Multiple platform build/check report for BioC 3.20 - BUILD BIN results for VariantFiltering on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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 VariantFiltering on kjohnson1

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

Version: 1.42.0

Command: rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantFiltering.buildbin-libdir

StartedAt: 2025-04-02 16:46:00 -0400 (Wed, 02 Apr 2025)

EndedAt: 2025-04-02 16:47:20 -0400 (Wed, 02 Apr 2025)

EllapsedTime: 80.1 seconds

RetCode: 0

Status: OK

PackageFile: VariantFiltering_1.42.0.tgz

PackageFileSize: 4.156 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf VariantFiltering.buildbin-libdir && mkdir VariantFiltering.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantFiltering_1.42.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantFiltering.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantFiltering.buildbin-libdir VariantFiltering_1.42.0.tar.gz'
>>>>>>> 

* installing *source* package ‘VariantFiltering’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_VariantFiltering.c -o R_init_VariantFiltering.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c methods-WeightMatrix.c -o methods-WeightMatrix.o
methods-WeightMatrix.c:341:9: warning: variable 'line' set but not used [-Wunused-but-set-variable]
  int   line=1;
        ^
methods-WeightMatrix.c:546:11: warning: variable 'line' set but not used [-Wunused-but-set-variable]
  int     line=1;
          ^
2 warnings generated.
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o VariantFiltering.so Biostrings_stubs.o R_init_VariantFiltering.o methods-WeightMatrix.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.20-bioc/meat/VariantFiltering.buildbin-libdir/00LOCK-VariantFiltering/00new/VariantFiltering/libs
** R
** 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 (VariantFiltering)


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

>>>>>>> Paths before fix:
VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so:
	VariantFiltering.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 4.4.3)
	/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so"

>>>>>>> Paths after fix:
VariantFiltering.buildbin-libdir/VariantFiltering/libs/VariantFiltering.so:
	VariantFiltering.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 4.4.3)
	/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)