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BUILD BIN report for csaw on merida1

This page was generated on 2019-04-16 11:58:05 -0400 (Tue, 16 Apr 2019).

Package 350/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
csaw 1.16.1
Aaron Lun
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/csaw
Branch: RELEASE_3_8
Last Commit: 63ef4a6
Last Changed Date: 2018-12-20 19:32:06 -0400 (Thu, 20 Dec 2018)
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: csaw
Version: 1.16.1
Command: rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh csaw_1.16.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R csaw.buildbin-libdir
StartedAt: 2019-04-16 03:54:33 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:56:51 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 138.2 seconds
RetCode: 0
Status:  OK 
PackageFile: csaw_1.16.1.tgz
PackageFileSize: 1.666 MiB

Command output

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###
### Running command:
###
###   rm -rf csaw.buildbin-libdir && mkdir csaw.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh csaw_1.16.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R csaw.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=csaw.buildbin-libdir csaw_1.16.1.tar.gz'
>>>>>>> 

* installing *source* package ‘csaw’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c annotator.cpp -o annotator.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c bam_utils.cpp -o bam_utils.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c best_in_cluster.cpp -o best_in_cluster.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c check_bimodality.cpp -o check_bimodality.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c correlate_reads.cpp -o correlate_reads.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c find_maxima.cpp -o find_maxima.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_cluster_stats.cpp -o get_cluster_stats.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_profile.cpp -o get_profile.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c get_rle_counts.cpp -o get_rle_counts.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/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/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c merge_windows.cpp -o merge_windows.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c pair_reads.cpp -o pair_reads.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c single_reads.cpp -o single_reads.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/zlibbioc/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/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 csaw.so annotator.o bam_utils.o best_in_cluster.o check_bimodality.o correlate_reads.o find_maxima.o get_cluster_stats.o get_profile.o get_rle_counts.o init.o merge_windows.o pair_reads.o single_reads.o utils.o /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhtslib/usrlib/libhts.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.8-bioc/meat/csaw.buildbin-libdir/csaw/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 (csaw)


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