Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 2056/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
switchBox 1.41.0 (landing page) Bahman Afsari
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
To the developers/maintainers of the switchBox package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/switchBox.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: switchBox |
Version: 1.41.0 |
Command: rm -rf switchBox.buildbin-libdir && mkdir switchBox.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh switchBox_1.41.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R switchBox.buildbin-libdir |
StartedAt: 2024-06-11 15:17:09 -0400 (Tue, 11 Jun 2024) |
EndedAt: 2024-06-11 15:17:18 -0400 (Tue, 11 Jun 2024) |
EllapsedTime: 8.9 seconds |
RetCode: 0 |
Status: OK |
PackageFile: switchBox_1.41.0.tgz |
PackageFileSize: 636.8 KiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf switchBox.buildbin-libdir && mkdir switchBox.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh switchBox_1.41.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R switchBox.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=switchBox.buildbin-libdir switchBox_1.41.0.tar.gz' >>>>>>> * installing *source* package ‘switchBox’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ 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 CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o CalculateSignedScoreCore.cc:36:26: warning: variable 'pairsNo' set but not used [-Wunused-but-set-variable] int i,j,l,countplace,pairsNo; ^ 1 warning generated. 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 CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable 'score1' [-Wunused-variable] double score1, score2, type; ^ 1 warning generated. 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 CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCore.cc:22:11: warning: variable 'countplace' set but not used [-Wunused-but-set-variable] int i,l,countplace,pairsNo; ^ 1 warning generated. 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 CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:11: warning: unused variable 'countplace' [-Wunused-variable] int i,l,countplace,pairsNo; ^ CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable 'score1' [-Wunused-variable] double score1, score2, type; ^ 2 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rinit.c -o rinit.o 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 vect2compC.cc -o vect2compC.o 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 switchBox.so CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/switchBox.buildbin-libdir/00LOCK-switchBox/00new/switchBox/libs ** R ** data ** 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 (switchBox) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR switchBox.buildbin-libdir/switchBox/libs/switchBox.so >>>>>>> >>>>>>> Paths before fix: switchBox.buildbin-libdir/switchBox/libs/switchBox.so: switchBox.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 4.4.0) /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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "switchBox.buildbin-libdir/switchBox/libs/switchBox.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "switchBox.buildbin-libdir/switchBox/libs/switchBox.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "switchBox.buildbin-libdir/switchBox/libs/switchBox.so" >>>>>>> Paths after fix: switchBox.buildbin-libdir/switchBox/libs/switchBox.so: switchBox.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 4.4.0) /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)