Martin Morgan
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/BiocParallel |
| git_branch: devel |
| git_last_commit: 0f688b6 |
| git_last_commit_date: 2024-10-29 09:43:33 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:44 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 188/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocParallel 1.41.0 (landing page) Martin Morgan
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | 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 | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the BiocParallel package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocParallel.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: BiocParallel |
| Version: 1.41.0 |
| Command: rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocParallel_1.41.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiocParallel.buildbin-libdir |
| StartedAt: 2024-12-23 22:20:17 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 22:20:27 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 10.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: BiocParallel_1.41.0.tgz |
| PackageFileSize: 1.551 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BiocParallel.buildbin-libdir && mkdir BiocParallel.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BiocParallel_1.41.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BiocParallel.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BiocParallel.buildbin-libdir BiocParallel_1.41.0.tar.gz' >>>>>>> * installing *source* package ‘BiocParallel’ ... ** using staged installation checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... yes checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed checking for library containing shm_open... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/mman.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c cpp11.cpp -o cpp11.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/cpp11/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ipcmutex.cpp -o ipcmutex.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o BiocParallel.so cpp11.o ipcmutex.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/BiocParallel.buildbin-libdir/00LOCK-BiocParallel/00new/BiocParallel/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 (BiocParallel) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BiocParallel.buildbin-libdir/BiocParallel/libs/BiocParallel.so >>>>>>> >>>>>>> Paths before fix: BiocParallel.buildbin-libdir/BiocParallel/libs/BiocParallel.so: BiocParallel.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 4.5.0) /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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "BiocParallel.buildbin-libdir/BiocParallel/libs/BiocParallel.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "BiocParallel.buildbin-libdir/BiocParallel/libs/BiocParallel.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "BiocParallel.buildbin-libdir/BiocParallel/libs/BiocParallel.so" >>>>>>> Paths after fix: BiocParallel.buildbin-libdir/BiocParallel/libs/BiocParallel.so: BiocParallel.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 4.5.0) /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)