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This page was generated on 2024-12-19 12:06 -0500 (Thu, 19 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4743
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4486
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4466
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 798/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneNetworkBuilder 1.48.0  (landing page)
Jianhong Ou
Snapshot Date: 2024-12-16 13:00 -0500 (Mon, 16 Dec 2024)
git_url: https://git.bioconductor.org/packages/GeneNetworkBuilder
git_branch: RELEASE_3_20
git_last_commit: b97fc69
git_last_commit_date: 2024-10-29 09:42:17 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

BUILD BIN results for GeneNetworkBuilder on merida1

To the developers/maintainers of the GeneNetworkBuilder package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneNetworkBuilder.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: GeneNetworkBuilder
Version: 1.48.0
Command: rm -rf GeneNetworkBuilder.buildbin-libdir && mkdir GeneNetworkBuilder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneNetworkBuilder_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeneNetworkBuilder.buildbin-libdir
StartedAt: 2024-12-17 12:09:56 -0500 (Tue, 17 Dec 2024)
EndedAt: 2024-12-17 12:10:41 -0500 (Tue, 17 Dec 2024)
EllapsedTime: 44.5 seconds
RetCode: 0
Status:   OK  
PackageFile: GeneNetworkBuilder_1.48.0.tgz
PackageFileSize: 7.694 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GeneNetworkBuilder.buildbin-libdir && mkdir GeneNetworkBuilder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GeneNetworkBuilder_1.48.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GeneNetworkBuilder.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GeneNetworkBuilder.buildbin-libdir GeneNetworkBuilder_1.48.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GeneNetworkBuilder’ ...
** 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 x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c geneTree.cpp -o geneTree.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c nodefilter.cpp -o nodefilter.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o GeneNetworkBuilder.so RcppExports.o geneTree.o nodefilter.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/GeneNetworkBuilder.buildbin-libdir/00LOCK-GeneNetworkBuilder/00new/GeneNetworkBuilder/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (GeneNetworkBuilder)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/GeneNetworkBuilder.so
>>>>>>> 

>>>>>>> Paths before fix:
GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/GeneNetworkBuilder.so:
	GeneNetworkBuilder.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/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/4.4-x86_64/Resources/lib/libgcc_s.1.1.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/GeneNetworkBuilder.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/GeneNetworkBuilder.so"

>>>>>>> Paths after fix:
GeneNetworkBuilder.buildbin-libdir/GeneNetworkBuilder/libs/GeneNetworkBuilder.so:
	GeneNetworkBuilder.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)