Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:06 -0500 (Wed, 20 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
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 1316/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
motifcounter 1.30.0 (landing page) Wolfgang Kopp
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the motifcounter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/motifcounter.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: motifcounter |
Version: 1.30.0 |
Command: rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifcounter_1.30.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifcounter.buildbin-libdir |
StartedAt: 2024-11-20 04:37:58 -0500 (Wed, 20 Nov 2024) |
EndedAt: 2024-11-20 04:38:24 -0500 (Wed, 20 Nov 2024) |
EllapsedTime: 26.3 seconds |
RetCode: 0 |
Status: OK |
PackageFile: motifcounter_1.30.0.tgz |
PackageFileSize: 742.3 KiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf motifcounter.buildbin-libdir && mkdir motifcounter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh motifcounter_1.30.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R motifcounter.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=motifcounter.buildbin-libdir motifcounter_1.30.0.tar.gz' >>>>>>> * installing *source* package ‘motifcounter’ ... ** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rbackground.c -o Rbackground.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rcombinatorial.c -o Rcombinatorial.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rcompoundpoisson.c -o Rcompoundpoisson.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rminmaxscore.c -o Rminmaxscore.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Roption.c -o Roption.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Roverlap.c -o Roverlap.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rscore1d.c -o Rscore1d.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rsequence.c -o Rsequence.o Rsequence.c:143:21: warning: unused variable 'noscores' [-Wunused-variable] int mins, maxs, noscores; ^ 1 warning generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c Rsimulate.c -o Rsimulate.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c background.c -o background.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c combinatorial.c -o combinatorial.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c compoundpoisson.c -o compoundpoisson.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c markovchain.c -o markovchain.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c markovchain_single.c -o markovchain_single.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c matrix.c -o matrix.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c mdist_register.c -o mdist_register.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c minmaxscore.c -o minmaxscore.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c overlap.c -o overlap.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c score1d.c -o score1d.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c score2d.c -o score2d.o score2d.c:597:25: warning: variable 'p1' set but not used [-Wunused-but-set-variable] double p, p0 = 0.0, p1 = 0.0, ptmp; ^ score2d.c:597:15: warning: variable 'p0' set but not used [-Wunused-but-set-variable] double p, p0 = 0.0, p1 = 0.0, ptmp; ^ 2 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c scorefunctions.c -o scorefunctions.o scorefunctions.c:84:22: warning: unused variable 'cindex' [-Wunused-variable] int j, i, index, cindex, ds; ^ scorefunctions.c:119:17: warning: unused variable 'cindex' [-Wunused-variable] int s, index, cindex; ^ scorefunctions.c:159:19: warning: unused variable 'cindex' [-Wunused-variable] int s, index, cindex; ^ 3 warnings generated. clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c sequence.c -o sequence.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -DIN_R -fPIC -falign-functions=64 -Wall -g -O2 -c simulate.c -o simulate.o clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o motifcounter.so Rbackground.o Rcombinatorial.o Rcompoundpoisson.o Rminmaxscore.o Roption.o Roverlap.o Rscore1d.o Rsequence.o Rsimulate.o background.o combinatorial.o compoundpoisson.o markovchain.o markovchain_single.o matrix.o mdist_register.o minmaxscore.o overlap.o score1d.o score2d.o scorefunctions.o sequence.o simulate.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/motifcounter.buildbin-libdir/00LOCK-motifcounter/00new/motifcounter/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 (motifcounter) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so >>>>>>> >>>>>>> Paths before fix: motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so: motifcounter.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/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-x86_64/Resources/lib/libgcc_s.1.1.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libgfortran.5.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libquadmath.0.dylib" "motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so" >>>>>>> Paths after fix: motifcounter.buildbin-libdir/motifcounter/libs/motifcounter.so: motifcounter.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.4-x86_64/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/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)