Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1145/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MANOR 1.78.0 (landing page) Pierre Neuvial
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the MANOR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MANOR.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: MANOR |
Version: 1.78.0 |
Command: rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MANOR_1.78.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R MANOR.buildbin-libdir |
StartedAt: 2024-12-21 15:29:46 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 15:29:54 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 8.1 seconds |
RetCode: 0 |
Status: OK |
PackageFile: MANOR_1.78.0.tgz |
PackageFileSize: 1.78 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf MANOR.buildbin-libdir && mkdir MANOR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh MANOR_1.78.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R MANOR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=MANOR.buildbin-libdir MANOR_1.78.0.tar.gz' >>>>>>> * installing *source* package ‘MANOR’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rnem_arg.c -o Rnem_arg.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Rnem_exe.c -o Rnem_exe.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c exememo.c -o exememo.o exememo.c:43:13: warning: format string is not a string literal (potentially insecure) [-Wformat-security] error(msg); ^~~ exememo.c:43:13: note: treat the string as an argument to avoid this error(msg); ^ "%s", exememo.c:40:13: warning: variable 'msg' is uninitialized when used here [-Wuninitialized] sprintf(msg, "Fatal: in %s, no memory for %s (%ld elements size %ld)\n", ^~~ /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk/usr/include/secure/_stdio.h:47:28: note: expanded from macro 'sprintf' __builtin___sprintf_chk (str, 0, __darwin_obsz(str), __VA_ARGS__) ^~~ exememo.c:39:14: note: initialize the variable 'msg' to silence this warning char* msg; ^ = NULL 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 nem_alg.c -o nem_alg.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nem_hlp.c -o nem_hlp.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nem_mod.c -o nem_mod.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nem_nei.c -o nem_nei.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nem_rnd.c -o nem_rnd.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c nem_ver.c -o nem_ver.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbols.c -o registerDynamicSymbols.o clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o MANOR.so Rnem_arg.o Rnem_exe.o exememo.o nem_alg.o nem_hlp.o nem_mod.o nem_nei.o nem_rnd.o nem_ver.o registerDynamicSymbols.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/MANOR.buildbin-libdir/00LOCK-MANOR/00new/MANOR/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 (MANOR) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR MANOR.buildbin-libdir/MANOR/libs/MANOR.so >>>>>>> >>>>>>> Paths before fix: MANOR.buildbin-libdir/MANOR/libs/MANOR.so: MANOR.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 4.4.2) /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-arm64/Resources/lib/libgcc_s.1.1.dylib" "MANOR.buildbin-libdir/MANOR/libs/MANOR.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "MANOR.buildbin-libdir/MANOR/libs/MANOR.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "MANOR.buildbin-libdir/MANOR/libs/MANOR.so" >>>>>>> Paths after fix: MANOR.buildbin-libdir/MANOR/libs/MANOR.so: MANOR.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 4.4.2) /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)