Back to Multiple platform build/check report for BioC 3.12
ABCDEF[G]HIJKLMNOPQRSTUVWXYZ

BUILD BIN report for GOSemSim on merida1

This page was generated on 2021-05-06 12:35:10 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the GOSemSim package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 763/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GOSemSim 2.16.1  (landing page)
Guangchuang Yu
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GOSemSim
Branch: RELEASE_3_12
Last Commit: 92f1d56
Last Changed Date: 2020-10-29 03:57:45 -0400 (Thu, 29 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GOSemSim
Version: 2.16.1
Command: rm -rf GOSemSim.buildbin-libdir && mkdir GOSemSim.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GOSemSim_2.16.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GOSemSim.buildbin-libdir
StartedAt: 2021-05-06 08:48:47 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 08:49:41 -0400 (Thu, 06 May 2021)
EllapsedTime: 53.6 seconds
RetCode: 0
Status:   OK  
PackageFile: GOSemSim_2.16.1.tgz
PackageFileSize: 831.5 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GOSemSim.buildbin-libdir && mkdir GOSemSim.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GOSemSim_2.16.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R GOSemSim.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GOSemSim.buildbin-libdir GOSemSim_2.16.1.tar.gz'
>>>>>>> 

* installing *source* package ‘GOSemSim’ ...
** 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/usr/local/include   -fPIC  -Wall -g -O2  -c ICmethod.cpp -o ICmethod.o
In file included from ICmethod.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
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 GOSemSim.so ICmethod.o RcppExports.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/GOSemSim.buildbin-libdir/00LOCK-GOSemSim/00new/GOSemSim/libs
** R
** data
** 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 (GOSemSim)


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