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Bug 928295 - media-libs/opencv-4.9.0 build failed: /usr/lib/gcc/x86_64-pc-linux-gnu/12/../../../../x86_64-pc-linux-gnu/bin/ld: /lib64/libz.so: error adding symbols: file in wrong format
Summary: media-libs/opencv-4.9.0 build failed: /usr/lib/gcc/x86_64-pc-linux-gnu/12/../...
Status: UNCONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: AMD64 Linux
: Normal normal (vote)
Assignee: Paul Zander
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2024-03-31 15:35 UTC by Yuriy V
Modified: 2024-04-03 20:16 UTC (History)
4 users (show)

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


Attachments
Build log (file_928295.txt,246.95 KB, text/plain)
2024-03-31 15:38 UTC, Yuriy V
Details
emerge --info sys-libs/zlib (file_928295.txt,12.48 KB, text/plain)
2024-03-31 18:29 UTC, Yuriy V
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Yuriy V 2024-03-31 15:35:39 UTC
emerge -pqv '=media-libs/opencv-4.9.0::gentoo'
[ebuild  r  U ] media-libs/opencv-4.9.0 [4.8.1-r1] USE="contrib contribdnn cuda eigen features2d ffmpeg gstreamer jpeg opencl opengl openmp png python qt5 qt6 tiff v4l vaapi webp -atlas% -contribcvv -contribfreetype -contribhdf (-contribovis) -contribsfm -contribxfeatures2d -cudnn -debug -dnnsamples -doc% -examples -gdal -gflags -glog -gphoto2 -gtk3 -ieee1394 -jasper% -java -jpeg2k -lapack -mkl% -non-free -opencvapps -openexr -quirc% -tbb -tesseract -test% -testprograms -vtk -xine" ABI_X86="32 (64) (-x32)" CPU_FLAGS_X86="avx avx2 f16c fma3 popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3 -avx512f" PYTHON_TARGETS="python3_11 -python3_10 -python3_12" VIDEO_CARDS="intel" 
[ebuild  rR   ] media-plugins/frei0r-plugins-1.8.0  USE="facedetect scale0tilt -doc" ABI_X86="32 (64) (-x32)" 

The following packages are causing rebuilds:

  (media-libs/opencv-4.9.0:0/4.9.0::gentoo, ebuild scheduled for merge) causes rebuilds for:
    (media-plugins/frei0r-plugins-1.8.0:0/0::gentoo, ebuild scheduled for merge)

 * IMPORTANT: 23 news items need reading for repository 'gentoo'.
 * Use eselect news read to view new items.


equery b /lib64/libz.so 
 * Searching for /lib64/libz.so ... 
sys-libs/zlib-1.3.1-r1 (/usr/lib64/libz.so.1.3.1)





emerge --info '=media-libs/opencv-4.9.0::gentoo'
Portage 3.0.63 (python 3.11.8-final-0, default/linux/amd64/23.0/desktop/plasma/systemd, gcc-12, glibc-2.39-r2, 6.8.0-pf1-custom2 x86_64)
=================================================================
                         System Settings
=================================================================
System uname: Linux-6.8.0-pf1-custom2-x86_64-Intel-R-_Core-TM-_i7-4790_CPU_@_3.60GHz-with-glibc2.39
KiB Mem:    16325248 total,   3752916 free
KiB Swap:   16777212 total,  16606812 free
Timestamp of repository gentoo: Sun, 31 Mar 2024 06:00:00 +0000
Head commit of repository gentoo: 1778e8c1ffd125e2992e345f1a83c0e65df6bae8
Timestamp of repository anomen: Fri, 29 Mar 2024 19:06:00 +0000
Head commit of repository anomen: a3c58d7dc94a0c1dd09daf1d013ca7aaab990849

Timestamp of repository brother-overlay: Fri, 29 Mar 2024 20:33:31 +0000
Head commit of repository brother-overlay: f2c2fc010da56f5eba7614a421801361ed2c3c7a

Timestamp of repository edgets: Fri, 29 Mar 2024 19:06:12 +0000
Head commit of repository edgets: 91eeb4ec05b7f7024d78dbe15d773cca3a963e04

Timestamp of repository gamerlay: Fri, 29 Mar 2024 19:05:49 +0000
Head commit of repository gamerlay: 4c79deb26f6bfced5a39353b9bcd3f8893658cd2

Timestamp of repository gentoo-zh: Sat, 30 Mar 2024 12:37:05 +0000
Head commit of repository gentoo-zh: 3ad67127d7667a26e083df892a71464ac3f5a179

Timestamp of repository guru: Sun, 31 Mar 2024 02:33:26 +0000
Head commit of repository guru: bca4c20383a32c8308a65695bd7752dda56974b1

Timestamp of repository java: Fri, 29 Mar 2024 19:05:49 +0000
Head commit of repository java: 340cf5509081b0188a2b090c57628af3030cf1d8

Timestamp of repository kde: Sat, 30 Mar 2024 21:18:26 +0000
Head commit of repository kde: 1118d034577e3551dbca4c552edb29f38dcea9fb

Timestamp of repository nest: Fri, 29 Mar 2024 19:06:04 +0000
Head commit of repository nest: abfc27d7523c20914d0adc360ce7ec472a809aff

Timestamp of repository pentoo: Fri, 29 Mar 2024 19:05:52 +0000
Head commit of repository pentoo: d032366e05c8d621a02c0db74100a1ef015cfc82

Timestamp of repository qt: Fri, 29 Mar 2024 19:05:55 +0000
Head commit of repository qt: eb9a85da1a127079e8b82eba581df880cac90ab0

Timestamp of repository rion: Sat, 30 Mar 2024 22:07:22 +0000
Head commit of repository rion: 506d8371f0567bbaba16ea89292bbb17bfc2d095

Head commit of repository somestuff: 89a3107268d5060b23a06acfa8f45b5f1e6314b2

Timestamp of repository steam-overlay: Fri, 29 Mar 2024 19:05:56 +0000
Head commit of repository steam-overlay: 1f8da0027213c6b8e79b4f2f4dfa113f418a1365

Timestamp of repository x11: Fri, 29 Mar 2024 19:05:58 +0000
Head commit of repository x11: 9e654e0cd473a04d04b655e3610d416c4ce4ce13

Timestamp of repository zugaina: Fri, 16 Jun 2023 08:32:15 +0000
Head commit of repository zugaina: a31fcec20b159a13ccd069d4e13b92d18bc0ffec

sh bash 5.2_p26
ld GNU ld (Gentoo 2.42 p3) 2.42.0
distcc 3.4 x86_64-pc-linux-gnu [enabled]
ccache version 4.9.1 [disabled]
app-misc/pax-utils:        1.3.7::gentoo
app-shells/bash:           5.2_p26::gentoo
dev-build/autoconf:        2.13-r8::gentoo, 2.72-r1::gentoo
dev-build/automake:        1.16.5-r2::gentoo
dev-build/cmake:           3.29.0::gentoo
dev-build/libtool:         2.4.7-r4::gentoo
dev-build/make:            4.4.1-r1::gentoo
dev-build/meson:           1.4.0-r1::gentoo
dev-java/java-config:      2.3.3-r1::gentoo
dev-lang/perl:             5.38.2-r2::gentoo
dev-lang/python:           3.11.8_p1::gentoo, 3.12.2_p1::gentoo
dev-lang/rust-bin:         1.76.0::gentoo
dev-util/ccache:           4.9.1-r1::gentoo
sys-apps/baselayout:       2.15::gentoo
sys-apps/sandbox:          2.38::gentoo
sys-apps/systemd:          255.4::gentoo
sys-devel/binutils:        2.42-r1::gentoo
sys-devel/binutils-config: 5.5::gentoo
sys-devel/clang:           17.0.6::gentoo, 18.1.2::gentoo
sys-devel/gcc:             12.3.1_p20240209::gentoo, 13.2.1_p20240210::gentoo
sys-devel/gcc-config:      2.11::gentoo
sys-devel/lld:             17.0.6::gentoo
sys-devel/llvm:            17.0.6::gentoo, 18.1.2::gentoo
sys-kernel/linux-headers:  6.7-r1::gentoo (virtual/os-headers)
sys-libs/glibc:            2.39-r2::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-jobs: 1
    sync-rsync-verify-metamanifest: yes
    sync-rsync-verify-max-age: 3
    sync-rsync-extra-opts: 

anomen
    location: /var/db/repos/anomen
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/anomen.git
    masters: gentoo
    volatile: False

brother-overlay
    location: /var/db/repos/brother-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/brother-overlay.git
    masters: gentoo
    volatile: False

edgets
    location: /var/db/repos/edgets
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/edgets.git
    masters: gentoo
    volatile: False

gamerlay
    location: /var/db/repos/gamerlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/gamerlay.git
    masters: gentoo
    volatile: False

gentoo-zh
    location: /var/db/repos/gentoo-zh
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/gentoo-zh.git
    masters: gentoo
    volatile: False

guru
    location: /var/db/repos/guru
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/guru.git
    masters: gentoo
    volatile: False

java
    location: /var/db/repos/java
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/java.git
    masters: gentoo
    volatile: False

kde
    location: /var/db/repos/kde
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/kde.git
    masters: gentoo
    volatile: False

nest
    location: /var/db/repos/nest
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/nest.git
    masters: gentoo
    volatile: False

pentoo
    location: /var/db/repos/pentoo
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/pentoo.git
    masters: gentoo
    volatile: False

qt
    location: /var/db/repos/qt
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/qt.git
    masters: gentoo
    volatile: False

rion
    location: /var/db/repos/rion
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/rion.git
    masters: gentoo
    volatile: False

somestuff
    location: /var/db/repos/somestuff
    sync-type: git
    sync-uri: https://github.com/m00r3ik/somestuff.git
    masters: gentoo
    volatile: False

steam-overlay
    location: /var/db/repos/steam-overlay
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/steam-overlay.git
    masters: gentoo
    volatile: False

x11
    location: /var/db/repos/x11
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/x11.git
    masters: gentoo
    volatile: False

zugaina
    location: /var/db/repos/zugaina
    sync-type: git
    sync-uri: https://github.com/gentoo-mirror/zugaina.git
    masters: gentoo
    volatile: False

Binary Repositories:

gentoobinhost
    priority: 1
    sync-uri: https://gentoo.osuosl.org/releases/amd64/binpackages/17.1/x86-64

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=haswell -O2 -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"
CXXFLAGS="-march=haswell -O2 -pipe"
DISTDIR="/var/cache/distfiles"
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="-march=haswell -O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live config-protect-if-modified distcc distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=haswell -O2 -pipe"
GENTOO_MIRRORS="http://ftp.vectranet.pl/gentoo/     http://gentoo.mirror.web4u.cz/     http://ftp.gwdg.de/pub/linux/gentoo/"
LANG="uk_UA.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs"
LEX="flex"
LINGUAS="uk ua ru"
MAKEOPTS="-j44"
PKGDIR="/var/cache/binpkgs"
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="7zip X a52 aac acl acpi activities aes alsa amd64 aspell avahi avx avx2 bash-completion bittorrent bluetooth branding bzip2 cairo cdda cdr cet crypt cuda cups dav1d dbus declarative designer device-mapper directx dlna dri dts dvb dvd dvdr efi egl emoji encode epub evdev exif f16c ffmpeg flac flatpak fma3 fontconfig gamepad gdbm geoip geolocation gif gnuefi gpm grub gstreamer gtk gui gzip hackrf hevc hwaccel iconv icu imagemagick jack joystick jpeg json kde kf6compat kwallet lcms libnotify libtirpc lm-sensors logrotate lvm lzma lzo mad midi mmx mmxext mng mp3 mp4 mpeg multilib ncurses networkmanager nfs nls nvenc ogg opencl opengl openh264 openmp openvpn opus p7zip pam pango pclmul pcre pdf pipewire plasma png policykit popcnt portaudio ppds pulseaudio qdbus qml qt5 qt6 rar raw rdrand readline samba screencast sdl seccomp semantic-desktop sensord sftp sound spell spotlight ssdp sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 startup-notification svg svt-av1 systemd tcmalloc test-rust theora threads tiff truetype udev udisks uefi unicode unrar unwind upnp upower usb v4l vaapi vdpau vorbis vulkan vulkan-overlay wacom wayland webp widgets wxwidgets x264 x265 xattr xcb xft xml xv xvid xz zeroconf zink zlib zstd" ABI_X86="32 64" ADA_TARGET="gcc_12" 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="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 ntrip navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" INPUT_DEVICES="joystick wacom evdev synaptics zink" KERNEL="linux" L10N="uk ua ru" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LLVM_TARGETS="directx" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-1" POSTGRES_TARGETS="postgres15" PYTHON_SINGLE_TARGET="python3_11" PYTHON_TARGETS="python3_11" RUBY_TARGETS="ruby31" VIDEO_CARDS="nvidia intel d3d12" 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, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
Comment 1 Yuriy V 2024-03-31 15:38:25 UTC
Created attachment 889089 [details]
Build log
Comment 2 Paul Zander 2024-03-31 16:06:06 UTC
 * Build directory  (BUILD_DIR):     "/var/tmp/portage/media-libs/opencv-4.9.0/work/opencv-4.9.0_build-abi_x86_32.x86"
-- Found ZLIB: /lib64/libz.so (found suitable version "1.3.1", minimum required is "1.2.3")
-- Found JPEG: /lib64/libjpeg.so (found version "62")
-- Found TIFF: /lib64/libtiff.so (found version "4.6.0")
-- Found WebP: /lib64/libwebp.so

I assume your /lib64 is symlinked to /usr/lib64?
Comment 3 Paul Zander 2024-03-31 16:13:04 UTC
You'll also find out that opencv won't compile with dev-util/nvidia-cuda-toolkit-12.4.0, see https://github.com/opencv/opencv_contrib/issues/3690. You'll have to downgrade to 12.3.2.
Comment 4 Eli Schwartz 2024-03-31 17:21:00 UTC
What is the output of:

```
file /lib64/libz.so*
```
Comment 5 Paul Zander 2024-03-31 18:26:13 UTC
Can you attach the output of `equery files sys-libs/zlib` and `emerge --info sys-libs/zlib` please?
Comment 6 Yuriy V 2024-03-31 18:29:53 UTC
Created attachment 889115 [details]
emerge --info sys-libs/zlib
Comment 7 Yuriy V 2024-03-31 18:31:16 UTC
(In reply to Eli Schwartz from comment #4)
> What is the output of:
> 
> ```
> file /lib64/libz.so*

file /lib64/libz.so*
/lib64/libz.so:       symbolic link to libz.so.1.3.1
/lib64/libz.so.1:     symbolic link to libz.so.1.3.1
/lib64/libz.so.1.3.1: ELF 64-bit LSB shared object, x86-64, version 1 (SYSV), dynamically linked, stripped
Comment 8 Paul Zander 2024-03-31 18:41:59 UTC
Please add the output of:

equery files sys-libs/zlib
Comment 9 Yuriy V 2024-03-31 19:25:30 UTC
(In reply to Paul Zander from comment #8)
> Please add the output of:
> 
> equery files sys-libs/zlib

equery files sys-libs/zlib
 * Searching for zlib in sys-libs ...
 * Contents of sys-libs/zlib-1.3.1-r1:
/usr
/usr/include
/usr/include/minizip
/usr/include/minizip/ioapi.h
/usr/include/minizip/mztools.h
/usr/include/minizip/unzip.h
/usr/include/minizip/zip.h
/usr/include/zconf.h
/usr/include/zlib.h
/usr/lib
/usr/lib/libminizip.so -> libminizip.so.1.0.0
/usr/lib/libminizip.so.1 -> libminizip.so.1.0.0
/usr/lib/libminizip.so.1.0.0
/usr/lib/libz.so -> libz.so.1.3.1
/usr/lib/libz.so.1 -> libz.so.1.3.1
/usr/lib/libz.so.1.3.1
/usr/lib/pkgconfig
/usr/lib/pkgconfig/minizip.pc
/usr/lib/pkgconfig/zlib.pc
/usr/lib64
/usr/lib64/libminizip.so -> libminizip.so.1.0.0
/usr/lib64/libminizip.so.1 -> libminizip.so.1.0.0
/usr/lib64/libminizip.so.1.0.0
/usr/lib64/libz.so -> libz.so.1.3.1
/usr/lib64/libz.so.1 -> libz.so.1.3.1
/usr/lib64/libz.so.1.3.1
/usr/lib64/pkgconfig
/usr/lib64/pkgconfig/minizip.pc
/usr/lib64/pkgconfig/zlib.pc
/usr/share
/usr/share/doc
/usr/share/doc/zlib-1.3.1-r1
/usr/share/doc/zlib-1.3.1-r1/ChangeLog.bz2
/usr/share/doc/zlib-1.3.1-r1/FAQ.bz2
/usr/share/doc/zlib-1.3.1-r1/MiniZip64_Changes.txt
/usr/share/doc/zlib-1.3.1-r1/MiniZip64_info.txt.bz2
/usr/share/doc/zlib-1.3.1-r1/README.bz2
/usr/share/doc/zlib-1.3.1-r1/algorithm.txt.bz2
/usr/share/doc/zlib-1.3.1-r1/rfc1950.txt.bz2
/usr/share/doc/zlib-1.3.1-r1/rfc1951.txt.bz2
/usr/share/doc/zlib-1.3.1-r1/rfc1952.txt.bz2
/usr/share/doc/zlib-1.3.1-r1/txtvsbin.txt.bz2
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/miniunzip.1.bz2
/usr/share/man/man1/minizip.1.bz2
/usr/share/man/man3
/usr/share/man/man3/zlib.3.bz2
Comment 10 Paul Zander 2024-03-31 19:53:02 UTC
Do 

/usr/lib/libz.so
/usr/lib/libz.so.1
/usr/lib/libz.so.1.3.1

exist?
Comment 11 Yuriy V 2024-04-02 20:40:45 UTC
(In reply to Paul Zander from comment #10)
> Do 
> 
> /usr/lib/libz.so
> /usr/lib/libz.so.1
> /usr/lib/libz.so.1.3.1
> 
> exist?

$ file /usr/lib/libz.so*
/usr/lib/libz.so:       symbolic link to libz.so.1.3.1
/usr/lib/libz.so.1:     symbolic link to libz.so.1.3.1
/usr/lib/libz.so.1.3.1: ELF 32-bit LSB shared object, Intel 80386, version 1 (SYSV), dynamically linked, stripped
Comment 12 Yuriy V 2024-04-03 20:16:46 UTC
The problem was solved by rollback to 4.8.1
After rebuilding the system with -veDN @system @world 
Will try again.