Kent Riemondy
| Snapshot Date: 2024-03-27 14:05:05 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/raer |
| git_branch: RELEASE_3_18 |
| git_last_commit: 852cee5 |
| git_last_commit_date: 2024-03-08 12:35:28 -0400 (Fri, 08 Mar 2024) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:38:07 -0400 (Fri, 29 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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 1649/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| raer 1.0.2 (landing page) Kent Riemondy
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the raer package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/raer.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: raer |
| Version: 1.0.2 |
| Command: rm -rf raer.buildbin-libdir && mkdir raer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh raer_1.0.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R raer.buildbin-libdir |
| StartedAt: 2024-03-28 12:11:30 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 12:13:17 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 106.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: raer_1.0.2.tgz |
| PackageFileSize: 2.844 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf raer.buildbin-libdir && mkdir raer.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh raer_1.0.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R raer.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=raer.buildbin-libdir raer_1.0.2.tar.gz' >>>>>>> * installing *source* package ‘raer’ ... ** 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 -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c plp.c -o plp.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c plp_data.c -o plp_data.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c plp_utils.c -o plp_utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c regfile.c -o regfile.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c sc-plp.c -o sc-plp.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ext/bcftools/bcftools-ext.c -o ext/bcftools/bcftools-ext.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ext/htsbox/htsbox-ext.c -o ext/htsbox/htsbox-ext.o clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ext/samtools/samtools-ext.c -o ext/samtools/samtools-ext.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 raer.so init.o plp.o plp_data.o plp_utils.o regfile.o sc-plp.o utils.o ext/bcftools/bcftools-ext.o ext/htsbox/htsbox-ext.o ext/samtools/samtools-ext.o /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.18-bioc/meat/raer.buildbin-libdir/00LOCK-raer/00new/raer/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 (raer) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR raer.buildbin-libdir/raer/libs/raer.so >>>>>>> >>>>>>> Paths before fix: raer.buildbin-libdir/raer/libs/raer.so: raer.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "raer.buildbin-libdir/raer/libs/raer.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libgfortran.5.dylib" "raer.buildbin-libdir/raer/libs/raer.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libquadmath.0.dylib" "raer.buildbin-libdir/raer/libs/raer.so" >>>>>>> Paths after fix: raer.buildbin-libdir/raer/libs/raer.so: raer.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libbz2.1.0.dylib (compatibility version 1.0.0, current version 1.0.5) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.3) /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)