Multiple platform build/check report for BioC 3.20 - BUILD BIN results for Mulcom on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
teran2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4505
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4506
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4538
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4486
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	4.4.1 (2024-06-14) -- "Race for Your Life"	4493
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 Mulcom on kjohnson3

To the developers/maintainers of the Mulcom package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Mulcom.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: Mulcom

Version: 1.56.0

Command: rm -rf Mulcom.buildbin-libdir && mkdir Mulcom.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Mulcom_1.56.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Mulcom.buildbin-libdir

StartedAt: 2024-11-09 17:00:59 -0500 (Sat, 09 Nov 2024)

EndedAt: 2024-11-09 17:01:03 -0500 (Sat, 09 Nov 2024)

EllapsedTime: 4.1 seconds

RetCode: 0

Status: OK

PackageFile: Mulcom_1.56.0.tgz

PackageFileSize: 1.187 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf Mulcom.buildbin-libdir && mkdir Mulcom.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Mulcom_1.56.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Mulcom.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Mulcom.buildbin-libdir Mulcom_1.56.0.tar.gz'
>>>>>>> 

* installing *source* package ‘Mulcom’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c mulLibs.cc -o mulLibs.o
mulLibs.cc:708:17: warning: expression result unused [-Wunused-value]
                current_cluster ;
                ^~~~~~~~~~~~~~~
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Mulcom.so mulLibs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/Mulcom.buildbin-libdir/00LOCK-Mulcom/00new/Mulcom/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 (Mulcom)


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

>>>>>>> Paths before fix:
Mulcom.buildbin-libdir/Mulcom/libs/Mulcom.so:
	Mulcom.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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-arm64/Resources/lib/libgcc_s.1.1.dylib" "Mulcom.buildbin-libdir/Mulcom/libs/Mulcom.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "Mulcom.buildbin-libdir/Mulcom/libs/Mulcom.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "Mulcom.buildbin-libdir/Mulcom/libs/Mulcom.so"

>>>>>>> Paths after fix:
Mulcom.buildbin-libdir/Mulcom/libs/Mulcom.so:
	Mulcom.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/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)