Michael Lawrence
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/rsbml |
| git_branch: devel |
| git_last_commit: 7671d4c |
| git_last_commit_date: 2025-04-15 09:41:01 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:07 -0400 (Fri, 24 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1849/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rsbml 2.67.0 (landing page) Michael Lawrence
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | ... NOT SUPPORTED ... | ||||||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | ... NOT SUPPORTED ... | ||||||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the rsbml package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rsbml.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: rsbml |
| Version: 2.67.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data rsbml |
| StartedAt: 2025-10-21 02:39:47 -0000 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 02:39:50 -0000 (Tue, 21 Oct 2025) |
| EllapsedTime: 3.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data rsbml
###
##############################################################################
##############################################################################
* checking for file ‘rsbml/DESCRIPTION’ ... OK
* preparing ‘rsbml’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘rsbml’ ...
** this is package ‘rsbml’ version ‘2.67.0’
** using staged installation
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for LIBSBML... yes
configure: === Begin local SOSLib build ===
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... config/config.guess: unable to guess system type
This script, last modified 2008-01-23, has failed to recognize
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from
http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
and
http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
If the version you run (config/config.guess) is already up to date, please
send the following data and any information you think might be
pertinent to <config-patches@gnu.org> in order to provide the needed
information to handle your system.
config.guess timestamp = 2008-01-23
uname -m = aarch64
uname -r = 6.6.0-72.0.0.64.oe2403.aarch64
uname -s = Linux
uname -v = #1 SMP Wed Dec 25 13:58:11 CST 2024
/usr/bin/uname -p = aarch64
/bin/uname -X =
hostinfo =
/bin/universe =
/usr/bin/arch -k =
/bin/arch = aarch64
/usr/bin/oslevel =
/usr/convex/getsysinfo =
UNAME_MACHINE = aarch64
UNAME_RELEASE = 6.6.0-72.0.0.64.oe2403.aarch64
UNAME_SYSTEM = Linux
UNAME_VERSION = #1 SMP Wed Dec 25 13:58:11 CST 2024
configure: error: cannot guess build type; you must specify one
configure: === End local SOSLib build ===
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (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-4.5.0/include" -DNDEBUG -I/home/biocbuild/libsbml-from-git/include -I/usr/include/libxml2 -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c StringMap.c -o StringMap.o
StringMap.c:52:10: fatal error: sbml/common/common.h: No such file or directory
52 | #include <sbml/common/common.h>
| ^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [/home/biocbuild/R/R-4.5.0/etc/Makeconf:202: StringMap.o] Error 1
ERROR: compilation failed for package ‘rsbml’
* removing ‘/home/biocbuild/tmp/RtmpUFWSSW/Rinst115c9e6e9686c1/rsbml’
-----------------------------------
ERROR: package installation failed