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This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 796/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GENIE3 1.22.0  (landing page)
Van Anh Huynh-Thu
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/GENIE3
git_branch: RELEASE_3_17
git_last_commit: 60f78fb
git_last_commit_date: 2023-08-24 05:09:04 -0400 (Thu, 24 Aug 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for GENIE3 on kjohnson2


To the developers/maintainers of the GENIE3 package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: GENIE3
Version: 1.22.0
Command: rm -rf GENIE3.buildbin-libdir && mkdir GENIE3.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GENIE3_1.22.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GENIE3.buildbin-libdir
StartedAt: 2023-10-19 13:36:12 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 13:36:25 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 12.6 seconds
RetCode: 0
Status:   OK  
PackageFile: GENIE3_1.22.0.tgz
PackageFileSize: 263.5 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_1.22.0.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_1.22.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GENIE3’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
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
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/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 PATHS TO DYNAMIC LIBRARIES FOR GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so
>>>>>>> 

>>>>>>> Paths before fix:
GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so:
	GENIE3.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so"

>>>>>>> Paths after fix:

GENIE3.buildbin-libdir/GENIE3/libs/GENIE3.so:
	GENIE3.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)