Joern P. Meier
| Snapshot Date: 2026-03-20 13:40 -0400 (Fri, 20 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/GraphAlignment |
| git_branch: devel |
| git_last_commit: c4f998f |
| git_last_commit_date: 2025-10-29 10:00:07 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-21 11:34 -0400 (Sat, 21 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4545 |
| 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 933/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GraphAlignment 1.75.0 (landing page) Joern P. Meier
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | ERROR | |||||||||
| See other builds for GraphAlignment in R Universe. | ||||||||||||||
|
To the developers/maintainers of the GraphAlignment package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GraphAlignment.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. |
| Package: GraphAlignment |
| Version: 1.75.0 |
| Command: rm -rf GraphAlignment.buildbin-libdir && mkdir GraphAlignment.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GraphAlignment_1.75.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GraphAlignment.buildbin-libdir |
| StartedAt: 2026-03-21 02:30:11 -0400 (Sat, 21 Mar 2026) |
| EndedAt: 2026-03-21 02:30:15 -0400 (Sat, 21 Mar 2026) |
| EllapsedTime: 4.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### rm -rf GraphAlignment.buildbin-libdir && mkdir GraphAlignment.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GraphAlignment_1.75.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GraphAlignment.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GraphAlignment.buildbin-libdir GraphAlignment_1.75.0.tar.gz'
>>>>>>>
* installing *source* package ‘GraphAlignment’ ...
** this is package ‘GraphAlignment’ version ‘1.75.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’
using SDK: ‘MacOSX26.2.sdk’
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GA_alloc.c -o GA_alloc.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GA_matrix.c -o GA_matrix.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GA_matrix_R.c -o GA_matrix_R.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GA_message.c -o GA_message.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GA_vector.c -o GA_vector.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GA_vector_R.c -o GA_vector_R.o
GA_vector_R.c:139:9: warning: unused variable 'size' [-Wunused-variable]
139 | int size = LENGTH(robj);
| ^~~~
1 warning generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GraphAlignment.c -o GraphAlignment.o
GraphAlignment.c:143:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
143 | } else
| ^
GraphAlignment.c:164:23: warning: add explicit braces to avoid dangling else [-Wdangling-else]
164 | } else
| ^
GraphAlignment.c:264:9: warning: unused variable 'size' [-Wunused-variable]
264 | int size = LENGTH(robj);
| ^~~~
3 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c lap.c -o lap.o
clang -arch arm64 -std=gnu23 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GraphAlignment.so GA_alloc.o GA_matrix.o GA_matrix_R.o GA_message.o GA_vector.o GA_vector_R.o GraphAlignment.o lap.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Users/biocbuild/bbs-3.23-bioc/meat/GraphAlignment.buildbin-libdir/00LOCK-GraphAlignment/00new/GraphAlignment/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 (GraphAlignment)
>>>>>>>
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GraphAlignment.buildbin-libdir/GraphAlignment/libs/GraphAlignment.so
>>>>>>>
>>>>>>> Paths before fix:
GraphAlignment.buildbin-libdir/GraphAlignment/libs/GraphAlignment.so:
GraphAlignment.so (compatibility version 0.0.0, current version 0.0.0)
/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0)
>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!