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Bug 656128 - revdep-rebuild fails finding broken references to `libgfortan.so.4`
Summary: revdep-rebuild fails finding broken references to `libgfortan.so.4`
Status: UNCONFIRMED
Alias: None
Product: Portage Development
Classification: Unclassified
Component: Tools (show other bugs)
Hardware: All Linux
: Normal normal with 1 vote (vote)
Assignee: Portage Tools Team
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2018-05-19 20:32 UTC by Niklas Haas
Modified: 2018-08-27 19:23 UTC (History)
1 user (show)

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


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Description Niklas Haas 2018-05-19 20:32:45 UTC
After upgrading gcc from 7.3 to 8.1, all references to `libgfortran.so.4` broke. For example, `sci-libs/blas-reference`:

    $ ldd /usr/lib64/blas/reference/libblas.so
    	linux-vdso.so.1 (0x00007ffc50d5d000)
    	libgfortran.so.4 => not found
    	libm.so.6 => /lib64/libm.so.6 (0x00007f46c3e58000)
    	libc.so.6 => /lib64/libc.so.6 (0x00007f46c3a82000)
    	/lib64/ld-linux-x86-64.so.2 (0x00007f46c43f3000)

revdep-rebuild insists my system is clean, even if I specifically ask it to check for references to this library:

    $ revdep-rebuild --library 'libgfortran.so.4'
     * This is the new python coded version
     * Please report any bugs found using it.
     * The original revdep-rebuild script is installed as revdep-rebuild.sh
     * Please file bugs at: https://bugs.gentoo.org/
     * Collecting system binaries and libraries
     * Checking dynamic linking consistency

    Your system is consistent

Manually re-building {c,}blas-reference solves the issue:

    $ emerge -1 {c,}blas-reference
    ...
    $ ldd /usr/lib64/blas/reference/libblas.so
	linux-vdso.so.1 (0x00007fff7f35f000)
	libgfortran.so.5 => /usr/lib/gcc/x86_64-pc-linux-gnu/8.1.0/libgfortran.so.5 (0x00007f8fa83e1000)
	libm.so.6 => /lib64/libm.so.6 (0x00007f8fa809a000)
	libc.so.6 => /lib64/libc.so.6 (0x00007f8fa7cc4000)
	libquadmath.so.0 => /usr/lib/gcc/x86_64-pc-linux-gnu/8.1.0/libquadmath.so.0 (0x00007f8fa7a83000)
	libz.so.1 => /lib64/libz.so.1 (0x00007f8fa786a000)
	libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/8.1.0/libgcc_s.so.1 (0x00007f8fa7652000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f8fa8aa7000)

It also worries me that portage didn't automatically preserve libgfortran.so.4 when unmerging gcc 7.3, like it normally does. Perhaps these two bugs are connected. In addition to this, even though I've rebuild blas-reference successfully, I presumably still have other broken references to libgfortan.so.4 *somewhere* on my system, since `import numpy` runs into the issue. So getting revdep-rebuild to work here would be useful.

    $ emerge --info gentoolkit
    Portage 2.3.38 (python 3.5.5-final-0, default/linux/amd64/17.0/hardened, gcc-8.1.0, glibc-2.26-r7, 4.16.8-gentoo-pcireset x86_64)
    =================================================================
                             System Settings
    =================================================================
    System uname: Linux-4.16.8-gentoo-pcireset-x86_64-AMD_Ryzen_Threadripper_1950X_16-Core_Processor-with-gentoo-2.4.1
    KiB Mem:    65926136 total,  20355064 free
    KiB Swap:          0 total,         0 free
    Timestamp of repository gentoo: Fri, 18 May 2018 02:15:01 +0000
    Head commit of repository gentoo: 6f378127e806e8e17f0692ed7e5064bcad06d24a
    sh dash 0.5.10.1-r2
    ld GNU ld (Gentoo 2.30 p2) 2.30.0
    app-shells/bash:          4.4_p19::gentoo
    dev-lang/perl:            5.26.2::gentoo
    dev-lang/python:          2.7.14-r2::gentoo, 3.5.5-r1::gentoo, 3.6.5-r1::gentoo
    dev-util/cmake:           3.11.1::gentoo
    dev-util/pkgconfig:       0.29.2::gentoo
    sys-apps/baselayout:      2.4.1-r2::gentoo
    sys-apps/sandbox:         2.13::gentoo
    sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
    sys-devel/automake:       1.16.1-r1::gentoo
    sys-devel/binutils:       2.30-r2::gentoo
    sys-devel/gcc:            8.1.0-r3::gentoo
    sys-devel/gcc-config:     1.9.1::gentoo
    sys-devel/libtool:        2.4.6-r5::gentoo
    sys-devel/make:           4.2.1-r3::gentoo
    sys-kernel/linux-headers: 4.16-r1::gentoo (virtual/os-headers)
    sys-libs/glibc:           2.26-r7::gentoo
    Repositories:

    tristelune
        location: /var/lib/layman/tristelune
        masters: gentoo
        priority: -5000

    gentoo
        location: /usr/portage
        sync-type: rsync
        sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage
        priority: -1000
        sync-rsync-verify-max-age: 24
        sync-rsync-extra-opts: 
        sync-rsync-verify-jobs: 1
        sync-rsync-verify-metamanifest: yes

    local_overlay
        location: /usr/local/portage
        masters: gentoo
        priority: 0

    crossdev
        location: /usr/crossdev/portage
        masters: gentoo
        priority: 1

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

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

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

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

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

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

    ACCEPT_KEYWORDS="amd64 ~amd64"
    ACCEPT_LICENSE="* -@EULA"
    CBUILD="x86_64-pc-linux-gnu"
    CFLAGS="-march=native -O2 -g"
    CHOST="x86_64-pc-linux-gnu"
    CONFIG_PROTECT="/etc /etc/omega.conf /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/i18n/locales /var/spool/munin-async/.ssh"
    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 /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
    CXXFLAGS="-march=native -O2 -g"
    DISTDIR="/var/cache/distfiles"
    EMERGE_DEFAULT_OPTS="--ask --ask-enter-invalid --alert --keep-going --quiet-unmerge-warn --quiet-build --quiet-fail --ignore-built-slot-operator-deps=y --jobs=10 --load-average=32 --tree --backtrack=3 --with-bdeps=y --nospinner"
    ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY 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="-O2 -pipe"
    FEATURES="assume-digests binpkg-logs cgroup collision-protect compressdebug config-protect-if-modified distlocks ebuild-locks fixlafiles installsources ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
    FFLAGS="-O2 -pipe"
    GENTOO_MIRRORS="http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://gentoo.modulix.net/gentoo/ http://gd.tuwien.ac.at/opsys/linux/gentoo/ http://tux.rainside.sk/gentoo/ http://ftp.halifax.rwth-aachen.de/gentoo/"
    LANG="en_US.UTF-8"
    LDFLAGS="-Wl,-O1 -Wl,--as-needed"
    LINGUAS="en"
    MAKEOPTS="-j32 -l32"
    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 aes amd64 aspell avx avx2 bash-completion bazaar branding btrfs bzip2 cairo caps cdr cjk clang color-management crypt cvs cxx darcs dri dts dvd dvdr emboss encode exif f16c fam ffmpeg firefox flac fma3 fontconfig gif git glamor gpg gpm gtk guile hardened http2 iconv icu idn ipv6 jbig jpeg jpeg2k lcms ldap libnotify libzfs littlecms llvm lm_sensors lua luajit lzma lzo mad mem-scramble mercurial mmx mmxext mng mp3 mp4 mpeg multilib ncurses nls nptl numa ogg opencl openexr opengl openmp otr pam pango pclmul pcre pdf perl pie png popcnt ppds pulseaudio python qt qt5 readline ruby sasl savedconfig scim sdl seccomp sha3 socks socks5 sound spell sse sse2 sse3 sse4_1 sse4_2 sse4a ssl ssp ssse3 subversion svg systemd theora threads tiff truetype tta udev unicode usb vaapi vdpau vim vim-syntax vorbis vulkan wavpack wxwidgets x264 xattr xcb xetex xfs xft xinerama xml xtpax xvid xz zfs zlib zsh zsh-completion" ABI_X86="64 32" 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 plan sheets stage 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 sse4a ssse3" CURL_SSL="openssl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="pc efi-64" INPUT_DEVICES="libinput" KERNEL="linux" L10N="en ja" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LLVM_TARGETS="AMDGPU BPF" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_5 python3_6" RUBY_TARGETS="ruby23 ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu radeonsi" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
    Unset:  CC, CPPFLAGS, CTARGET, CXX, INSTALL_MASK, LC_ALL, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

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

    app-portage/gentoolkit-0.4.2-r1::gentoo was built with the following:
    USE="" ABI_X86="(64)" PYTHON_TARGETS="python2_7 python3_5 python3_6 -pypy -python3_4"
Comment 1 poinck 2018-07-10 14:17:48 UTC
I had a similar problem when upgrading to the new stable gcc-7.3.0-r3 from gcc-6.4:

The new "revdep-rebuild" (python-version) reported that my system is consistent. After using R-3.4.1 (current stable version), a broken reference showed up:

"libgfortan.so.3"

After recompiling R, the problem was gone. I immediatly issued the legacy "revdep-rebuild.sh" (shell-version) which found additional broken packages:

sys-cluster/openmpi-2.0.2
ci-libs/blas-reference-20070226-r4
sci-libs/lapack-reference-3.2.1-r4

The rebuilds were successful.


```emerge --info
Portage 2.3.40 (python 3.4.8-final-0, default/linux/amd64/17.0/desktop/gnome/systemd, gcc-7.3.0, glibc-2.26-r7, 4.14.52-gentoo x86_64)
=================================================================
System uname: Linux-4.14.52-gentoo-x86_64-Intel-R-_Core-TM-_i5-3570K_CPU_@_3.40GHz-with-gentoo-2.4.1
KiB Swap:   20479996 total,  20453644 free
Timestamp of repository gentoo: Tue, 10 Jul 2018 13:00:01 +0000
Head commit of repository gentoo: c9b3acfe37ba4c772c1671a36ace6de6c2e17651
sh bash 4.4_p12
ld GNU ld (Gentoo 2.30 p2) 2.30.0
distcc 3.2rc1 x86_64-pc-linux-gnu [enabled]
app-shells/bash:          4.4_p12::gentoo
dev-java/java-config:     2.2.0-r4::gentoo
dev-lang/perl:            5.24.3-r1::gentoo
dev-lang/python:          2.7.14-r1::gentoo, 3.4.8::gentoo, 3.5.5::gentoo, 3.6.5::gentoo
dev-util/cmake:           3.9.6::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.4.1-r2::gentoo
sys-apps/sandbox:         2.13::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.11.6-r3::gentoo, 1.15.1-r2::gentoo
sys-devel/binutils:       2.30-r2::gentoo
sys-devel/gcc:            7.3.0-r3::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r3::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.13::gentoo (virtual/os-headers)
sys-libs/glibc:           2.26-r7::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000
    sync-rsync-extra-opts: 
    sync-rsync-verify-jobs: 1
    sync-rsync-verify-max-age: 24
    sync-rsync-verify-metamanifest: yes

lokal
    location: /usr/local/portage
    masters: gentoo
    priority: 0

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

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

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

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=core-avx-i -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/easy-rsa /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/php/apache2-php7.0/ext-active/ /etc/php/apache2-php7.1/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cgi-php7.1/ext-active/ /etc/php/cli-php7.0/ext-active/ /etc/php/cli-php7.1/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c"
CXXFLAGS="-march=core-avx-i -O2 -pipe"
DISTDIR="/usr/portage/distfiles"
ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY 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="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distcc distlocks ebuild-locks fixlafiles merge-sync multilib-strict news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="ftp://mirror.netcologne.de/gentoo/ ftp://ftp.uni-erlangen.de/pub/mirrors/gentoo ftp://ftp.wh2.tu-dresden.de/pub/mirrors/gentoo ftp://gentoo.imj.fr/pub/gentoo/ http://linux.rz.ruhr-uni-bochum.de/download/gentoo-mirror/"
LANG="de_DE.UTF-8"
LC_ALL="de_DE.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de"
MAKEOPTS="-j5"
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 alsa amd64 amdgpu autoipd avahi bash-completion berkdb branding bzip2 cairo cdda cli clock collada colord crypt cups cxx cycles dbus dri drm dts dvd dvdr eds egl emboss encode evo exif fam ffmpeg flac fortran gbm gcrypt gdbm gflags gif git glamor gles gnome gnome-keyring gnome-online-accounts gnutls gpm gstreamer gtk gtk3 iconv icu introspection ipv6 jack jit jpeg kdrive ladpsa lcms ldap libkms libnotify libsecret libtirpc mad mmx mng modemmanager modules mp3 mp4 mpeg multilib nautilus ncurses netcdf nls nptl ogg openal opencl opengl openmp pam pango pch pcre pdf perl pie png policykit ppds pulseaudio python readline sdl seccomp sndfile spell sqlite sse sse2 ssl ssse3 startup-notification subversion svg symlink systemd taglib tcpd theora tiff truetype udev udisks unicode upower usb uxa vaapi vala virt-network visualizer vorbis vulkan winbind wxwidgets x264 xa xattr xcb xml xv xvid xvmc zlib" ABI_X86="64" 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 plan sheets stage words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="evdev synaptics" KERNEL="linux" L10N="de" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5 postgres10" PYTHON_SINGLE_TARGET="python3_5" PYTHON_TARGETS="python2_7 python3_4 python3_5" RUBY_TARGETS="ruby23" SANE_BACKENDS="mustek mustek_pp mustek_usb mustek_usb2 plustek plustek_pp" USERLAND="GNU" VIDEO_CARDS="intel i965 amdgpu radeonsi radeon" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account"
Unset:  CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
```