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Bug 815222 - media-gfx/gmic-2.9.9 undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'
Summary: media-gfx/gmic-2.9.9 undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'
Status: RESOLVED CANTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal
Assignee: Marek Szuba (RETIRED)
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2021-09-28 08:19 UTC by Anton Gubarkov
Modified: 2021-11-22 14:05 UTC (History)
1 user (show)

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


Attachments
build log (build.log,272.03 KB, text/plain)
2021-09-28 08:21 UTC, Anton Gubarkov
Details

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Description Anton Gubarkov 2021-09-28 08:19:58 UTC
the build of gmic-2.9.9 fails with clang

/usr/bin/x86_64-pc-linux-gnu-ld: CMakeFiles/gmic_qt.dir/src/CroppedImageListProxy.cpp.o: undefined reference to symbol 'pthread_create@@GLIBC_2.2.5'
/usr/bin/x86_64-pc-linux-gnu-ld: /lib64/libpthread.so.0: error adding symbols: DSO missing from command line
clang-12: error: linker command failed with exit code 1 (use -v to see invocation)
Comment 1 Anton Gubarkov 2021-09-28 08:20:19 UTC
PF16W6Y2 ~ # emerge --info gmic
Portage 3.0.24 (python 3.9.7-final-0, default/linux/amd64/17.1/desktop/gnome/systemd, gcc-11.2.0, glibc-2.33-r7, 5.14.7-gentoo x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-5.14.7-gentoo-x86_64-Intel-R-_Core-TM-_i7-8850H_CPU_@_2.60GHz-with-glibc2.33
KiB Mem:    32564672 total,   2378456 free
KiB Swap:   33554428 total,  32459004 free
Timestamp of repository gentoo: Tue, 28 Sep 2021 06:51:27 +0000
Head commit of repository gentoo: 1c3a9b6264f2129ff6d2b81adb75e12ba0d93126

Head commit of repository audio-overlay: 67c8fbcd0681d09261860c2f1bac1e9cb8fab08e

Head commit of repository lto-overlay: dde13f77f390545d64b1a64430f23b4bf10b65eb

Head commit of repository mv: f0bfe79d76c3f987220abd1ccdc77f52103fce1a

sh bash 5.1_p8
ld GNU ld (Gentoo 2.36.1 p4) 2.36.1
ccache version 4.4.1 [disabled]
app-shells/bash:          5.1_p8::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.34.0-r2::gentoo
dev-lang/python:          2.7.18_p13::gentoo, 3.8.12::gentoo, 3.9.7::gentoo, 3.10.0_rc2::gentoo
dev-lang/rust:            1.55.0::gentoo
dev-util/ccache:          4.4.1::gentoo
dev-util/cmake:           3.21.3::gentoo
sys-apps/baselayout:      2.7-r3::gentoo
sys-apps/sandbox:         2.25::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.71-r1::gentoo
sys-devel/automake:       1.16.4::gentoo
sys-devel/binutils:       2.36.1-r2::gentoo, 2.37_p1::gentoo
sys-devel/gcc:            8.4.0-r2::gentoo, 10.3.0-r2::gentoo, 11.2.0::gentoo
sys-devel/gcc-config:     2.4::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.14::gentoo (virtual/os-headers)
sys-libs/glibc:           2.33-r7::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: git
    sync-uri: git://github.com/gentoo-mirror/gentoo.git
    priority: -1000

audio-overlay
    location: /var/lib/layman/audio-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/audio-overlay.git
    masters: gentoo
    priority: 50

calculate
    location: /var/lib/layman/calculate
    masters: gentoo
    priority: 50

dlang
    location: /var/lib/layman/dlang
    masters: gentoo
    priority: 50

gentoo-zh
    location: /var/lib/layman/gentoo-zh
    masters: gentoo
    priority: 50

go-overlay
    location: /var/lib/layman/go-overlay
    masters: gentoo
    priority: 50

lto-overlay
    location: /var/lib/layman/lto-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/lto-overlay.git
    masters: gentoo mv
    priority: 50

mv
    location: /var/lib/layman/mv
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/mv.git
    masters: gentoo
    priority: 50

steam-overlay
    location: /var/lib/layman/steam-overlay
    masters: gentoo
    priority: 50

tlp
    location: /var/lib/layman/tlp
    masters: gentoo
    priority: 50

rugubara
    location: /var/lib/layman/rugubara
    masters: gentoo
    priority: 100

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA Vivaldi"
CBUILD="x86_64-pc-linux-gnu"
CC="clang"
CFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
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"
CXX="clang++"
CXXFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
DISTDIR="/usr/portage/distfiles"
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"
FCFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance config-protect-if-modified distlocks 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"
FFLAGS="-march=native -O3 -fno-semantic-interposition -fgraphite-identity -floop-nest-optimize  -flto=12 -fuse-linker-plugin -falign-functions=32 -pipe"
GENTOO_MIRRORS="http://gentoo.bloodhost.ru/ rsync://gentoo.bloodhost.ru/gentoo-distfiles http://ftp.ntua.gr/pub/linux/gentoo/"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j6"
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 acl acpi aio alsa amd64 ap bash-completion bluetooth branding bzip2 cacert cairo caps cdda cdr cgroup-hybrid chromecast clang cli client colord crypt cups dbus djvu dri dri3 dts dvd dvdr eds egl emboss encode evo exif fat ffmpeg fftw flac fortran gdbm gif gimp gles2 gnome gnome-keyring gnome-online-accounts gpm graphite gstreamer gtk gtk3 gui heif iconv icu introspection io-uring ipv6 jack jpeg jpeg2k lcms libglvnd libnotify libsecret libtirpc libzfs lm_sensors lto lv2 mad mng mp3 mp4 mpeg multilib native-headset nautilus ncat ncurses networkmanager nfs nls nptl ntfs nvenc nvme ogg opencl opengl openmp opus p2p pam pango pcre pdf png policykit ppds pulseaudio qt5 raw readline sdl sdl2 seccomp smp sna sound spell spice split-usr ssl startup-notification svg synaptics sysprof systemd tcpd thunderbolt tiff tracker truetype udev udisks uefi unicode upower usb usbredir user-session vaapi vala vdpau virgl vlc vorbis vulkan wayland webdav wireguard wxwidgets x264 x265 xattr xcb xml xv xvid zeroconf zfs zlib" ABI_X86="64" ADA_TARGET="gnat_2019" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" 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" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" 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 wacom" KERNEL="linux" L10N="en ru" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-3 php7-4" POSTGRES_TARGETS="postgres12 postgres13" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_8 python3_9" RUBY_TARGETS="ruby26 ruby27 ruby30" USERLAND="GNU" VIDEO_CARDS="intel i965 iris nvidia" 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:  CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, RUSTFLAGS

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

media-gfx/gmic-2.9.8::gentoo was built with the following:
USE="X cli ffmpeg fftw gimp jpeg openmp png qt5 tiff zlib -curl -graphicsmagick -krita -opencv -openexr -static-libs" ABI_X86="(64)"
CFLAGS="-O2 -pipe -mtune=native"
CXXFLAGS="-O2 -pipe -mtune=native"
Comment 2 Anton Gubarkov 2021-09-28 08:21:49 UTC
Created attachment 741774 [details]
build log
Comment 3 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2021-10-26 05:10:55 UTC
Comment on attachment 741774 [details]
build log

For me, it happily realises it needs pthread for the main variant:
>-- Looking for pthread.h
>-- Looking for pthread.h - found
>-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
>-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
>-- Found Threads: TRUE

and for the Qt bit, I only have:
>-- Found FFTW3_CORE
>-- FFTW core Found Libraries: /usr/lib64/libfftw3.so
>-- Found FFTW3_THREADS
>-- FFTW threads Found Libraries: /usr/lib64/libfftw3_threads.so
Comment 4 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2021-10-26 05:12:49 UTC
Would be interesting if it's any different with gcc.
Comment 5 Marek Szuba (RETIRED) archtester gentoo-dev 2021-11-19 15:26:16 UTC
With gcc, cmake moves on to trying to link against libpthread as expected:

>-- Looking for pthread.h
>-- Looking for pthread.h - found
>-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
>-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
>-- Looking for pthread_create in pthreads
>-- Looking for pthread_create in pthreads - not found
>-- Looking for pthread_create in pthread
>-- Looking for pthread_create in pthread - found
>-- Found Threads: TRUE  

Anyway:
 - when I took a bare amd64 stage3 system (or to be precise, our official Docker image), emerged sys-devel/clang, then emerged media-gfx/gmic and all its dependency using clang - no issues
 - when I attempted to emerge media-gfx/gmic using clang on a gcc-based system which had all the already installed - reproduced the error

This suggests the culprit here is an incomplete (or possibly incorrect) switch from gcc to clang - which is something we cannot enforce at ebuild level.
Comment 6 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2021-11-19 15:29:13 UTC
(In reply to Marek Szuba from comment #5)
> With gcc, cmake moves on to trying to link against libpthread as expected:
> 
> >-- Looking for pthread.h
> >-- Looking for pthread.h - found
> >-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
> >-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
> >-- Looking for pthread_create in pthreads
> >-- Looking for pthread_create in pthreads - not found
> >-- Looking for pthread_create in pthread
> >-- Looking for pthread_create in pthread - found
> >-- Found Threads: TRUE  
> 
> Anyway:
>  - when I took a bare amd64 stage3 system (or to be precise, our official
> Docker image), emerged sys-devel/clang, then emerged media-gfx/gmic and all
> its dependency using clang - no issues
>  - when I attempted to emerge media-gfx/gmic using clang on a gcc-based
> system which had all the already installed - reproduced the error
> 
> This suggests the culprit here is an incomplete (or possibly incorrect)
> switch from gcc to clang - which is something we cannot enforce at ebuild
> level.

That’s actually rather interesting. It should be OK to just use Clang for some packages. Problems may come in with compiler-rt and libcxx. Could you let me know if you did anything interesting to repro it?

Or just set CC and CXX?
Comment 7 Marek Szuba (RETIRED) archtester gentoo-dev 2021-11-19 15:37:39 UTC
I've just set CC and CXX, having assumed from Comment 1 that this is how Anton switched to clang in this case.
Comment 8 Anton Gubarkov 2021-11-22 14:05:40 UTC
I've set CC and CXX globally. When certain package fails, I switch to gcc using package.env