Jiri Hon
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/triplex |
| git_branch: devel |
| git_last_commit: cc51819 |
| git_last_commit_date: 2024-10-29 09:45:50 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| 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 2183/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| triplex 1.47.0 (landing page) Jiri Hon
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the triplex package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/triplex.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: triplex |
| Version: 1.47.0 |
| Command: rm -rf triplex.buildbin-libdir && mkdir triplex.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh triplex_1.47.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R triplex.buildbin-libdir |
| StartedAt: 2024-12-23 22:47:47 -0500 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 22:47:56 -0500 (Mon, 23 Dec 2024) |
| EllapsedTime: 9.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: triplex_1.47.0.tgz |
| PackageFileSize: 939.1 KiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf triplex.buildbin-libdir && mkdir triplex.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh triplex_1.47.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R triplex.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=triplex.buildbin-libdir triplex_1.47.0.tar.gz' >>>>>>> * installing *source* package ‘triplex’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_triplex.c -o R_init_triplex.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align.c -o align.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align_interface.c -o align_interface.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dl_list.c -o dl_list.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c interval.c -o interval.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c libtriplex.c -o libtriplex.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progress.c -o progress.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c search.c -o search.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c search_interface.c -o search_interface.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 triplex.so Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o XVector_stubs.o align.o align_interface.o dl_list.o interval.o libtriplex.o progress.o search.o search_interface.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/meat/triplex.buildbin-libdir/00LOCK-triplex/00new/triplex/libs ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’ ** testing if installed package keeps a record of temporary installation path * DONE (triplex) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR triplex.buildbin-libdir/triplex/libs/triplex.so >>>>>>> >>>>>>> Paths before fix: triplex.buildbin-libdir/triplex/libs/triplex.so: triplex.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "triplex.buildbin-libdir/triplex/libs/triplex.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "triplex.buildbin-libdir/triplex/libs/triplex.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "triplex.buildbin-libdir/triplex/libs/triplex.so" >>>>>>> Paths after fix: triplex.buildbin-libdir/triplex/libs/triplex.so: triplex.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /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)