| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-03-21 11:35 -0400 (Sat, 21 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences" | 4866 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-20 r89666) -- "Unsuffered Consequences" | 4545 |
| 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 2312/2368 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantAnnotation 1.57.1 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | ERROR | |||||||||
| See other builds for VariantAnnotation in R Universe. | ||||||||||||||
|
To the developers/maintainers of the VariantAnnotation package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VariantAnnotation.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: VariantAnnotation |
| Version: 1.57.1 |
| Command: rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantAnnotation_1.57.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantAnnotation.buildbin-libdir |
| StartedAt: 2026-03-21 02:51:47 -0400 (Sat, 21 Mar 2026) |
| EndedAt: 2026-03-21 02:52:24 -0400 (Sat, 21 Mar 2026) |
| EllapsedTime: 37.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf VariantAnnotation.buildbin-libdir && mkdir VariantAnnotation.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VariantAnnotation_1.57.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VariantAnnotation.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VariantAnnotation.buildbin-libdir VariantAnnotation_1.57.1.tar.gz' >>>>>>> * installing *source* package ‘VariantAnnotation’ ... ** this is package ‘VariantAnnotation’ version ‘1.57.1’ ** using staged installation ** libs using C compiler: ‘Apple clang version 17.0.0 (clang-1700.6.4.2)’ using SDK: ‘MacOSX26.2.sdk’ clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c XVector_stubs.c -o XVector_stubs.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c dna_hash.c -o dna_hash.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c rle.c -o rle.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c strhash.c -o strhash.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utilities.c -o utilities.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcffile.c -o vcffile.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vcftype.c -o vcftype.o clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/IRanges/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XVector/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Biostrings/include' -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c writevcf.c -o writevcf.o clang -arch arm64 -std=gnu23 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R installing to /Users/biocbuild/bbs-3.23-bioc/meat/VariantAnnotation.buildbin-libdir/00LOCK-VariantAnnotation/00new/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** 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 (VariantAnnotation) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.so >>>>>>> >>>>>>> Paths before fix: VariantAnnotation.buildbin-libdir/VariantAnnotation/libs/VariantAnnotation.so: VariantAnnotation.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 1.0.8) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.12) /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1356.0.0) >>>>>>> Fix with install_name_tool: ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libR.dylib not found!