Jitao David Zhang
| Snapshot Date: 2025-12-07 13:40 -0500 (Sun, 07 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/BioQC |
| git_branch: devel |
| git_last_commit: c2f01e7 |
| git_last_commit_date: 2025-10-29 10:28:57 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-08 11:35 -0500 (Mon, 08 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 220/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BioQC 1.39.0 (landing page) Jitao David Zhang
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the BioQC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.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: BioQC |
| Version: 1.39.0 |
| Command: rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BioQC_1.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BioQC.buildbin-libdir |
| StartedAt: 2025-12-07 23:23:07 -0500 (Sun, 07 Dec 2025) |
| EndedAt: 2025-12-07 23:23:15 -0500 (Sun, 07 Dec 2025) |
| EllapsedTime: 8.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: BioQC_1.39.0.tgz |
| PackageFileSize: 4.12 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh BioQC_1.39.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R BioQC.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=BioQC.buildbin-libdir BioQC_1.39.0.tar.gz' >>>>>>> * installing *source* package ‘BioQC’ ... ** this is package ‘BioQC’ version ‘1.39.0’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gini.c -o gini.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c read_gmt.cpp -o read_gmt.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c stat_rank.c -o stat_rank.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG `/Library/Frameworks/R.framework/Resources/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c wmw_test.c -o wmw_test.o 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 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 BioQC.so gini.o init.o read_gmt.o stat_rank.o wmw_test.o -F/Library/Frameworks/R.framework/.. -framework R 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. installing to /Users/biocbuild/bbs-3.23-bioc/meat/BioQC.buildbin-libdir/00LOCK-BioQC/00new/BioQC/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (BioQC) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR BioQC.buildbin-libdir/BioQC/libs/BioQC.so >>>>>>> >>>>>>> Paths before fix: BioQC.buildbin-libdir/BioQC/libs/BioQC.so: BioQC.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0) /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/4.6-arm64/Resources/lib/libgcc_s.1.1.dylib" "BioQC.buildbin-libdir/BioQC/libs/BioQC.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libgfortran.5.dylib" "BioQC.buildbin-libdir/BioQC/libs/BioQC.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libquadmath.0.dylib" "BioQC.buildbin-libdir/BioQC/libs/BioQC.so" >>>>>>> Paths after fix: BioQC.buildbin-libdir/BioQC/libs/BioQC.so: BioQC.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0) /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)