| Back to Multiple platform build/check report for BioC 3.23: simplified long |
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This page was generated on 2026-04-18 11:38 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 2346/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| VariantAnnotation 1.57.1 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
| 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: VariantAnnotation |
| Version: 1.57.1 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data VariantAnnotation |
| StartedAt: 2026-04-17 02:24:01 -0000 (Fri, 17 Apr 2026) |
| EndedAt: 2026-04-17 02:24:09 -0000 (Fri, 17 Apr 2026) |
| EllapsedTime: 8.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data VariantAnnotation
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* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* preparing ‘VariantAnnotation’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘VariantAnnotation’ ...
** this is package ‘VariantAnnotation’ version ‘1.57.1’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c dna_hash.c -o dna_hash.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rle.c -o rle.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c strhash.c -o strhash.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utilities.c -o utilities.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c vcffile.c -o vcffile.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c vcftype.c -o vcftype.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c writevcf.c -o writevcf.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/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 /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/R/R/lib -lR
/usr/bin/ld: cannot find -lcurl: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [/home/biocbuild/R/R/share/make/shlib.mk:10: VariantAnnotation.so] Error 1
ERROR: compilation failed for package ‘VariantAnnotation’
* removing ‘/home/biocbuild/tmp/RtmpZpodwe/Rinst13e7d64ab7f319/VariantAnnotation’
-----------------------------------
ERROR: package installation failed