Jiri Hon
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/pqsfinder |
| git_branch: RELEASE_3_17 |
| git_last_commit: a798b81 |
| git_last_commit_date: 2023-04-25 10:46:21 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:37:23 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 1547/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pqsfinder 2.16.0 (landing page) Jiri Hon
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the pqsfinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pqsfinder.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: pqsfinder |
| Version: 2.16.0 |
| Command: rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pqsfinder_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R pqsfinder.buildbin-libdir |
| StartedAt: 2023-10-16 09:56:40 -0400 (Mon, 16 Oct 2023) |
| EndedAt: 2023-10-16 09:59:03 -0400 (Mon, 16 Oct 2023) |
| EllapsedTime: 143.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: pqsfinder_2.16.0.tgz |
| PackageFileSize: 1.578 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf pqsfinder.buildbin-libdir && mkdir pqsfinder.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pqsfinder_2.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R pqsfinder.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=pqsfinder.buildbin-libdir pqsfinder_2.16.0.tar.gz' >>>>>>> * installing *source* package ‘pqsfinder’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pqsfinder.cpp -o pqsfinder.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_regex/regex.cpp -o boost_regex/regex.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o mkdir -p "/Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib" ar rs "/Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/static_mutex.o boost_regex/wide_posix_api.o ar: creating archive /Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a /Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a(regex.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a(regex_debug.o) has no symbols /Library/Developer/CommandLineTools/usr/bin/ranlib: file: /Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a(static_mutex.o) has no symbols clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o pqsfinder.so RcppExports.o pqsfinder.o /Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.17-bioc/meat/pqsfinder.buildbin-libdir/00LOCK-pqsfinder/00new/pqsfinder/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 (pqsfinder) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR pqsfinder.buildbin-libdir/pqsfinder/libs/pqsfinder.so >>>>>>> >>>>>>> Paths before fix: pqsfinder.buildbin-libdir/pqsfinder/libs/pqsfinder.so: pqsfinder.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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/4.3-x86_64/Resources/lib/libgcc_s.1.1.dylib" "pqsfinder.buildbin-libdir/pqsfinder/libs/pqsfinder.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" "pqsfinder.buildbin-libdir/pqsfinder/libs/pqsfinder.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" "pqsfinder.buildbin-libdir/pqsfinder/libs/pqsfinder.so" >>>>>>> Paths after fix: pqsfinder.buildbin-libdir/pqsfinder/libs/pqsfinder.so: pqsfinder.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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)