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Bug 733988

Summary: dev-db/mariadb-10.4.13-r1 fails to install in place of dev-db/mariadb-10.4.13 citing file collisions
Product: Gentoo Linux Reporter: Phil Stracchino (Unix Ronin) <phils>
Component: Current packagesAssignee: Gentoo Linux MySQL bugs team <mysql-bugs>
Status: RESOLVED DUPLICATE    
Severity: normal    
Priority: Normal    
Version: unspecified   
Hardware: All   
OS: Linux   
Whiteboard:
Package list:
Runtime testing required: ---

Description Phil Stracchino (Unix Ronin) 2020-07-26 18:50:44 UTC 
dev-db/mariadb-10.4.13-r1 refuses to install as an update to dev-db/mariadb-10.4.13 due to file collisions.  Of course there's going to be file collisions.  How could there not be?  Portage even correctly identifies that the "conflicting" files belong to dev-db/mariadb-10.4.13.  Something is definitely wrong here, but I don't know whether it's in the ebuild or in portage itself.  No other ebuild appears to be affected, though.

Reproducible: Always

Actual Results:  
* Searching all installed packages for file collisions...
 *
 * Press Ctrl-C to Stop
 *
 * dev-db/mariadb-10.4.13:0::gentoo
 *      /usr/share/mariadb/binary-configure
 *      /usr/share/mariadb/errmsg-utf8.txt
 *      /usr/share/mariadb/fill_help_tables.sql
 *      /usr/share/mariadb/install_spider.sql
 *      /usr/share/mariadb/magic
 *      /usr/share/mariadb/maria_add_gis_sp.sql
 *      /usr/share/mariadb/maria_add_gis_sp_bootstrap.sql
 *      /usr/share/mariadb/mysql-log-rotate
 *      /usr/share/mariadb/mysql.server
 *      /usr/share/mariadb/mysql_performance_tables.sql
 *      /usr/share/mariadb/mysql_system_tables.sql
 *      /usr/share/mariadb/mysql_system_tables_data.sql
 *      /usr/share/mariadb/mysql_test_data_timezone.sql
 *      /usr/share/mariadb/mysql_test_db.sql
 *      /usr/share/mariadb/mysql_to_mariadb.sql
 *      /usr/share/mariadb/mysqld_multi.server
 *      /usr/share/mariadb/wsrep.cnf
 *      /usr/share/mariadb/wsrep_notify
 *      /usr/share/pam_user_map.so
 *      /usr/share/user_map.conf
 *
 * Package 'dev-db/mariadb-10.4.13-r1' NOT merged due to file collisions.



minbar:root:~:2 # emerge --info
Portage 2.3.103 (python 3.7.8-final-0, default/linux/amd64/17.1, gcc-9.3.0, glibc-2.30-r8, 5.6.19-gentoo-minbar x86_64)
=================================================================
System uname: Linux-5.6.19-gentoo-minbar-x86_64-Intel-R-_Xeon-R-_CPU_E5620_@_2.40GHz-with-gentoo-2.6
KiB Mem:    24619476 total,   7289320 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Sun, 26 Jul 2020 06:00:01 +0000
Head commit of repository gentoo: b405f9d294376d9a7884d3f523ef75ebdff27eb0
Head commit of repository mysql: 4fc991d753db5c2c0c319acf981b4609c2ee64bb

Head commit of repository palemoon: a3c55e23cac2de9c76f7c3021d586154886d614b

sh bash 5.0_p17
ld GNU ld (Gentoo 2.33.1 p2) 2.33.1
app-shells/bash:          5.0_p17::gentoo
dev-java/java-config:     2.3.1::gentoo
dev-lang/perl:            5.30.3::gentoo
dev-lang/python:          2.7.18-r1::gentoo, 3.6.11-r2::gentoo, 3.7.8-r2::gentoo, 3.8.4-r1::gentoo
dev-util/cmake:           3.18.0::gentoo
dev-util/pkgconfig:       0.29.2::gentoo
sys-apps/baselayout:      2.6-r1::gentoo
sys-apps/openrc:          0.42.1::gentoo
sys-apps/sandbox:         2.18::gentoo
sys-devel/autoconf:       2.13-r1::gentoo, 2.69-r4::gentoo
sys-devel/automake:       1.16.1-r1::gentoo
sys-devel/binutils:       2.33.1-r1::gentoo
sys-devel/gcc:            9.3.0-r1::gentoo
sys-devel/gcc-config:     2.3.1::gentoo
sys-devel/libtool:        2.4.6-r6::gentoo
sys-devel/make:           4.2.1-r4::gentoo
sys-kernel/linux-headers: 5.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.30-r8::gentoo
Repositories:

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

mysql
    location: /var/db/repos/mysql
    sync-type: git
    sync-uri: https://anongit.gentoo.org/git/proj/mysql.git
    masters: gentoo

palemoon
    location: /var/db/repos/palemoon
    sync-type: git
    sync-uri: https://github.com/deu/palemoon-overlay.git
    masters: gentoo

gentoo-dev-alaric
    location: /var/db/repos/alaric
    sync-type: rsync
    sync-uri: rsync://babylon5/dev-alaric
    masters: gentoo
    priority: 60
    sync-rsync-extra-opts:
    sync-rsync-vcs-ignore: true

ACCEPT_KEYWORDS="amd64"
ACCEPT_LICENSE="*"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=native -O2 -pipe -mfpmath=sse -mcx16 -mpopcnt"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/bind"
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 -mfpmath=sse -mcx16 -mpopcnt"
DISTDIR="/usr/portage/distfiles"
EMERGE_DEFAULT_OPTS="--with-bdeps=y --verbose-conflicts --keep-going"
ENV_UNSET="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="-O2 -pipe"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs 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 xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://gentoo.osuosl.org                 http://www.gtlib.gatech.edu/pub/gentoo                 http://mirrors.cs.wmich.edu/gentoo                 http://distfiles.gentoo.org                 "
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="en_US en"
MAKEOPTS="-j16"
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="acl aes amd64 bash-completion berkdb bzip2 cdda cddb cli crypt dri elogind fltk fortran gdbm iconv id3tag imagemagick ipv6 jpeg2k libtirpc mmx mmxext multilib mysql ncurses nls nptl nsplugin openmp opus pam pcre readline seccomp speex split-usr sse sse2 sse4 sse4_1 sse4_2 ssl tcpd theora threads tk tools unicode utils v4l v4l2 vdpau vorbis x264 xattr xpm 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="actions alias auth_basic authn_core authn_alias authn_anon authn_dbm authn_default authn_file authz_core 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 proxy proxy_html proxy_http rewrite setenvif socache_shmcb speling status unixd unique_id userdir vhost_alias xml2enc" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes mmx mmxext 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="evdev keyboard mouse" KERNEL="linux" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php7-2 php7-3" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python2_7 python3_7" RUBY_TARGETS="ruby25" USERLAND="GNU" VIDEO_CARDS="mga" 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
Comment 1 Dirkjan Ochtman (RETIRED) gentoo-dev 2020-07-26 20:44:03 UTC 
Also seeing this on my (stable) server.
Comment 2 Arfrever Frehtes Taifersar Arahesis 2020-07-26 21:44:31 UTC 

*** This bug has been marked as a duplicate of bug 733928 ***