Bug 738972 – dev-python/cython-0.29.20-r2 with dev-python/numpy-1.19.0 fails tests

• Product: Gentoo Linux
• Status: RESOLVED OBSOLETE

[Description Paolo Pedroni 2020-08-25 16:39:46 UTC]

Created attachment 656642 [details]
cython-0.29.20-r2:20200825-135306.log.gz

======================================================================
ERROR: runTest (__main__.CythonRunTestCase)
compiling (c) and running numpy_test
----------------------------------------------------------------------
Traceback (most recent call last):
  File "runtests.py", line 1252, in run
    ext_so_path = self.runCompileTest()
  File "runtests.py", line 930, in runCompileTest
    self.test_directory, self.expect_errors, self.expect_warnings, self.annotate)
  File "runtests.py", line 1173, in compile
    self._match_output(expected_errors, errors, tostderr)
  File "runtests.py", line 1222, in _match_output
    self.assertEqual(None, unexpected)
AssertionError: None != "962:69: Cannot convert 'void *' to Python object"

======================================================================
ERROR: runTest (__main__.CythonRunTestCase)
compiling (cpp) and running numpy_test
----------------------------------------------------------------------
Traceback (most recent call last):
  File "runtests.py", line 1252, in run
    ext_so_path = self.runCompileTest()
  File "runtests.py", line 930, in runCompileTest
    self.test_directory, self.expect_errors, self.expect_warnings, self.annotate)
  File "runtests.py", line 1173, in compile
    self._match_output(expected_errors, errors, tostderr)
  File "runtests.py", line 1222, in _match_output
    self.assertEqual(None, unexpected)
AssertionError: None != "962:69: Cannot convert 'void *' to Python object"

----------------------------------------------------------------------

With numpy-1.18.5 it used to work fine. cython-0.29.21 gives the same error.

# emerge --info =dev-python/cython-0.29.20-r2
Portage 2.3.103 (python 3.7.8-final-0, default/linux/amd64/17.1/desktop/plasma/systemd, gcc-9.3.0, glibc-2.31-r6, 5.4.48-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.4.48-gentoo-x86_64-AMD_Phenom-tm-_II_X6_1100T_Processor-with-gentoo-2.6
KiB Mem:    16138344 total,   1220440 free
KiB Swap:   12550140 total,  12372988 free
Timestamp of repository gentoo: Wed, 19 Aug 2020 14:15:01 +0000
Head commit of repository gentoo: bb1337bcb30f2ffbdef74e9e667ad7ca3495c3f7
sh dash 0.5.11.1
ld GNU gold (Gentoo 2.33.1 p2 2.33.1) 1.16
distcc 3.3.3 x86_64-pc-linux-gnu [enabled]
ccache version 3.7.10 [disabled]
app-shells/bash:          5.0_p17::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.30.3::gentoo
dev-lang/python:          2.7.18-r1::gentoo, 3.7.8-r2::gentoo, 3.8.5::gentoo
dev-util/ccache:          3.7.10::gentoo
dev-util/cmake:           3.16.5::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/sandbox:         2.18::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.16.1-r1::gentoo
sys-devel/binutils:       2.33.1-r1::gentoo
sys-devel/gcc:            9.3.0-r1::gentoo
sys-devel/gcc-config:     2.3.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.4-r1::gentoo (virtual/os-headers)
sys-libs/glibc:           2.31-r6::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.europe.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-extra-opts: 
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-jobs: 1

x-portage
    location: /usr/local/portage
    masters: gentoo
    priority: 0

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe -frecord-gcc-switches -march=amdfam10 -flto=7"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /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 /etc/terminfo"
CXXFLAGS="-O2 -pipe -frecord-gcc-switches -march=amdfam10 -flto=7"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going y --with-bdeps y"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY 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"
FCFLAGS="-O2 -pipe -frecord-gcc-switches -march=amdfam10 -flto=7"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs cgroup compress-build-logs config-protect-if-modified distcc 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 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=amdfam10 -flto=7"
GENTOO_MIRRORS="http://mirrors.soeasyto.com/distfiles.gentoo.org/ http://mirrors.evowise.com/gentoo/ http://gentoo.modulix.net/gentoo/ https://mirrors.soeasyto.com/distfiles.gentoo.org/ https://mirrors.evowise.com/gentoo/"
LANG="it_IT.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu -Wl,--sort-common -flto=7"
LINGUAS="it it_IT"
MAKEOPTS="-j12 -l6"
PKGDIR="/usr/portage/packages"
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"
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 emboss encode exif expat fbcon ffmpeg fftw flac fontconfig fortran ftp gd gdbm geoip gif gimp gmp gnutls gphoto2 gpm graphviz gtk handbook iconv icu idn imagemagick imlib introspection ipv6 java javascript jbig jemalloc jpeg jpeg2k kde kipi kwallet lame lcms libass libglvnd libnotify libsamplerate libtirpc lm_sensors lua lzma lzo mad mmap mng mp3 mp4 mpeg mplayer multilib musicbrainz ncurses nls nptl nsplugin offensive ogg openal opengl openmp pam pango pcre pdf phonon plasma png policykit postscript ppds pulseaudio qml qt5 rdesktop readline recode samba sctp sdl seccomp sndfile sockets speex spell split-usr sqlite sqlite3 ssl startup-notification svg symlink syslog systemd sysvipc taglib telemetry test theora threads tidy tiff truetype udev udisks unicode upower usb vaapi vala vdpau vim-syntax vnc vorbis wavpack wayland widgets win32codecs wmf wxwidgets x264 xattr xcb xine xml xpm xscreensaver xv xvid yahoo zlib zstd" ABI_X86="64" ADA_TARGET="gnat_2018" 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="kodak ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext popcnt sse sse2 sse3 sse4a" 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" GRUB_PLATFORMS="pc" INPUT_DEVICES="libinput" KERNEL="linux" L10N="it en" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="nlpsolver" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2 php7-3" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python3_7" RUBY_TARGETS="ruby25" SANE_BACKENDS="epson epson2" USERLAND="GNU" VIDEO_CARDS="radeon r600" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

=================================================================
                        Package Settings
=================================================================

dev-python/cython-0.29.20-r2::gentoo was built with the following:
USE="test -doc -emacs" ABI_X86="(64)" PYTHON_TARGETS="python3_7 (-pypy3) -python2_7 -python3_6 -python3_8 (-python3_9)"

# emerge -1pqv =dev-python/cython-0.29.20-r2
[ebuild   R   ] dev-python/cython-0.29.20-r2  USE="test -doc -emacs" PYTHON_TARGETS="python3_7 (-pypy3) -python2_7 -python3_6 -python3_8 (-python3_9)"