Hervé Pagès
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/pwalign |
| git_branch: RELEASE_3_20 |
| git_last_commit: 9d0fa61 |
| git_last_commit_date: 2024-10-29 11:29:52 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:08 -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 1622/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pwalign 1.2.0 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the pwalign package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pwalign.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: pwalign |
| Version: 1.2.0 |
| Command: rm -rf pwalign.buildbin-libdir && mkdir pwalign.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pwalign_1.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R pwalign.buildbin-libdir |
| StartedAt: 2024-12-21 16:05:51 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 16:06:12 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 21.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: pwalign_1.2.0.tgz |
| PackageFileSize: 755.8 KiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf pwalign.buildbin-libdir && mkdir pwalign.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh pwalign_1.2.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R pwalign.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=pwalign.buildbin-libdir pwalign_1.2.0.tar.gz' >>>>>>> * installing *source* package ‘pwalign’ ... ** 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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_pairwiseAlignment.c -o R_init_pairwiseAlignment.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Biostrings/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c align_utils.c -o align_utils.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 pwalign.so Biostrings_stubs.o IRanges_stubs.o R_init_pairwiseAlignment.o S4Vectors_stubs.o XVector_stubs.o align_pairwiseAlignment.o align_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.20-bioc/meat/pwalign.buildbin-libdir/00LOCK-pwalign/00new/pwalign/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘insertion’ in package ‘pwalign’ Creating a new generic function for ‘deletion’ in package ‘pwalign’ Creating a new generic function for ‘unaligned’ in package ‘pwalign’ Creating a new generic function for ‘aligned’ in package ‘pwalign’ Creating a new generic function for ‘indel’ in package ‘pwalign’ Creating a new generic function for ‘nindel’ in package ‘pwalign’ Creating a new generic function for ‘PairwiseAlignments’ in package ‘pwalign’ Creating a new generic function for ‘alignedPattern’ in package ‘pwalign’ Creating a new generic function for ‘alignedSubject’ in package ‘pwalign’ Creating a new generic function for ‘PairwiseAlignmentsSingleSubject’ in package ‘pwalign’ Creating a new generic function for ‘nedit’ in package ‘pwalign’ Creating a new generic function for ‘mismatchTable’ in package ‘pwalign’ Creating a new generic function for ‘mismatchSummary’ in package ‘pwalign’ Creating a new generic function for ‘compareStrings’ in package ‘pwalign’ Creating a new generic function for ‘pid’ in package ‘pwalign’ Creating a new generic function for ‘pairwiseAlignment’ in package ‘pwalign’ Creating a new generic function for ‘stringDist’ in package ‘pwalign’ ** 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 (pwalign) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR pwalign.buildbin-libdir/pwalign/libs/pwalign.so >>>>>>> >>>>>>> Paths before fix: pwalign.buildbin-libdir/pwalign/libs/pwalign.so: pwalign.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" "pwalign.buildbin-libdir/pwalign/libs/pwalign.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "pwalign.buildbin-libdir/pwalign/libs/pwalign.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "pwalign.buildbin-libdir/pwalign/libs/pwalign.so" >>>>>>> Paths after fix: pwalign.buildbin-libdir/pwalign/libs/pwalign.so: pwalign.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)