Kylie Ariel Bemis
| Snapshot Date: 2025-10-29 19:52 -0400 (Wed, 29 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/CardinalIO |
| git_branch: RELEASE_3_22 |
| git_last_commit: 0a719c9 |
| git_last_commit_date: 2025-10-29 11:24:36 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-30 12:35 -0400 (Thu, 30 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| 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 282/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CardinalIO 1.8.0 (landing page) Kylie Ariel Bemis
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the CardinalIO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CardinalIO.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: CardinalIO |
| Version: 1.8.0 |
| Command: rm -rf CardinalIO.buildbin-libdir && mkdir CardinalIO.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CardinalIO_1.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CardinalIO.buildbin-libdir |
| StartedAt: 2025-10-30 08:07:28 -0400 (Thu, 30 Oct 2025) |
| EndedAt: 2025-10-30 08:07:56 -0400 (Thu, 30 Oct 2025) |
| EllapsedTime: 27.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: CardinalIO_1.8.0.tgz |
| PackageFileSize: 1.255 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf CardinalIO.buildbin-libdir && mkdir CardinalIO.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh CardinalIO_1.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R CardinalIO.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=CardinalIO.buildbin-libdir CardinalIO_1.8.0.tar.gz' >>>>>>> * installing *source* package ‘CardinalIO’ ... ** this is package ‘CardinalIO’ version ‘1.8.0’ ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CardinalIO.cpp -o CardinalIO.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.cpp -o init.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pugixml.cpp -o pugixml.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 CardinalIO.so CardinalIO.o init.o pugixml.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.22-bioc/meat/CardinalIO.buildbin-libdir/00LOCK-CardinalIO/00new/CardinalIO/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 (CardinalIO) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so >>>>>>> >>>>>>> Paths before fix: CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so: CardinalIO.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so" >>>>>>> Paths after fix: CardinalIO.buildbin-libdir/CardinalIO/libs/CardinalIO.so: CardinalIO.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.1) /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)