Hi, seems the install process writes directly into the filesystem instead of ${DESTDIR}. >>> Emerging (3 of 19) dev-python/tables-3.9.2::gentoo * tables-3.9.2.tar.gz BLAKE2B SHA512 size ;-) ... [ ok ] >>> Unpacking source... >>> Unpacking tables-3.9.2.tar.gz to /var/tmp/portage/dev-python/tables-3.9.2/work >>> Source unpacked in /var/tmp/portage/dev-python/tables-3.9.2/work >>> Preparing source in /var/tmp/portage/dev-python/tables-3.9.2/work/tables-3.9.2 ... * Build system packages: * dev-python/gpep517 : 15 * dev-python/installer : 0.7.0 * dev-python/cython : 3.0.8 * dev-python/setuptools : 68.0.0-r1 * dev-python/setuptools-rust : 1.6.0 * dev-python/setuptools-scm : 7.1.0 * dev-python/wheel : 0.40.0 >>> Source prepared. >>> Configuring source in /var/tmp/portage/dev-python/tables-3.9.2/work/tables-3.9.2 ... >>> Source configured. >>> Compiling source in /var/tmp/portage/dev-python/tables-3.9.2/work/tables-3.9.2 ... * python3_10: running distutils-r1_run_phase distutils-r1_python_compile * Building the wheel for tables-3.9.2 via setuptools.build_meta python3.10 -m gpep517 build-wheel --prefix=/usr --backend setuptools.build_meta --output-fd 3 --wheel-dir /var/tmp/portage/dev-python/tables-3.9.2/work/tables-3.9.2-python3_10/wheel 2024-01-17 12:34:30,131 gpep517 INFO Building wheel via backend setuptools.build_meta Traceback (most recent call last): File "/usr/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "/usr/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals) File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 429, in <module> sys.exit(main()) File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 425, in main return func(args) File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 215, in build_wheel print(build_wheel_impl(args, args.wheel_dir), file=out) File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 207, in build_wheel_impl wheel_name = backend.build_wheel(str(wheel_dir), args.config_json) File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 416, in build_wheel return self._build_with_temp_dir(['bdist_wheel'], '.whl', File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 401, in _build_with_temp_dir self.run_setup() File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 817, in <module> File "<string>", line 459, in find_directories File "<string>", line 342, in find_header_path File "<string>", line 209, in _find_file_path File "/usr/lib/python3.10/pathlib.py", line 1322, in is_file return S_ISREG(self.stat().st_mode) File "/usr/lib/python3.10/pathlib.py", line 1097, in stat return self._accessor.stat(self, follow_symlinks=follow_symlinks) PermissionError: [Errno 13] Permission denied: '/opt/include/H5public.h' * Using Python 3.10.13 (main, Dec 28 2023, 03:07:56) [GCC 13.2.1 20231014] * Found cython 3.0.8 * USE_PKGCONFIG: True * ERROR: dev-python/tables-3.9.2::gentoo failed (compile phase): * Wheel build failed * * Call stack: * ebuild.sh, line 136: Called src_compile * environment, line 4098: Called distutils-r1_src_compile * environment, line 1950: Called _distutils-r1_run_foreach_impl 'distutils-r1_python_compile' * environment, line 764: Called python_foreach_impl 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3701: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3191: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 3189: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'distutils-r1_python_compile' * environment, line 1235: Called distutils-r1_run_phase 'distutils-r1_python_compile' * environment, line 1932: Called distutils-r1_python_compile * environment, line 1747: Called distutils_pep517_install '/var/tmp/portage/dev-python/tables-3.9.2/work/tables-3.9.2-python3_10/install' * environment, line 2288: Called die * The specific snippet of code: * local wheel=$("${cmd[@]}" 3>&1 1>&2 || die "Wheel build failed"); * * If you need support, post the output of `emerge --info '=dev-python/tables-3.9.2::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-python/tables-3.9.2::gentoo'`. * The complete build log is located at '/var/tmp/portage/dev-python/tables-3.9.2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/dev-python/tables-3.9.2/temp/environment'. * Working directory: '/var/tmp/portage/dev-python/tables-3.9.2/work/tables-3.9.2' * S: '/var/tmp/portage/dev-python/tables-3.9.2/work/tables-3.9.2' Blocks: https://bugs.gentoo.org/920021
And I wonder why /opt/include/H5public.h is being attempted if /usr/include/H5public.h is already installed by sci-libs/hdf5-1.14.3-r1 # emerge --info '=dev-python/tables-3.9.2::gentoo' Portage 3.0.61 (python 3.11.7-final-0, default/linux/amd64/17.1/no-multilib, gcc-13, glibc-2.38-r1, 6.6.11 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.6.11-x86_64-Intel-R-_Core-TM-_i7-7820HQ_CPU_@_2.90GHz-with-glibc2.38 KiB Mem: 32735000 total, 6634724 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Mon, 15 Jan 2024 19:00:01 +0000 Head commit of repository gentoo: b24167aa561016cbe3dc6e8e23e45e0a016e17e4 Head commit of repository jgenco: 6c0e9d29ad9b0322809b663afd4cdb401f0c0f87 Head commit of repository randall: 1878db2875a45dfa0a8c37a1f38035da7deb5cbc sh bash 5.2_p26 ld GNU ld (Gentoo 2.39 p5) 2.39.0 app-misc/pax-utils: 1.3.7::gentoo app-shells/bash: 5.2_p26::gentoo dev-build/autoconf: 2.13-r8::gentoo, 2.69-r5::gentoo, 2.71-r7::gentoo, 2.72-r1::gentoo dev-build/automake: 1.14.1-r2::gentoo, 1.15.1-r2::gentoo, 1.16.5-r1::gentoo dev-build/cmake: 3.27.4::gentoo dev-build/libtool: 2.4.7-r2::gentoo dev-build/make: 4.4.1-r1::gentoo dev-build/meson: 1.3.1::gentoo dev-java/java-config: 2.3.3-r1::gentoo dev-lang/perl: 5.36.0::gentoo dev-lang/python: 2.7.18_p112::stefantalpalaru, 3.10.13::gentoo, 3.11.7::gentoo, 3.12.1_p1::gentoo dev-lang/rust: 1.70.0::gentoo sys-apps/baselayout: 2.14-r1::gentoo sys-apps/openrc: 0.53::gentoo sys-apps/sandbox: 2.38::gentoo sys-devel/binutils: 2.39-r4::gentoo, 2.40-r6::gentoo, 2.41-r4::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 14.0.6-r4::gentoo, 15.0.7-r3::gentoo, 16.0.6::gentoo sys-devel/gcc: 10.3.0::gentoo, 11.3.0::gentoo, 12.2.1_p20230304::gentoo, 13.2.1_p20231216::gentoo sys-devel/gcc-config: 2.11::gentoo sys-devel/lld: 14.0.6-r1::gentoo, 15.0.7::gentoo, 16.0.6::gentoo sys-devel/llvm: 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/etc/php/fpm-php8.3/ext-active/ /etc/php/phpdbg-php8.1/ext-active/ /etc/php/phpdbg-php8.2/ext-active/ /etc/php/phpdbg-php8.3/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c /etc/vmware-installer" CXXFLAGS="-O2 -pipe -march=native -ftree-vectorize" DISTDIR="/usr/portage/distfiles" ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME" FCFLAGS="-O2 -pipe -march=native -ftree-vectorize" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news nostrip parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox 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I don't think it's writing anything, it's trying to find a header. I suspect that you have /opt/include that isn't accessible to Portage.
(In reply to Michał Górny from comment #2) > I don't think it's writing anything, it's trying to find a header. I > suspect that you have /opt/include that isn't accessible to Portage. Thank, you are right. One package outside of portage screwed my permissions on /opt and its child subdirs.
