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BUILD BIN report for bcSeq on merida1

This page was generated on 2020-08-10 12:41:45 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bcSeq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 123/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bcSeq 1.11.0
Jiaxing Lin
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/bcSeq
Branch: master
Last Commit: ed5bf3d
Last Changed Date: 2020-04-27 15:12:22 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: bcSeq
Version: 1.11.0
Command: rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bcSeq_1.11.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bcSeq.buildbin-libdir
StartedAt: 2020-08-10 07:26:20 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 07:27:18 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 58.3 seconds
RetCode: 0
Status:  OK 
PackageFile: bcSeq_1.11.0.tgz
PackageFileSize: 345.9 KiB

Command output

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###
### Running command:
###
###   rm -rf bcSeq.buildbin-libdir && mkdir bcSeq.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bcSeq_1.11.0.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_1.11.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bcSeq’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c CRISPR_matching.cpp -o CRISPR_matching.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c Trie_edit.cpp -o Trie_edit.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c Trie_hamming.cpp -o Trie_hamming.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c Trie_util.cpp -o Trie_util.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c alignment.cpp -o alignment.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c trimRead.cpp -o trimRead.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Matrix/include' -I/usr/local/include  -pthread -fPIC  -Wall -g -O2  -c uniqueBar.cpp -o uniqueBar.o
clang++ -mmacosx-version-min=10.13 -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-3.12-bioc/meat/bcSeq.buildbin-libdir/00LOCK-bcSeq/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* 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/4.0/Resources/lib/libgcc_s.1.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "bcSeq.buildbin-libdir/bcSeq/libs/bcSeq.so"