Likun Wang
| Snapshot Date: 2024-11-27 13:40 -0500 (Wed, 27 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/cisPath |
| git_branch: devel |
| git_last_commit: 7d721c8 |
| git_last_commit_date: 2024-10-29 09:44:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-28 12:16 -0500 (Thu, 28 Nov 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" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| 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 350/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cisPath 1.47.0 (landing page) Likun Wang
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
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: 1.47.0 |
| Command: rm -rf cisPath.buildbin-libdir && mkdir cisPath.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cisPath_1.47.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cisPath.buildbin-libdir |
| StartedAt: 2024-11-28 03:53:46 -0500 (Thu, 28 Nov 2024) |
| EndedAt: 2024-11-28 03:54:07 -0500 (Thu, 28 Nov 2024) |
| EllapsedTime: 20.8 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: cisPath_1.47.0.tgz |
| PackageFileSize: 1.089 MiB |
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### Running command:
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### rm -rf cisPath.buildbin-libdir && mkdir cisPath.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cisPath_1.47.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R cisPath.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cisPath.buildbin-libdir cisPath_1.47.0.tar.gz'
>>>>>>>
* installing *source* package ‘cisPath’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.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 -DR_NO_REMAP -c cisPath.cpp -o cisPath.o
cisPath.cpp:945:14: warning: explicitly assigning value of variable of type 'std::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",
2 warnings generated.
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 cisPath.so cisPath.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-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/4.5-x86_64/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)
/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)
>>>>>>> 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" "cisPath.buildbin-libdir/cisPath/libs/cisPath.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" "cisPath.buildbin-libdir/cisPath/libs/cisPath.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" "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/4.5-x86_64/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)
/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)