Created attachment 868448 [details] cython-3.0.0-r1:20230822-091646.log.gz Sharded tests run in 585 seconds (9.8 minutes) Errors found in shards 3 Errors from shard 3: ====================================================================== FAIL: runTest (__main__.EndToEndTest.runTest) [3] End-to-end coverage_cmd_src_pkg_layout ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/tmp/portage/dev-python/cython-3.0.0-r1/work/cython-3.0.0/runtests.py", line 2041, in runTest self.assertEqual(0, res, "non-zero exit status, last output was:\n%r\n-- stdout:%s\n-- stderr:%s\n" % ( AssertionError: 0 != 1 : non-zero exit status, last output was: '/usr/bin/python3.11 -m pip install .' -- stdout: -- stderr:error: externally-managed-environment [...] * ERROR: dev-python/cython-3.0.0-r1::gentoo failed (test phase): * Tests fail with python3.11 # emerge --info =dev-python/cython-3.0.0-r1 Portage 3.0.49 (python 3.11.4-final-0, default/linux/amd64/17.1/desktop/plasma/systemd/merged-usr, gcc-12, glibc-2.37-r3, 6.1.41-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.1.41-gentoo-x86_64-AMD_Ryzen_7_5700G_with_Radeon_Graphics-with-glibc2.37 KiB Mem: 65120636 total, 1237292 free KiB Swap: 67108860 total, 67104252 free Timestamp of repository gentoo: Tue, 22 Aug 2023 06:45:01 +0000 Head commit of repository gentoo: 8a9889b3e6f61269efc5dced9abe9c45b33335a9 sh dash 0.5.12 ld GNU ld (Gentoo 2.40 p5) 2.40.0 distcc 3.4 x86_64-pc-linux-gnu [disabled] ccache version 4.8.2 [disabled] app-misc/pax-utils: 1.3.5::gentoo app-shells/bash: 5.1_p16-r6::gentoo dev-java/java-config: 2.3.1-r1::gentoo dev-lang/perl: 5.36.1-r3::gentoo dev-lang/python: 3.11.4::gentoo dev-lang/rust: 1.70.0::gentoo dev-util/ccache: 4.8.2::gentoo dev-util/cmake: 3.26.5-r2::gentoo dev-util/meson: 1.1.1::gentoo sys-apps/baselayout: 2.14::gentoo sys-apps/sandbox: 2.37::gentoo sys-apps/systemd: 253.6::gentoo sys-devel/autoconf: 2.71-r6::gentoo sys-devel/automake: 1.16.5-r1::gentoo sys-devel/binutils: 2.40-r5::gentoo sys-devel/binutils-config: 5.5::gentoo sys-devel/clang: 15.0.7-r3::gentoo, 16.0.6::gentoo sys-devel/gcc: 12.3.1_p20230526::gentoo sys-devel/gcc-config: 2.11::gentoo sys-devel/libtool: 2.4.7-r1::gentoo sys-devel/lld: 15.0.7::gentoo, 16.0.6::gentoo sys-devel/llvm: 15.0.7-r3::gentoo, 16.0.6::gentoo sys-devel/make: 4.4.1-r1::gentoo sys-kernel/linux-headers: 6.1::gentoo (virtual/os-headers) sys-libs/glibc: 2.37-r3::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.europe.gentoo.org/gentoo-portage priority: -1000 volatile: True sync-rsync-extra-opts: sync-rsync-verify-jobs: 1 sync-rsync-verify-metamanifest: yes sync-rsync-verify-max-age: 24 x-portage location: /usr/local/portage masters: gentoo priority: 0 volatile: True ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="@FREE" AR="/usr/bin/gcc-ar" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -frecord-gcc-switches -march=znver3 -ftree-vectorize -flto=8" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d" CXXFLAGS="-O2 -pipe -frecord-gcc-switches -march=znver3 -ftree-vectorize -flto=8" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--keep-going y --with-bdeps y" 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 -frecord-gcc-switches -march=znver3 -ftree-vectorize -flto=8" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live cgroup compress-build-logs config-protect-if-modified distlocks ebuild-locks ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-elog split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe -frecord-gcc-switches -march=znver3 -ftree-vectorize -flto=8" GENTOO_MIRRORS="http://ftp.tu-ilmenau.de/mirror/gentoo/ https://ftp.tu-ilmenau.de/mirror/gentoo/ http://mirror.init7.net/gentoo/ https://mirror.init7.net/gentoo/ntoo/" LANG="it_IT.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -Wl,--sort-common -ftree-vectorize -flto=8" LEX="flex" LINGUAS="it it_IT" MAKEOPTS="-j16 -l16" NM="/usr/bin/gcc-nm" PKGDIR="/var/cache/binpkgs" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" PORTAGE_TMPDIR="/var/tmp" RANLIB="/usr/bin/gcc-ranlib" SHELL="/bin/bash" USE="X a52 aac aalib acl acpi activities adns alsa amd64 ao audiofile bash-completion bluetooth branding brotli bzip2 cairo caps cdda cddb cdparanoia cdr cli crypt css cups curl dbus declarative dga djvu dri dts dvd dvdr encode exif expat fbcon ffmpeg fftw flac fontconfig foomaticdb fortran ftp gd gdbm geoip gif gimp gmp gnutls gphoto2 gpm graphviz gstreamer gtk gui guile handbook iconv icu idn imagemagick imlib introspection ipv6 java javascript jbig jemalloc jpeg jpeg2k kde kwallet lame lcms libass libnotify libsamplerate libtirpc lm-sensors lua lz4 lzma lzo mad magic mhash mmap mng mp3 mp4 mpeg multilib musicbrainz ncurses nls nptl offensive ogg openal opengl openmp opus pam pango pcre pdf pipewire plasma png policykit postscript ppds pulseaudio qml qt5 rdesktop readline recode samba screencast sctp sdl seccomp sndfile sockets sound speex spell sqlite ssl startup-notification svg symlink syslog systemd sysvipc taglib telemetry test test-rust theora threads tidy tiff truetype udev udisks unicode upower usb v4l vaapi vala verify-sig vim-syntax vnc vorbis vulkan wavpack wayland webp widgets win32codecs wmf wxwidgets x264 xattr xcb xft xinerama xml xpm xscreensaver xv xvid yahoo zip zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2021" ALSA_CARDS="hda-intel virmidi" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sha sse sse2 sse3 sse4_1 sse4_2 sse4a ssse3" CURL_SSL="gnutls" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" KERNEL="linux" L10N="it en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="AMDGPU" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" RUBY_TARGETS="ruby31" VIDEO_CARDS="amdgpu radeon radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq proto steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: ADDR2LINE, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS # emerge -1pqv =dev-python/cython-3.0.0-r1 [ebuild U ] dev-python/cython-3.0.0-r1 [0.29.36] USE="test -debug -doc (-emacs%)" PYTHON_TARGETS="python3_11 (-pypy3) -python3_10 (-python3_12)"
Maybe another reason for us to change our mind on the PEP thing...
Created attachment 875254 [details] Portage Tracks Getting the same on cython-3.0.2-r1. Also, _test_cython_pyximport.pyx seems to drop the work/cython-3.0.2 directories from the path building pyxbuild.pyx_to_dll for visibility: ALL DONE (6/9) Sharded tests run in 713 seconds (11.9 minutes) Errors found in shards 7, 5 Errors from shard 7: ====================================================================== ERROR: test_cython_pyximport (Cython.Build.Tests.TestIpythonMagic.TestIPythonMagic.test_cython_pyximport) ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/pyximport/_pyximport3.py", line 314, in create_module so_path = build_module(spec.name, pyxfilename=spec.origin, pyxbuild_dir=self._pyxbuild_dir, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/pyximport/_pyximport3.py", line 197, in build_module so_path = pyxbuild.pyx_to_dll(pyxfilename, extension_mod, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/pyximport/pyxbuild.py", line 27, in pyx_to_dll assert os.path.exists(filename), "Could not find %s" % os.path.abspath(filename) AssertionError: Could not find /var/tmp/portage/dev-python/cython-3.0.2-r1/_test_cython_pyximport.pyx During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/Cython/Build/Tests/TestIpythonMagic.py", line 122, in test_cython_pyximport ip.run_cell_magic('cython_pyximport', module_name, code) File "/usr/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 2493, in run_cell_magic result = fn(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^ File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/Cython/Build/IpythonMagic.py", line 179, in cython_pyximport __import__(module_name) File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/pyximport/_pyximport3.py", line 332, in create_module raise exc.with_traceback(tb) File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/pyximport/_pyximport3.py", line 314, in create_module so_path = build_module(spec.name, pyxfilename=spec.origin, pyxbuild_dir=self._pyxbuild_dir, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/pyximport/_pyximport3.py", line 197, in build_module so_path = pyxbuild.pyx_to_dll(pyxfilename, extension_mod, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/pyximport/pyxbuild.py", line 27, in pyx_to_dll assert os.path.exists(filename), "Could not find %s" % os.path.abspath(filename) ImportError: Building module _test_cython_pyximport failed: ['AssertionError: Could not find /var/tmp/portage/dev-python/cython-3.0.2-r1/_test_cython_pyximport.pyx\n'] Errors from shard 5: ====================================================================== FAIL: runTest (__main__.EndToEndTest.runTest) [5] End-to-end coverage_cmd_src_pkg_layout ---------------------------------------------------------------------- Traceback (most recent call last): File "/var/tmp/portage/dev-python/cython-3.0.2-r1/work/cython-3.0.2/runtests.py", line 2047, in runTest self.assertEqual(0, res, "non-zero exit status, last output was:\n%r\n-- stdout:%s\n-- stderr:%s\n" % ( AssertionError: 0 != 1 : non-zero exit status, last output was: '/usr/bin/python3.11 -m pip install .' -- stdout: -- stderr:error: externally-managed-environment × This environment is externally managed ╰─> The system-wide Python installation in Gentoo should be maintained using the system package manager (e.g. emerge). If the package in question is not packaged for Gentoo, please consider installing it inside a virtual environment, e.g.: python -m venv /path/to/venv . /path/to/venv/bin/activate pip install mypackage To exit the virtual environment, run: deactivate The virtual environment is not deleted, and can be re-entered by re-sourcing the activate file. note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages. hint: See PEP 668 for the detailed specification.
Created attachment 875255 [details] Portage Settings
Created attachment 880264 [details, diff] Patch to fix test_cython_pyximport test error I was not able to reproduce the "coverage_cmd_src_pkg_layout" error originally mentioned in the bug. However, I was able to reproduce the "test_cython_pyximport" error mentioned by bschnzl on cython-3.0.6 and cython-3.0.7. Running the tests manually from the "${WORKDIR}/${P}" directory using the same test command failing in the ebuild did not produce any errors. I suspected this to be a path traversal issue instigated by something in the portage build environment which wasn't present in an interactive shell. The errors I received from cython-3.0.6 are below. > ERROR: test_cython_pyximport (Cython.Build.Tests.TestIpythonMagic.TestIPythonMagic.test_cython_pyximport) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/pyximport/_pyximport3.py", line 314, in create_module > so_path = build_module(spec.name, pyxfilename=spec.origin, pyxbuild_dir=self._pyxbuild_dir, > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/pyximport/_pyximport3.py", line 197, in build_module > so_path = pyxbuild.pyx_to_dll(pyxfilename, extension_mod, > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/pyximport/pyxbuild.py", line 27, in pyx_to_dll > assert os.path.exists(filename), "Could not find %s" % os.path.abspath(filename) > AssertionError: Could not find /var/tmp/portage/dev-python/cython-3.0.6/_test_cython_pyximport.pyx > > During handling of the above exception, another exception occurred: > > Traceback (most recent call last): > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/Cython/Build/Tests/TestIpythonMagic.py", line 122, in test_cython_pyximport > ip.run_cell_magic('cython_pyximport', module_name, code) > File "/usr/lib/python3.11/site-packages/IPython/core/interactiveshell.py", line 2517, in run_cell_magic > result = fn(*args, **kwargs) > ^^^^^^^^^^^^^^^^^^^ > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/Cython/Build/IpythonMagic.py", line 179, in cython_pyximport > __import__(module_name) > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/pyximport/_pyximport3.py", line 332, in create_module > raise exc.with_traceback(tb) > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/pyximport/_pyximport3.py", line 314, in create_module > so_path = build_module(spec.name, pyxfilename=spec.origin, pyxbuild_dir=self._pyxbuild_dir, > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/pyximport/_pyximport3.py", line 197, in build_module > so_path = pyxbuild.pyx_to_dll(pyxfilename, extension_mod, > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/var/tmp/portage/dev-python/cython-3.0.6/work/cython-3.0.6/pyximport/pyxbuild.py", line 27, in pyx_to_dll > assert os.path.exists(filename), "Could not find %s" % os.path.abspath(filename) > ImportError: Building module _test_cython_pyximport failed: ['AssertionError: Could not find /var/tmp/portage/dev-python/cython-3.0.6/_test_cython_pyximport.pyx\n'] Investigating the second traceback above, I found that the build_module function in _pyximport3.py has a fair amount of logic around changing the directory. That logic was introduced in the below PR from upstream to ensure Windows paths don't go beyond the supported length. https://github.com/cython/cython/pull/4630 It appears that upstream considered constraining that logic to Windows only, but ultimately decided to "keep it general and see if it actually causes problems that way." See the below comment. https://github.com/cython/cython/pull/4630#issuecomment-1186580262 Leaving that logic general does indeed cause problems. I confirmed this by creating a patch reverting the PR (attached) and attempting to emerge cython again. The patch resolved the "test_cython_pyximport" testing failure on both cython-3.0.6 and cython-3.0.7. I did a cursory review of the open cython issues on GitHub and it doesn't appear that others are running into this. I believe the root cause to be something specific to how portage interacts with the logic from the PR, but I am not sure. More testing and debugging would be needed. Does anyone see any value in me opening an issue upstream for the "test_cython_pyximport" testing failure?
Created attachment 881118 [details, diff] Patch to fix coverage_cmd_src_pkg_layout test I'm not sure why I didn't run into it sooner, but I hit the coverage_cmd_src_pkg_layout test failure doing a @world rebuild. I applied this patch to work past it. There may be a more elegant solution, but this didn't seem to cause any issues for my system.
