Bug 954182

Summary:	dev-python/lmdb-1.6.2: fails tests
Product:	Gentoo Linux	Reporter:	Sam James <sam>
Component:	Current packages	Assignee:	Python Gentoo Team <python>
Status:	CONFIRMED ---
Severity:	normal	CC:	mgorny
Priority:	Normal	Keywords:	TESTFAILURE
Version:	unspecified
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---
Bug Depends on:
Bug Blocks:	948759
Attachments:	build.log

Description Sam James archtester

2025-04-22 05:13:30 UTC

Created attachment 925652 [details]
build.log

```
[...]
FAILED tests/txn_test.py::PutTest::test_dupdata_no_dupsort - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testg6cpr7r_: Invalid argument
FAILED tests/txn_test.py::PutTest::test_dupsort - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testfgjnf28s: Invalid argument
FAILED tests/txn_test.py::PutTest::test_empty_key_value - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_test7wh2mwtb: Invalid argument
FAILED tests/txn_test.py::PutTest::test_ro_txn - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_test44m1rem8: Invalid argument
FAILED tests/txn_test.py::ReplaceTest::test_bad_env - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_test63wl9juc: Invalid argument
FAILED tests/txn_test.py::ReplaceTest::test_bad_txn - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testw5d_ffth: Invalid argument
FAILED tests/txn_test.py::ReplaceTest::test_dupdata_no_dupsort - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_test0jyrgiu0: Invalid argument
FAILED tests/txn_test.py::ReplaceTest::test_dupsort_del_none - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_tests_kco96z: Invalid argument
FAILED tests/txn_test.py::ReplaceTest::test_dupsort_noexist - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testsofaief2: Invalid argument
FAILED tests/txn_test.py::ReplaceTest::test_empty_key_value - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testlnex1pv4: Invalid argument
FAILED tests/txn_test.py::ReplaceTest::test_ro_txn - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testgp61_0jd: Invalid argument
FAILED tests/txn_test.py::LeakTest::test_open_close - lmdb.InvalidParameterError: /var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testrkobcdx6: Invalid argument
=================== 180 failed, 9 passed, 1 skipped in 3.69s ===================
 * ERROR: dev-python/lmdb-1.6.2::gentoo failed (test phase):
 *   pytest failed with python3.12
 * 
```

---

# emerge --info
Portage 3.0.67 (python 3.12.9-final-0, default/linux/amd64/23.0/desktop/plasma/systemd, gcc-14, glibc-2.40-r8, 6.14.3 x86_64)
=================================================================
System uname: Linux-6.14.3-x86_64-AMD_Ryzen_9_3950X_16-Core_Processor-with-glibc2.40
KiB Mem:    65737644 total,   3536472 free
KiB Swap:   16662520 total,    107728 free
Timestamp of repository gentoo: Tue, 22 Apr 2025 03:35:10 +0000
sh bash 5.2_p37
ld GNU ld (Gentoo 2.44 p1) 2.44.0
app-misc/pax-utils:        1.3.8::gentoo
app-shells/bash:           5.2_p37::gentoo
dev-build/autoconf:        2.72-r1::gentoo
dev-build/automake:        1.17-r1::gentoo
dev-build/cmake:           3.31.5::gentoo
dev-build/libtool:         2.5.4::gentoo
dev-build/make:            4.4.1-r100::gentoo
dev-build/meson:           1.7.0::gentoo
dev-lang/perl:             5.40.0-r1::gentoo
dev-lang/python:           3.12.9::gentoo, 3.13.2::gentoo
dev-lang/rust:             1.85.1::gentoo
dev-lang/rust-bin:         1.84.1-r2::gentoo, 1.85.1::gentoo
llvm-core/clang:           19.1.7::gentoo
llvm-core/llvm:            19.1.7::gentoo
sys-apps/baselayout:       2.17::gentoo
sys-apps/sandbox:          2.39::gentoo
sys-apps/systemd:          256.10::gentoo
sys-devel/binutils:        2.44::gentoo
sys-devel/binutils-config: 5.5.2::gentoo
sys-devel/gcc:             11.5.0::gentoo, 12.4.1_p20241219::gentoo, 13.3.1_p20241220::gentoo, 14.2.1_p20241221::gentoo
sys-devel/gcc-config:      2.12.1::gentoo
sys-kernel/linux-headers:  6.12::gentoo (virtual/os-headers)
sys-libs/glibc:            2.40-r8::gentoo
Repositories:

gentoo
    location: /var/db/repos/gentoo
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    volatile: False
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-jobs: 1
    sync-rsync-extra-opts: 
    sync-rsync-verify-max-age: 3

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="@FREE"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /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/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-O2 -pipe"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--keep-going --complete-graph --usepkg=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"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg buildpkg-live clean-logs config-protect-if-modified distlocks fixlafiles ipc-sandbox merge-wait multilib-strict network-sandbox news parallel-fetch parallel-install pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox split-elog split-log strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="https://www.mirrorservice.org/sites/distfiles.gentoo.org/ https://mirror.bytemark.co.uk/gentoo/ https://mirrors.soeasyto.com/distfiles.gentoo.org/ https://mirrors.gethosted.online/gentoo/"
LANG="C.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs"
LEX="flex"
MAKEOPTS="-j4 -l4"
PKGDIR="/var/cache/binpkgs"
PORTAGE_COMPRESS="xz"
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"
SHELL="/bin/bash"
USE="X a52 aac acl acpi activities alsa amd64 bindist bluetooth branding bzip2 cairo cdda cdr cet crypt cups dbus declarative dri dts dvd dvdr encode exif flac gdbm gif gpm gtk gui iconv icu ipv6 jpeg kde kf6compat kwallet lcms libnotify libtirpc mad mng mp3 mp4 mpeg multilib ncurses networkmanager nls ogg opengl openmp pam pango pcre pdf pipewire plasma png policykit ppds pulseaudio qml qt5 qt6 readline screencast sdl seccomp semantic-desktop sound spell ssl startup-notification svg systemd test-rust tiff truetype udev udisks unicode upower usb vorbis vulkan wayland widgets wxwidgets x264 xattr xcb xft xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gcc_14" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" GUILE_SINGLE_TARGET="3-0" GUILE_TARGETS="3-0" INPUT_DEVICES="libinput" KERNEL="linux" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-2" POSTGRES_TARGETS="postgres17" PYTHON_SINGLE_TARGET="python3_12" PYTHON_TARGETS="python3_12" RUBY_TARGETS="ruby32" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto logmark ipmark dhcpmac delude chaos account"
Unset:  ADDR2LINE, AR, 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, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS

Comment 1 Michał Górny archtester

2025-04-22 09:16:49 UTC

That's some kind of devbox container issue.  They pass outside it — but they also pass in my local dev container.  Perhaps we need to upgrade systemd on devbox.

Comment 2 Sam James archtester

2025-04-22 09:18:32 UTC

Let me investigate. I hit it locally too...

Comment 3 Sam James archtester

2025-04-22 09:18:43 UTC

(In reply to Sam James from comment #2)
> Let me investigate. I hit it locally too...

(in nspawn, not outside). Seccomp again?

Comment 4 Sam James archtester

2025-04-22 09:25:42 UTC

0ve57o/data.mdb", 0x7ffd89285c10, 1023) = -1 EINVAL (Invalid argument)
559056:2509501 openat(AT_FDCWD, "/var/tmp/portage/dev-python/lmdb-1.6.2/temp/lmdb_testd10ve57o/data.mdb", O_WRONLY|O_DSYNC|O_CLOEXEC) = -1 EINVAL (Invalid argument)

It's because of --suppress-sync in my nspawn container vs O_DSYNC.

Comment 5 Michał Górny archtester

2025-04-22 09:29:41 UTC

That's systemd issue, not lmdb upstream issue, correct?

Comment 6 Sam James archtester

2025-04-22 09:31:50 UTC

(In reply to Michał Górny from comment #5)
> That's systemd issue, not lmdb upstream issue, correct?

Correct. I'd prefer it if systemd pretended it succeeded / swallowed O_DSYNC, but I don't know if they'll be open to that.