Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 357/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
cisPath 1.46.0 (landing page) Likun Wang
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the cisPath package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cisPath.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: cisPath |
Version: 1.46.0 |
Command: rm -rf cisPath.buildbin-libdir && mkdir cisPath.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cisPath_1.46.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cisPath.buildbin-libdir |
StartedAt: 2024-11-09 16:42:18 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 16:42:23 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 5.1 seconds |
RetCode: 0 |
Status: OK |
PackageFile: cisPath_1.46.0.tgz |
PackageFileSize: 1.078 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf cisPath.buildbin-libdir && mkdir cisPath.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cisPath_1.46.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cisPath.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cisPath.buildbin-libdir cisPath_1.46.0.tar.gz' >>>>>>> * installing *source* package ‘cisPath’ ... ** 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=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c cisPath.cpp -o cisPath.o cisPath.cpp:714:9: warning: variable 'lineCount' set but not used [-Wunused-but-set-variable] int lineCount = 1; ^ cisPath.cpp:945:14: warning: explicitly assigning value of variable of type 'string' (aka 'basic_string<char, char_traits<char>, allocator<char>>') to itself [-Wself-assign-overloaded] Name = Name; ~~~~ ^ ~~~~ cisPath.cpp:3555:27: warning: format string is not a string literal (potentially insecure) [-Wformat-security] PRINTFUNCTION(buffer); ^~~~~~ cisPath.cpp:3555:27: note: treat the string as an argument to avoid this PRINTFUNCTION(buffer); ^ "%s", 3 warnings generated. clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o cisPath.so cisPath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/cisPath.buildbin-libdir/00LOCK-cisPath/00new/cisPath/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 (cisPath) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR cisPath.buildbin-libdir/cisPath/libs/cisPath.so >>>>>>> >>>>>>> Paths before fix: cisPath.buildbin-libdir/cisPath/libs/cisPath.so: cisPath.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 4.4.1) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "cisPath.buildbin-libdir/cisPath/libs/cisPath.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "cisPath.buildbin-libdir/cisPath/libs/cisPath.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "cisPath.buildbin-libdir/cisPath/libs/cisPath.so" >>>>>>> Paths after fix: cisPath.buildbin-libdir/cisPath/libs/cisPath.so: cisPath.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 4.4.1) /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)