pqsfinder.buildbin-libdir/pqsfinder/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 (pqsfinder)


>>>>>>> 
>>>>>>> FIXING LINKS FOR pqsfinder.buildbin-libdir/pqsfinder/libs//pqsfinder.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" "pqsfinder.buildbin-libdir/pqsfinder/libs//pqsfinder.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "pqsfinder.buildbin-libdir/pqsfinder/libs//pqsfinder.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" "pqsfinder.buildbin-libdir/pqsfinder/libs//pqsfinder.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "pqsfinder.buildbin-libdir/pqsfinder/libs//pqsfinder.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "pqsfinder.buildbin-libdir/pqsfinder/libs//pqsfinder.so"