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BUILD BIN report for scater on machv2

This page was generated on 2020-10-17 11:59:31 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE scater PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1584/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.16.2
Davis McCarthy
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_11
Last Commit: e01dfed
Last Changed Date: 2020-06-26 14:17:15 -0400 (Fri, 26 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.16.2
Command: rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scater_1.16.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
StartedAt: 2020-10-17 07:55:29 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 07:56:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 77.3 seconds
RetCode: 0
Status:  OK 
PackageFile: scater_1.16.2.tgz
PackageFileSize: 1.263 MiB

Command output

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### Running command:
###
###   rm -rf scater.buildbin-libdir && mkdir scater.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh scater_1.16.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R scater.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=scater.buildbin-libdir scater_1.16.2.tar.gz'
>>>>>>> 

* installing *source* package ‘scater’ ...
** 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/beachmat/include' -I/usr/local/include   -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/beachmat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c combined_qc.cpp -o combined_qc.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/beachmat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sum_counts.cpp -o sum_counts.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/beachmat/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.cpp -o utils.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 scater.so RcppExports.o combined_qc.o sum_counts.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.11-bioc/meat/scater.buildbin-libdir/00LOCK-scater/00new/scater/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 (scater)


>>>>>>> 
>>>>>>> FIXING LINKS FOR scater.buildbin-libdir/scater/libs/scater.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" "scater.buildbin-libdir/scater/libs/scater.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "scater.buildbin-libdir/scater/libs/scater.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "scater.buildbin-libdir/scater/libs/scater.so"