Robert Castelo
| Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/GSVA |
| git_branch: devel |
| git_last_commit: a603221 |
| git_last_commit_date: 2025-04-23 13:02:32 -0400 (Wed, 23 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 926/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GSVA 2.3.1 (landing page) Robert Castelo
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the GSVA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSVA.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: GSVA |
| Version: 2.3.1 |
| Command: rm -rf GSVA.buildbin-libdir && mkdir GSVA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GSVA_2.3.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GSVA.buildbin-libdir |
| StartedAt: 2025-08-08 22:34:01 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 22:34:18 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 17.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: GSVA_2.3.1.tgz |
| PackageFileSize: 2.509 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf GSVA.buildbin-libdir && mkdir GSVA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GSVA_2.3.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GSVA.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GSVA.buildbin-libdir GSVA_2.3.1.tar.gz' >>>>>>> * installing *source* package ‘GSVA’ ... ** this is package ‘GSVA’ version ‘2.3.1’ ** 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=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ecdfvals.c -o ecdfvals.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kcdfvals.c -o kcdfvals.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kernel_estimation.c -o kernel_estimation.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ks_test.c -o ks_test.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c register_cmethods.c -o register_cmethods.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GSVA.so ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o utils.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.22-bioc/meat/GSVA.buildbin-libdir/00LOCK-GSVA/00new/GSVA/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 (GSVA) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GSVA.buildbin-libdir/GSVA/libs/GSVA.so >>>>>>> >>>>>>> Paths before fix: GSVA.buildbin-libdir/GSVA/libs/GSVA.so: GSVA.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "GSVA.buildbin-libdir/GSVA/libs/GSVA.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "GSVA.buildbin-libdir/GSVA/libs/GSVA.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "GSVA.buildbin-libdir/GSVA/libs/GSVA.so" >>>>>>> Paths after fix: GSVA.buildbin-libdir/GSVA/libs/GSVA.so: GSVA.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)