Multiple platform build/check report for BioC 3.20 - INSTALL results for rsbml on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4358
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*

INSTALL results for rsbml on taishan

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.

raw results

Summary

Package: rsbml

Version: 2.64.0

Command: /home/biocbuild/R/R/bin/R CMD INSTALL rsbml

StartedAt: 2025-01-08 19:54:51 -0000 (Wed, 08 Jan 2025)

EndedAt: 2025-01-08 19:54:53 -0000 (Wed, 08 Jan 2025)

EllapsedTime: 2.3 seconds

RetCode: 1

Status: ERROR

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL rsbml
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘rsbml’ ...
** 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 = 6.6.0-64.0.0.61.oe2403.aarch64
uname -s = Linux
uname -v = #1 SMP Wed Dec 11 15:43:03 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 = 6.6.0-64.0.0.61.oe2403.aarch64
UNAME_SYSTEM  = Linux
UNAME_VERSION = #1 SMP Wed Dec 11 15:43:03 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 -I"/home/biocbuild/R/R/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/etc/Makeconf:195: StringMap.o] Error 1
ERROR: compilation failed for package ‘rsbml’
* removing ‘/home/biocbuild/R/R-4.4.2/site-library/rsbml’