Hervé Pagès
| Snapshot Date: 2026-03-09 13:40 -0400 (Mon, 09 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/Rhtslib |
| git_branch: devel |
| git_last_commit: 0dcad2a |
| git_last_commit_date: 2025-10-29 14:52:40 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-03-10 11:33 -0400 (Tue, 10 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" | 4522 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences" | 2847 |
| 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 1796/2360 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhtslib 3.7.0 (landing page) Hervé Pagès
| 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 Rhtslib in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Rhtslib package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhtslib.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: Rhtslib |
| Version: 3.7.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhtslib |
| StartedAt: 2026-03-09 15:03:05 -0400 (Mon, 09 Mar 2026) |
| EndedAt: 2026-03-09 15:03:07 -0400 (Mon, 09 Mar 2026) |
| EllapsedTime: 1.5 seconds |
| RetCode: 1 |
| Status: ERROR |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rhtslib ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘Rhtslib’ ... ** this is package ‘Rhtslib’ version ‘3.7.0’ ** using non-staged installation via StagedInstall field ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’ using SDK: ‘MacOSX14.4.sdk’ cd "htslib-1.18" && make -f "Makefile.Rhtslib" echo '/* Default config.h generated by Makefile */' > config.h echo '#ifndef _XOPEN_SOURCE' >> config.h echo '#define _XOPEN_SOURCE 600' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBBZ2 1' >> config.h echo '#define HAVE_LIBLZMA 1' >> config.h echo '#ifndef __APPLE__' >> config.h echo '#define HAVE_LZMA_H 1' >> config.h echo '#endif' >> config.h echo '#define HAVE_LIBCURL 1' >> config.h if [ "x" != "x" ] && \ [ "x" != "x" ] && \ [ "x" != "x" ]; then \ echo '#define HAVE_POPCNT 1' >> config.h ; \ echo '#define HAVE_SSE4_1 1' >> config.h ; \ echo '#define HAVE_SSSE3 1' >> config.h ; \ echo '#if defined(HTS_ALLOW_UNALIGNED) && HTS_ALLOW_UNALIGNED == 0' >> config.h ; \ echo '#define UBSAN 1' >> config.h ; \ echo '#endif' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX2 1' >> config.h ; \ fi if [ "x" != "x" ] ; then \ echo '#define HAVE_AVX512 1' >> config.h ; \ fi clang -arch arm64 -std=gnu23 -falign-functions=64 -Wall -g -O2 -fpic -fvisibility=hidden -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c 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[1]: *** [kfunc.o] Error 1 make: *** [htslib] Error 2 ERROR: compilation failed for package ‘Rhtslib’ * removing ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rhtslib’