Xiuwen Zheng
| Snapshot Date: 2026-03-11 13:40 -0400 (Wed, 11 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/HIBAG |
| git_branch: devel |
| git_last_commit: 5a359df |
| git_last_commit_date: 2025-10-29 10:23:56 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-12 11:34 -0400 (Thu, 12 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" | 4806 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 4049 |
| 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 979/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HIBAG 1.47.0 (landing page) Xiuwen Zheng
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ERROR | ERROR | skipped | skipped | |||||||||
| See other builds for HIBAG in R Universe. | ||||||||||||||
|
To the developers/maintainers of the HIBAG package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HIBAG.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: HIBAG |
| Version: 1.47.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HIBAG |
| StartedAt: 2026-03-11 16:17:03 -0400 (Wed, 11 Mar 2026) |
| EndedAt: 2026-03-11 16:17:10 -0400 (Wed, 11 Mar 2026) |
| EllapsedTime: 7.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HIBAG
###
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* checking for file ‘HIBAG/DESCRIPTION’ ... OK
* preparing ‘HIBAG’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
-----------------------------------
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘HIBAG’ ...
** this is package ‘HIBAG’ version ‘1.47.0’
** using staged installation
** libs
specified C++11
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘MacOSX14.4.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c HIBAG.cpp -o HIBAG.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA.cpp -o LibHLA.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx512bw.cpp -o LibHLA_ext_avx512bw.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx512f.cpp -o LibHLA_ext_avx512f.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_avx512vpopcnt.cpp -o LibHLA_ext_avx512vpopcnt.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o
error: invalid value 'gnu23' in '-std=gnu23'
note: use 'c89', 'c90', or 'iso9899:1990' for 'ISO C 1990' standard
note: use 'iso9899:199409' for 'ISO C 1990 with amendment 1' standard
note: use 'gnu89' or 'gnu90' for 'ISO C 1990 with GNU extensions' standard
note: use 'c99' or 'iso9899:1999' for 'ISO C 1999' standard
note: use 'gnu99' for 'ISO C 1999 with GNU extensions' standard
note: use 'c11' or 'iso9899:2011' for 'ISO C 2011' standard
note: use 'gnu11' for 'ISO C 2011 with GNU extensions' standard
note: use 'c17', 'iso9899:2017', 'c18', or 'iso9899:2018' for 'ISO C 2017' standard
note: use 'gnu17' or 'gnu18' for 'ISO C 2017 with GNU extensions' standard
note: use 'c2x' for 'Working Draft for ISO C2x' standard
note: use 'gnu2x' for 'Working Draft for ISO C2x with GNU extensions' standard
make: *** [samtools_ext.o] Error 1
ERROR: compilation failed for package ‘HIBAG’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpHchnzN/Rinst1a1465ff7183/HIBAG’
-----------------------------------
ERROR: package installation failed