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Bug 743295 - dev-python/scipy fails test test_bisplev_integer_overflow Fatal Python error: Segmentation fault
Summary: dev-python/scipy fails test test_bisplev_integer_overflow Fatal Python error:...
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal with 1 vote (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: 742929 778140
  Show dependency tree
 
Reported: 2020-09-18 10:19 UTC by Agostino Sarubbo
Modified: 2021-03-30 02:16 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log.bz2 (build.log.bz2,81.52 KB, application/x-bzip-compressed-tar)
2020-09-18 10:19 UTC, Agostino Sarubbo
Details
gdb backtrace (bt.log,130.93 KB, text/plain)
2020-10-25 19:39 UTC, Thomas Deutschmann
Details
1.5.2-build.log x86 (build.log.gz,112.14 KB, application/x-gzip)
2020-10-25 19:40 UTC, Thomas Deutschmann
Details
build.log.xz (1.6.0, ppc) (scipy-1.6.0:20210306-190422.log.xz,92.22 KB, application/x-xz)
2021-03-06 19:41 UTC, ernsteiswuerfel
Details

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Description Agostino Sarubbo gentoo-dev 2020-09-18 10:19:06 UTC
https://blogs.gentoo.org/ago/2020/07/04/gentoo-tinderbox/

Issue: sci-libs/scipy-1.4.1 fails tests.
Discovered on: ppc (internal ref: ppc_at)
Comment 1 Agostino Sarubbo gentoo-dev 2020-09-18 10:19:08 UTC
Created attachment 661119 [details]
build.log.bz2

build log and emerge --info
Comment 2 Thomas Deutschmann gentoo-dev Security 2020-10-25 19:39:39 UTC
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"
Comment 3 Thomas Deutschmann gentoo-dev Security 2020-10-25 19:40:07 UTC
Created attachment 668525 [details]
1.5.2-build.log x86
Comment 4 ernsteiswuerfel 2021-03-06 19:41:03 UTC
Created attachment 689697 [details]
build.log.xz (1.6.0, ppc)

Same for 1.6.0 on ppc.
Comment 5 Thomas Deutschmann gentoo-dev Security 2021-03-30 02:16:58 UTC
1.6.1 still failing.