Sage 10.9 fails to build on my Ubuntu 24.04 computer, both as an incremental build from Sage 10.9.beta8 (which built and ran OK) or as a full build from a fresh git clone; this is due to the package rpy2_rinterface-3.6.6:
Attempting to download package rpy2_rinterface-3.6.6.tar.gz from mirrors
https://github.com/sagemath/sage/releases/download/10.9/rpy2_rinterface-3.6.6.tar.gz[......................................................................]
Setting up build directory /home/eric/sage/10.9/local/var/tmp/sage/build/rpy2_rinterface-3.6.6
No patch files found in ../patches
Host system: Linux tensor 6.8.0-110-generic #110-Ubuntu SMP PREEMPT_DYNAMIC Thu Mar 19 15:09:20 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux
C compiler: gcc, Using built-in specs., COLLECT_GCC=gcc, COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-linux-gnu/13/lto-wrapper, OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa, OFFLOAD_TARGET_DEFAULT=1, Target: x86_64-linux-gnu, Configured with: ../src/configure -v --with-pkgversion='Ubuntu 13.3.0-6ubuntu2~24.04.1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-libstdcxx-backtrace --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --enable-cet --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-13-EldibY/gcc-13-13.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-13-EldibY/gcc-13-13.3.0/debian/tmp-gcn/usr --enable-offload-defaulted --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-serialization=2, Thread model: posix, Supported LTO compression algorithms: zlib zstd, gcc version 13.3.0 (Ubuntu 13.3.0-6ubuntu2~24.04.1)
No stamp file for package 'rpy2_rinterface' in /home/eric/sage/10.9/local/var/lib/sage/installed
No spkg-legacy-uninstall script; nothing to do
[spkg-install] Installing rpy2_rinterface-3.6.6
[spkg-install] * Creating isolated environment: venv+pip...
[spkg-install] * Installing packages in isolated environment:
[spkg-install] - cffi>=1.15.0
[spkg-install] - packaging;platform_system=='Windows'
[spkg-install] - setuptools >= 75;python_version=='3.8'
[spkg-install] - setuptools >= 77;python_version>'3.8'
[spkg-install] - wheel
[spkg-install] > /home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/bin/python3 -m pip
[spkg-install] --python /tmp/build-env-_7leyfog/bin/python install --use-pep517 --no-warn-
[spkg-install] script-location --no-compile -r /tmp/build-requirements-fztpkgbu.txt
[spkg-install] < Looking in links: /home/eric/sage/10.9/local/var/lib/sage/wheels
[spkg-install] < Ignoring packaging: markers 'platform_system == "Windows"' don't match your
[spkg-install] environment
[spkg-install] < Ignoring setuptools: markers 'python_version == "3.8"' don't match your
[spkg-install] environment
[spkg-install] < ERROR: Could not find a version that satisfies the requirement wheel (from
[spkg-install] versions: none)
[spkg-install] < ERROR: No matching distribution found for wheel
[spkg-install]
[spkg-install] Traceback (most recent call last):
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 203, in _handle_build_error
[spkg-install] yield
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 601, in main
[spkg-install] built = build(
[spkg-install] ^^^^^^
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 264, in build_package
[spkg-install] out = _build(
[spkg-install] ^^^^^^^
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 187, in _build
[spkg-install] with _bootstrap_build_env(
[spkg-install] File "/usr/lib/python3.12/contextlib.py", line 137, in __enter__
[spkg-install] return next(self.gen)
[spkg-install] ^^^^^^^^^^^^^^
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/__main__.py", line 153, in _bootstrap_build_env
[spkg-install] install(builder.build_system_requires)
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/env.py", line 148, in install
[spkg-install] self._env_backend.install_dependencies(requirements, constraints)
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/env.py", line 309, in install_dependencies
[spkg-install] run_subprocess(cmd)
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/build/_ctx.py", line 71, in run_subprocess
[spkg-install] subprocess.run(cmd, capture_output=True, check=True, cwd=cwd, env=env)
[spkg-install] File "/usr/lib/python3.12/subprocess.py", line 571, in run
[spkg-install] raise CalledProcessError(retcode, process.args,
[spkg-install] subprocess.CalledProcessError: Command '['/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/bin/python3', '-m', 'pip', '--python', '/tmp/build-env-_7leyfog/bin/python', 'install', '--use-pep517', '--no-warn-script-location', '--no-compile', '-r', '/tmp/build-requirements-fztpkgbu.txt']' returned non-zero exit status 1.
[spkg-install]
[spkg-install] ERROR Command '['/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/bin/python3', '-m', 'pip', '--python', '/tmp/build-env-_7leyfog/bin/python', 'install', '--use-pep517', '--no-warn-script-location', '--no-compile', '-r', '/tmp/build-requirements-fztpkgbu.txt']' returned non-zero exit status 1.
[spkg-install] Warning: building with "python3 -m build --wheel --outdir=dist ." failed.
[spkg-install] Retrying with "python3 -m build --wheel --outdir=dist --no-isolation --skip-dependency-check .".
[spkg-install] * Building wheel...
[spkg-install] /usr/bin/ld: cannot find -ltirpc: No such file or directory
[spkg-install] collect2: error: ld returned 1 exit status
[spkg-install] Traceback (most recent call last):
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/_distutils/spawn.py", line 83, in spawn
[spkg-install] subprocess.check_call(cmd, env=_inject_macos_ver(env))
[spkg-install] File "/usr/lib/python3.12/subprocess.py", line 413, in check_call
[spkg-install] raise CalledProcessError(retcode, cmd)
[spkg-install] subprocess.CalledProcessError: Command '['/usr/bin/gcc', '/tmp/tmp_pw_r_imyi8wgw/tmp/tmp_pw_r_imyi8wgw/test_pw_r.o', '-L/usr/lib/R/lib', '-lR', '-lpcre2-8', '-llzma', '-lbz2', '-lz', '-ltirpc', '-lrt', '-ldl', '-lm', '-licuuc', '-licui18n', '-o', '/tmp/tmp_pw_r_imyi8wgw/test_pw_r']' returned non-zero exit status 1.
[spkg-install]
[spkg-install] The above exception was the direct cause of the following exception:
[spkg-install]
[spkg-install] Traceback (most recent call last):
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/_distutils/compilers/C/unix.py", line 307, in link
[spkg-install] self.spawn(linker + ld_args)
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/_distutils/compilers/C/base.py", line 1151, in spawn
[spkg-install] spawn(cmd, **kwargs)
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/_distutils/spawn.py", line 89, in spawn
[spkg-install] raise DistutilsExecError(
[spkg-install] distutils.errors.DistutilsExecError: command '/usr/bin/gcc' failed with exit code 1
[spkg-install]
[spkg-install] During handling of the above exception, another exception occurred:
[spkg-install]
[spkg-install] Traceback (most recent call last):
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
[spkg-install] main()
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 373, in main
[spkg-install] json_out["return_val"] = hook(**hook_input["kwargs"])
[spkg-install] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/pyproject_hooks/_in_process/_in_process.py", line 280, in build_wheel
[spkg-install] return _build_backend().build_wheel(
[spkg-install] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/build_meta.py", line 438, in build_wheel
[spkg-install] return _build(['bdist_wheel'])
[spkg-install] ^^^^^^^^^^^^^^^^^^^^^^^
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/build_meta.py", line 429, in _build
[spkg-install] return self._build_with_temp_dir(
[spkg-install] ^^^^^^^^^^^^^^^^^^^^^^^^^^
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/build_meta.py", line 410, in _build_with_temp_dir
[spkg-install] self.run_setup()
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/build_meta.py", line 317, in run_setup
[spkg-install] exec(code, locals())
[spkg-install] File "<string>", line 165, in <module>
[spkg-install] File "<string>", line 145, in get_r_c_extension_status
[spkg-install] File "<string>", line 106, in get_c_extension_status
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/_distutils/compilers/C/base.py", line 834, in link_executable
[spkg-install] self.link(
[spkg-install] File "/home/eric/sage/10.9/local/var/lib/sage/venv-python3.12/lib/python3.12/site-packages/setuptools/_distutils/compilers/C/unix.py", line 309, in link
[spkg-install] raise LinkError(msg)
[spkg-install] distutils.compilers.C.errors.LinkError: command '/usr/bin/gcc' failed with exit code 1
[spkg-install]
[spkg-install] ERROR Backend subprocess exited when trying to invoke build_wheel
[spkg-install] ********************************************************************************
[spkg-install] Error building a wheel for rpy2_rinterface-3.6.6
[spkg-install] ********************************************************************************
************************************************************************
Error installing package rpy2_rinterface-3.6.6
************************************************************************
Please email sage-devel (
http://groups.google.com/group/sage-devel)
explaining the problem and including the log files
/home/eric/sage/10.9/logs/pkgs/rpy2_rinterface-3.6.6.log
and
/home/eric/sage/10.9/config.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/eric/sage/10.9/local/var/tmp/sage/build/rpy2_rinterface-3.6.6 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/home/eric/sage/10.9/local/var/tmp/sage/build/rpy2_rinterface-3.6.6' && '/home/eric/sage/10.9/sage' --buildsh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************