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Bug 593662 - dev-libs/link-grammar: ebuilds build and install bundled copy of sci-mathematics/minisat
Summary: dev-libs/link-grammar: ebuilds build and install bundled copy of sci-mathemat...
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Linux Gnome Desktop Team
Depends on:
Blocks: bundled-libs
  Show dependency tree
Reported: 2016-09-13 13:38 UTC by Toralf Förster
Modified: 2020-05-28 13:48 UTC (History)
3 users (show)

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

emerge-history.txt (emerge-history.txt,260.90 KB, text/plain)
2016-09-13 13:39 UTC, Toralf Förster
sci-mathematics:minisat-2.2.0_p20130925:20160913-132447.log (sci-mathematics:minisat-2.2.0_p20130925:20160913-132447.log,13.29 KB, text/plain)
2016-09-13 13:39 UTC, Toralf Förster

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Description Toralf Förster gentoo-dev 2016-09-13 13:38:57 UTC
 * Detected file collision(s):
 * 	/usr/lib64/
 * 	/usr/lib64/
 * Searching all installed packages for file collisions...
 * Press Ctrl-C to Stop
 * dev-libs/link-grammar-5.3.9:0::gentoo
 * 	/usr/lib64/
 * 	/usr/lib64/
 * Package 'sci-mathematics/minisat-2.2.0_p20130925' NOT merged due to

$ cat emerge-info.txt

  This is an unstable amd64 chroot image (named amd64-13.0-unstable_20160909-160103) at a hardened host acting as a tinderbox.

  USE flags ...

  ... in make.conf:
USE="  pax_kernel xtpax -cdinstall -oci8 -bindist apache2 -avcodec cdb compat csc designer egl git glamor gnuplot gtk gtk2 gtk3 -gtkstyle hpn icu ipv6 isag jadetex jpeg -kerberos latex libkms libvirtd mad mdnsresponder-compat minimal ncurses nscd opencv -openexr openssl -postproc pwquality qemu qml qt3support -semantic-desktop sockets sqlite3 ssl sslv2 sslv3 -swscale -system-icu -system-libs tcpd -theora thinkpad threads -tls -v4l2 vim wav x265 xcb xinerama xinetd xscreensaver xvfb xz zenmap"

  ... in /etc/portage/package.use/*:
  mail-mta/ssmtp      ssl mta
  net-misc/wget       ssl
  app-crypt/pinentry  -qt4
  app-editors/emacs   -dbus -svg -ssl -gtk -gtk3
  app-text/xmlto      -latex
  dev-libs/boehm-gc   threads
  dev-libs/libpcre    pcre16
  net-nds/openldap    -sasl
  dev-util/cmake      -qt4 -qt5
  dev-vcs/git         -perl
  gnome-base/librsvg  -tools
  media-libs/mesa     -vaapi
  <=net-misc/openssh-7.3_p1-r2    -hpn
  net-misc/iputils -caps -filecaps
  >=x11-libs/cairo-1.14.6 X
  >=x11-libs/gdk-pixbuf-2.34.0 X

  entries in /etc/portage/package.unmask/*:


gcc-config -l:
 [1] x86_64-pc-linux-gnu-4.9.3
 [2] x86_64-pc-linux-gnu-5.4.0 *

Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python3.5 (fallback)
  [3]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby20 (with Rubygems)
  [2]   ruby21 (with Rubygems) *

Portage 2.3.0 (python 3.4.5-final-0, default/linux/amd64/13.0, gcc-5.4.0, glibc-2.23-r2, 4.7.3-hardened x86_64)
                         System Settings
System uname: Linux-4.7.3-hardened-x86_64-Intel-R-_Core-TM-_i7-3930K_CPU_@_3.20GHz-with-gentoo-2.3
KiB Mem:    65285352 total,   1316692 free
KiB Swap:   67108860 total,  67087936 free
Timestamp of repository gentoo: Tue, 13 Sep 2016 13:14:41 +0000
sh bash 4.3_p46
ld GNU ld (Gentoo 2.26.1 p1.0) 2.26.1
app-shells/bash:          4.3_p46::gentoo
dev-lang/perl:            5.24.0-r1::gentoo
dev-lang/python:          2.7.12::gentoo, 3.4.5::gentoo, 3.5.2::gentoo
dev-util/cmake:           3.6.2::gentoo
dev-util/pkgconfig:       0.29.1::gentoo
sys-apps/baselayout:      2.3::gentoo
sys-apps/openrc:          0.21.7::gentoo
sys-apps/sandbox:         2.10-r2::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r2::gentoo
sys-devel/automake:       1.10.3-r2::gentoo, 1.11.6-r2::gentoo, 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo
sys-devel/binutils:       2.26.1::gentoo
sys-devel/gcc:            4.9.3::gentoo, 5.4.0::gentoo
sys-devel/gcc-config:     1.8-r1::gentoo
sys-devel/libtool:        2.4.6-r2::gentoo
sys-devel/make:           4.2.1::gentoo
sys-kernel/linux-headers: 4.7::gentoo (virtual/os-headers)
sys-libs/glibc:           2.23-r2::gentoo

    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://
    priority: 1

    location: /usr/local/portage
    masters: gentoo
    priority: 2

ACCEPT_KEYWORDS="amd64 ~amd64"
CFLAGS="-march=native -O2 -pipe"
CONFIG_PROTECT="/etc /etc/stunnel/stunnel.conf /usr/share/config /usr/share/easy-rsa /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/apache2-php7.0/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cgi-php7.0/ext-active/ /etc/php/cli-php5.6/ext-active/ /etc/php/cli-php7.0/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=native -O2 -pipe"
EMERGE_DEFAULT_OPTS="--verbose --verbose-conflicts --color=n --nospinner --tree --quiet-build"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync network-sandbox parallel-fetch preserve-libs protect-owned sandbox sfperms strict test-fail-continue unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS=" rsync:// rsync://"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
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"
USE="acl amd64 apache2 berkdb bzip2 cdb cli compat cracklib crypt csc cxx designer dri egl fortran gdbm git glamor gnuplot gtk gtk2 gtk3 hpn iconv icu ipv6 isag jadetex jpeg latex libkms libvirtd mad mdnsresponder-compat minimal mmx mmxext modules multilib ncurses nls nptl nscd opencv openmp openssl pam pax_kernel pcre pwquality qemu qml qt3support readline seccomp session sockets sqlite3 sse sse2 ssl sslv2 sslv3 tcpd thinkpad threads unicode vim wav x265 xattr xcb xinerama xinetd xscreensaver xtpax xvfb xz zenmap 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="kexi words flow plan sheets stage tables krita karbon braindump author" CAMERAS="ptp2" 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 itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" L10N="ca-valencia da ga ia la mai ml ro sd" 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" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" 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"
Comment 1 Toralf Förster gentoo-dev 2016-09-13 13:39:00 UTC
Created attachment 445604 [details]
Comment 2 Toralf Förster gentoo-dev 2016-09-13 13:39:03 UTC
Created attachment 445606 [details]
Comment 3 Marek Szuba gentoo-dev 2016-09-13 13:57:28 UTC
I have just confirmed that stable dev-libs/link-grammar-5.3.7 installs its own copy of libminisat as well. Unfortunately there doesn't seem to be any way of preventing this without patching the build scripts.
Comment 4 David Seifert gentoo-dev 2016-09-14 11:57:15 UTC
Simple solution: add RDEPEND blocks for stable stuff, revbump all colliding packages and unbundle minisat.
Comment 5 Marek Szuba gentoo-dev 2016-09-19 10:26:48 UTC
Reassigning the bug to maintainers of dev-libs/link-grammar.

For the record, it seems that the version of minisat bundled with link-grammar is quite old.
Comment 6 René Rhéaume 2016-10-13 10:03:32 UTC
According to , version older than 5.3.11 were using a bundled minisat 2.0 . It is now possible to use a system minisat 2.2
Comment 7 Gilles Dartiguelongue gentoo-dev 2016-10-16 22:02:26 UTC
I don't know which minisat-2.2 release they used but none of the version in tree are supported it seems. I'll push a proper bug report after bumping link-grammar.
Comment 8 Pacho Ramos gentoo-dev 2016-12-05 11:50:10 UTC
Gilles, it seems this was solved in 5.3.13... are you going to look into it or could I go ahead? (I am unsure if you have any ebuild prepared)