| Summary: | dev-python/scipy fails test test_bisplev_integer_overflow Fatal Python error: Segmentation fault | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Agostino Sarubbo <ago> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | CONFIRMED --- | ||
| Severity: | normal | CC: | jsmolic, mgorny, python, sam, whissi |
| Priority: | Normal | Keywords: | TESTFAILURE |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| See Also: |
https://github.com/scipy/scipy/issues/12401 https://github.com/scipy/scipy/issues/12471 https://github.com/scipy/scipy/issues/9245 |
||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
build.log.bz2
gdb backtrace 1.5.2-build.log x86 build.log.xz (1.6.0, ppc) build.log.xz (arm, 1.7.1) build.log.xz (ppc, 1.6.3) |
||
|
Description
Agostino Sarubbo
2020-09-18 10:19:06 UTC
Created attachment 661119 [details]
build.log.bz2
build log and emerge --info
Created attachment 668522 [details] gdb backtrace Same on x86 with =dev-python/scipy-1.5.2: > scipy-1.5.2-py3.7-linux-i686.egg/scipy/interpolate/tests/test_fitpack.py::test_bisplev_integer_overflow Fatal Python error: Segmentation fault > > Current thread 0xb79dc940 (most recent call first): > File "/var/tmp/portage/dev-python/scipy-1.5.2/work/scipy-1.5.2-python3_7/build/test/lib/scipy-1.5.2-py3.7-linux-i686.egg/scipy/interpolate/_fitpack_impl.py", line 1048 in bisplev > File "/usr/lib/python3.7/site-packages/_pytest/python_api.py", line 706 in raises > File "/var/tmp/portage/dev-python/scipy-1.5.2/work/scipy-1.5.2-python3_7/build/test/lib/scipy-1.5.2-py3.7-linux-i686.egg/scipy/interpolate/tests/test_fitpack.py", line 491 in test_bisplev_integer_overflow > File "/usr/lib/python3.7/site-packages/_pytest/python.py", line 180 in pytest_pyfunc_call > File "/usr/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda> > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec > File "/usr/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__ > File "/usr/lib/python3.7/site-packages/_pytest/python.py", line 1567 in runtest > File "/usr/lib/python3.7/site-packages/_pytest/runner.py", line 153 in pytest_runtest_call > File "/usr/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda> > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec > File "/usr/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__ > File "/usr/lib/python3.7/site-packages/_pytest/runner.py", line 247 in <lambda> > File "/usr/lib/python3.7/site-packages/_pytest/runner.py", line 294 in from_call > File "/usr/lib/python3.7/site-packages/_pytest/runner.py", line 247 in call_runtest_hook > File "/usr/lib/python3.7/site-packages/_pytest/runner.py", line 207 in call_and_report > File "/usr/lib/python3.7/site-packages/_pytest/runner.py", line 117 in runtestprotocol > File "/usr/lib/python3.7/site-packages/_pytest/runner.py", line 100 in pytest_runtest_protocol > File "/usr/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda> > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec > File "/usr/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__ > File "/usr/lib/python3.7/site-packages/_pytest/main.py", line 321 in pytest_runtestloop > File "/usr/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda> > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec > File "/usr/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__ > File "/usr/lib/python3.7/site-packages/_pytest/main.py", line 296 in _main > File "/usr/lib/python3.7/site-packages/_pytest/main.py", line 240 in wrap_session > File "/usr/lib/python3.7/site-packages/_pytest/main.py", line 289 in pytest_cmdline_main > File "/usr/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda> > File "/usr/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec > File "/usr/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__ > File "/usr/lib/python3.7/site-packages/_pytest/config/__init__.py", line 158 in main > File "/var/tmp/portage/dev-python/scipy-1.5.2/work/scipy-1.5.2-python3_7/build/test/lib/scipy-1.5.2-py3.7-linux-i686.egg/scipy/_lib/_testutils.py", line 67 in __call__ > File "<string>", line 3 in <module> > /var/tmp/portage/dev-python/scipy-1.5.2/temp/environment: line 4267: 147 Segmentation fault (core dumped) PYTHONPATH=. "${EPYTHON}" -c " > import scipy, sys > r = scipy.test('fast', verbose=2) > sys.exit(0 if r else 1)" > * ERROR: dev-python/scipy-1.5.2::gentoo failed (test phase): > * Tests fail with python3.7 Portage 3.0.8 (python 3.7.9-final-0, default/linux/x86/17.0, gcc-9.3.0, glibc-2.31-r6, 5.4.72-gentoo-x86 i686) ================================================================= System uname: Linux-5.4.72-gentoo-x86-i686-with-gentoo-2.7 KiB Mem: 3106076 total, 199080 free KiB Swap: 8875836 total, 8856264 free Timestamp of repository gentoo: Sun, 25 Oct 2020 13:05:31 +0000 Head commit of repository gentoo: 0040a4b7a79b32b59b1b0c791d4b17bf491fba71 sh bash 5.0_p18 ld GNU ld (Gentoo 2.34 p6) 2.34.0 app-shells/bash: 5.0_p18::gentoo dev-lang/perl: 5.30.3::gentoo dev-lang/python: 2.7.18-r4::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo dev-util/cmake: 3.17.4-r1::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.18::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.1-r1::gentoo sys-devel/binutils: 2.34-r2::gentoo sys-devel/gcc: 9.3.0-r1::gentoo sys-devel/gcc-config: 2.3.2::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: git sync-uri: https://anongit.gentoo.org/git/repo/sync/gentoo.git priority: -1000 ABI="x86" ABI_X86="32" ACCEPT_KEYWORDS="x86" ACCEPT_LICENSE="*" ACCEPT_PROPERTIES="*" ACCEPT_RESTRICT="*" ADA_TARGET="gnat_2018" ARCH="x86" BINPKG_COMPRESS="bzip2" BROOT="" CBUILD="i686-pc-linux-gnu" CFLAGS="-O2 -pipe -march=pentium4m -mtune=pentium4m -Wno-error=jump-misses-init -Wno-error=sign-compare" CHOST="i686-pc-linux-gnu" CHOST_x86="i686-pc-linux-gnu" COLLISION_IGNORE="/lib/modules/*" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt" CPU_FLAGS_X86="mmx mmxext sse sse2" CXXFLAGS="-O2 -pipe -march=pentium4m -mtune=pentium4m -Wno-error=jump-misses-init -Wno-error=sign-compare" DEFAULT_ABI="x86" EDITOR="/usr/bin/mcedit" ELIBC="glibc" ENV_UNSET="CARGO_HOME 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" EPREFIX="" EROOT="/" ESYSROOT="/" FCFLAGS="-O2 -march=i686 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs cgroup config-protect-if-modified distlocks downgrade-backup ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -march=i686 -pipe" GCC_SPECS="" GRUB_PLATFORMS="efi-32 pc" GSETTINGS_BACKEND="dconf" HOME="/root" INFOPATH="/usr/share/gcc-data/i686-pc-linux-gnu/9.3.0/info:/usr/share/binutils-data/i686-pc-linux-gnu/2.34/info:/usr/share/info" INPUT_DEVICES="libinput" IUSE_IMPLICIT="abi_x86_32 prefix prefix-guest prefix-stack" KERNEL="linux" L10N="en en-US de de-DE" LANG="en_US.UTF-8" LC_ALL="en_US.UTF-8" LC_MESSAGES="C" LC_PAPER="de_DE.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LIBDIR_x86="lib" LINGUAS="en de" LOGNAME="root" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" MAIL="/var/mail/root" MAKEOPTS="--jobs 5 --load-average 7.95" MANPAGER="manpager" MOTD_SHOWN="pam" MULTILIB_ABIS="x86" NOCOLOR="true" OFFICE_IMPLEMENTATION="libreoffice" OPENCL_PROFILE="ocl-icd" OPENGL_PROFILE="xorg-x11" PAGER="/usr/bin/less" PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/lib/llvm/10/bin" PHP_TARGETS="php7-2 php7-3" POSTGRES_TARGETS="postgres10 postgres11" PWD="/root" PYTHONDONTWRITEBYTECODE="1" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" QT_GRAPHICSSYSTEM="raster" ROOT="/" ROOTPATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/bin:/usr/lib/llvm/10/bin" RUBY_TARGETS="ruby25 ruby26" SHELL="/bin/bash" SHLVL="2" SSH_TTY="/dev/pts/0" SYSROOT="/" TERM="tmux-256color" TMUX="/tmp//tmux-0/default,3586,0" TMUX_PANE="%2" TWISTED_DISABLE_WRITING_OF_PLUGIN_CACHE="1" USER="root" USERLAND="GNU" VIDEO_CARDS="vmware" XDG_CONFIG_DIRS="/etc/xdg" XDG_DATA_DIRS="/usr/local/share:/usr/share" XDG_RUNTIME_DIR="/run/user/0" XDG_SESSION_CLASS="user" XDG_SESSION_ID="3" XDG_SESSION_TYPE="tty" Created attachment 668525 [details]
1.5.2-build.log x86
Created attachment 689697 [details]
build.log.xz (1.6.0, ppc)
Same for 1.6.0 on ppc.
1.6.1 still failing. 1.6.3 on sparc b0rked as well Same on s390 in 1.6.3. Created attachment 743004 [details]
build.log.xz (arm, 1.7.1)
Created attachment 747957 [details]
build.log.xz (ppc, 1.6.3)
Same for 1.6.3 and 1.7.1 on ppc
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=24ca452f3ebb5b0e05cf5159137c272a554bff99 commit 24ca452f3ebb5b0e05cf5159137c272a554bff99 Author: Sam James <sam@gentoo.org> AuthorDate: 2021-11-05 02:26:48 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-11-05 02:28:19 +0000 dev-python/scipy: skip known-failing longstanding test failure Known broken upstream for years (ditto in Gentoo). Other tests seem okay and we're going to have to hope that's sufficient until there's a resolution upstream. Other distros are trying to battle this too. Bug: https://bugs.gentoo.org/743295 Bug: https://github.com/scipy/scipy/issues/9245 Bug: https://github.com/scipy/scipy/issues/12401 Bug: https://github.com/scipy/scipy/issues/12471 Signed-off-by: Sam James <sam@gentoo.org> dev-python/scipy/scipy-1.7.1.ebuild | 5 +++++ 1 file changed, 5 insertions(+) The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e5d8f69e3fc6dcc375a0c7d2ce6137dabe2addd1 commit e5d8f69e3fc6dcc375a0c7d2ce6137dabe2addd1 Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2021-11-11 09:16:17 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2021-11-11 09:18:21 +0000 dev-python/scipy: Skip broken test_fitpack on 1.6.3 as well Bug: https://bugs.gentoo.org/743295 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> dev-python/scipy/scipy-1.6.3.ebuild | 4 ++++ 1 file changed, 4 insertions(+) |
