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This page was generated on 2023-04-19 11:01:54 -0400 (Wed, 19 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnsonmacOS 13.0 Venturaarm644.2.2 (2022-10-31) -- "Innocent and Trusting" 4256
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for GENIE3 on kjohnson


To the developers/maintainers of the GENIE3 package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 775/2183HostnameOS / ArchINSTALLBUILDBUILD BIN
GENIE3 1.20.0  (landing page)
Van Anh Huynh-Thu
Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023)
git_url: https://git.bioconductor.org/packages/GENIE3
git_branch: RELEASE_3_16
git_last_commit: aea2e68
git_last_commit_date: 2022-11-01 11:16:03 -0400 (Tue, 01 Nov 2022)
kjohnsonmacOS 13.0 Ventura / arm64  OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GENIE3
Version: 1.20.0
Command: rm -rf GENIE3.buildbin-libdir && mkdir GENIE3.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GENIE3_1.20.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GENIE3.buildbin-libdir
StartedAt: 2023-04-18 16:02:01 -0400 (Tue, 18 Apr 2023)
EndedAt: 2023-04-18 16:02:17 -0400 (Tue, 18 Apr 2023)
EllapsedTime: 16.2 seconds
RetCode: 0
Status:   OK  
PackageFile: GENIE3_1.20.0.tgz
PackageFileSize: 261.1 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf GENIE3.buildbin-libdir && mkdir GENIE3.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GENIE3_1.20.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GENIE3.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GENIE3.buildbin-libdir GENIE3_1.20.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GENIE3’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c GENIE3.c -o GENIE3.o
GENIE3.c:984:7: warning: variable 'sum_complexity' set but not used [-Wunused-but-set-variable]
  int sum_complexity=0;
      ^
1 warning generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GENIE3.so GENIE3.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/GENIE3.buildbin-libdir/00LOCK-GENIE3/00new/GENIE3/libs
** R
** inst
** byte-compile and prepare package for lazy loading
in method for ‘GENIE3’ with signature ‘"SummarizedExperiment"’: no definition for class “SummarizedExperiment”
in method for ‘GENIE3’ with signature ‘"ExpressionSet"’: no definition for class “ExpressionSet”
** 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 (GENIE3)


>>>>>>> 
>>>>>>> FIXING LINKS FOR GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so
>>>>>>> 

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so"