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BUILD BIN report for chimera on merida1

This page was generated on 2020-08-10 12:34:15 -0400 (Mon, 10 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE chimera PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 268/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.31.1
Raffaele A Calogero
Snapshot Date: 2020-08-09 14:51:29 -0400 (Sun, 09 Aug 2020)
URL: https://git.bioconductor.org/packages/chimera
Branch: master
Last Commit: f48abc1
Last Changed Date: 2020-06-01 10:00:40 -0400 (Mon, 01 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS 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  ERROR  skipped  skipped 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: chimera
Version: 1.31.1
Command: rm -rf chimera.buildbin-libdir && mkdir chimera.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chimera_1.31.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chimera.buildbin-libdir
StartedAt: 2020-08-10 06:27:40 -0400 (Mon, 10 Aug 2020)
EndedAt: 2020-08-10 06:28:51 -0400 (Mon, 10 Aug 2020)
EllapsedTime: 70.5 seconds
RetCode: 0
Status:  OK 
PackageFile: chimera_1.31.1.tgz
PackageFileSize: 2.662 MiB

Command output

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### Running command:
###
###   rm -rf chimera.buildbin-libdir && mkdir chimera.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh chimera_1.31.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R chimera.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=chimera.buildbin-libdir chimera_1.31.1.tar.gz'
>>>>>>> 

* installing *source* package ‘chimera’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c StarParser.cpp -o StarParser.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 chimera.so StarParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/chimera.buildbin-libdir/00LOCK-chimera/00new/chimera/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
Warning: Package 'chimera' is deprecated and will be removed from Bioconductor
  version 3.13
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'chimera' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path
* DONE (chimera)


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