Bug 765376 – dev-libs/libpcre2-10.36 (file collisions) None of the installed packages claim the file(s)

• Product: Gentoo Linux
• Status: RESOLVED INVALID

[Description Gabriel 2021-01-14 01:24:05 UTC]

An update to app-misc / fdupes-2.1.2 is pulling this package into the installation, but it is generating this type of conflict even with some portage features enabled, in this case, collision-protect and protect-owned.

Portage 3.0.13 (python 3.8.7-final-0, default/linux/amd64/17.1/desktop/gnome, gcc-10.2.0, glibc-2.32-r7, 5.10.6 x86_64)
=================================================================
System uname: Linux-5.10.6-x86_64-Intel-R-_Core-TM-_i5-2450M_CPU_@_2.50GHz-with-glibc2.2.5
KiB Mem:     8062520 total,   1056264 free
KiB Swap:          0 total,         0 free
Head commit of repository gentoo: e4f6f85c63c1743f35d80031547b517480de8f95

sh bash 5.1_p4
ld GNU ld (Gentoo 2.35.1 p2) 2.35.1
app-shells/bash:          5.1_p4::gentoo
dev-lang/perl:            5.32.0-r1::gentoo
dev-lang/python:          3.8.7::gentoo, 3.9.1::gentoo
dev-util/cmake:           3.19.2::gentoo
sys-apps/baselayout:      2.7-r1::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.20::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r5::gentoo
sys-devel/automake:       1.16.3-r1::gentoo
sys-devel/binutils:       2.35.1-r1::gentoo
sys-devel/gcc:            10.2.0-r5::gentoo
sys-devel/gcc-config:     2.3.2-r1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.3::gentoo
sys-kernel/linux-headers: 5.10::gentoo (virtual/os-headers)
sys-libs/glibc:           2.32-r7::gentoo
Repositories:

gentoo
    location: /var/db/repos/gentoo
    sync-type: git
    sync-uri: https://github.com/gentoo/gentoo.git
    priority: -1000

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

stha09
    location: /var/lib/layman/stha09
    masters: gentoo
    priority: 50

ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS=" -march=native -O2 -pipe"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /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"
CXXFLAGS=" -march=native -O2 -pipe"
DISTDIR="/var/cache/distfiles"
EMERGE_DEFAULT_OPTS="--ask --jobs 4 --load-average 4"
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 -O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg cgroup collision-protect config-protect-if-modified distlocks downgrade-backup ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch parallel-install pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS=" -march=native -O2 -pipe"
GENTOO_MIRRORS="https://gentoo.c3sl.ufpr.br/ http://gentoo.c3sl.ufpr.br/ rsync://gentoo.c3sl.ufpr.br/gentoo/"
LANG="pt_BR.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j4 -l4"
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"
USE="X a52 aac acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord crypt dbus dri dts dvd dvdr eds elogind emboss encode evo exif flac fortran gdbm gif gnome gnome-keyring gnome-online-accounts gpm gstreamer gtk gui iconv icu introspection ipv6 jpeg lcms libglvnd libnotify libressl libsecret libtirpc mad mng mp3 mp4 mpeg multilib nautilus ncurses networkmanager nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt5 readline sdl seccomp spell split-usr ssl startup-notification svg sysprof tcpd tiff tracker truetype udev udisks unicode upower usb vaapi vorbis wayland wxwidgets x264 xattr xcb xml xv xvid zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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="mmx mmxext sse sse2" CURL_SSL="libressl" 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" KERNEL="linux" L10N="pt-BR" 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="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_8" PYTHON_TARGETS="python2_7 python3_8" RUBY_TARGETS="ruby25 ruby26" USERLAND="GNU" VIDEO_CARDS="intel i965 radeon r600" 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, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Gabriel 2021-01-14 01:29:00 UTC]

Created attachment 682780 [details]
emerge_output

[Comment 2 Ionen Wolkens 2021-01-14 09:57:32 UTC]

If at some point you've manually installed libpcre2 (without portage) or deleted some data from /var/db/pkg/, it would explain why portage doesn't know about these.

Support areas may be able to help with this better:
https://www.gentoo.org/support/

[Comment 3 Brian Evans (RETIRED) 2021-01-14 13:53:16 UTC]

I agree that it appears some damage or corruption happened on this system.

On top of which, the collision-protect FEATURE was manually enabled which stops fixing such things.  Normally just protect-owned is on by default which stops overwriting of 2 different packages.

Not a bug that I can tell.