Bug 547030 – sci-mathematics/topcom-0.17.4 : file collision(s) media-libs/lib3ds-2.0.0_rc1

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Toralf Förster 2015-04-18 18:32:32 UTC]

usr/bin/chiro2finetriang
   usr/bin/chiro2finetriangs
   usr/bin/chiro2mintriang
   usr/bin/chiro2nallfinetriangs
   usr/bin/chiro2nalltriangs
   usr/bin/chiro2nfinetriangs
   usr/bin/chiro2ntriangs
   usr/bin/chiro2placingtriang
   usr/bin/chiro2triangs
   usr/bin/cocircuits2facets
   usr/bin/cross
   usr/bin/cube
   usr/bin/cyclic
   usr/bin/hypersimplex
   usr/bin/lattice
   usr/bin/points2allfinetriangs
   usr/bin/points2alltriangs
   usr/bin/points2chiro
   usr/bin/points2facets
   usr/bin/points2finetriang
   usr/bin/points2finetriangs
   usr/bin/points2flips
   usr/bin/points2nallfinetriangs
   usr/bin/points2nalltriangs
   usr/bin/points2nfinetriangs
   usr/bin/points2nflips
   usr/bin/points2ntriangs
   usr/bin/points2placingtriang
   usr/bin/points2triangs
   usr/bin/points2volume
   usr/bin/santos_triang
   usr/bin/santos_dim4_triang
   usr/bin/santos_22_triang
ecompressdir: bzip2 -9 /usr/share/doc
 * This package will overwrite one or more files that may belong to other
 * packages (see list below). You can use a command such as `portageq
 * owners / <filename>` to identify the installed package that owns a
 * file. If portageq reports that only one package owns a file then do
 * NOT file a bug report. A bug report is only useful if it identifies at
 * least two or more packages that are known to install the same file(s).
 * If a collision occurs and you can not explain where the file came from
 * then you should simply ignore the collision since there is not enough
 * information to determine if a real problem exists. Please do NOT file
 * a bug report at http://bugs.gentoo.org unless you report exactly which
 * two packages install the same file(s). See
 * http://wiki.gentoo.org/wiki/Knowledge_Base:Blockers for tips on how to
 * solve the problem. And once again, please do NOT file a bug report
 * unless you have completely understood the above message.
 * 
 * Detected file collision(s):
 * 
 * 	/usr/bin/cube
 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * media-libs/lib3ds-2.0.0_rc1:0::gentoo
 * 	/usr/bin/cube
 * 
 * Package 'sci-mathematics/topcom-0.17.4' NOT merged due to file
 * collisions. If necessary, refer to your elog messages for the whole
 * content of the above message.

 * GNU info directory index is up-to-date.

The log is stored in /var/log/portage/_emerge_20150418-203001.log.
quick search: https://bugs.gentoo.org/buglist.cgi?quicksearch=sci-mathematics%2Ftopcom
Maintainer :  [e-mail] [e-mail]
maintainer : [e-mail]
herd       : sci

This is an unstable amd64 chroot image (named amd64-unstable_20150414) at a hardened host acting as a tinderbox.

Portage 2.2.18 (python 2.7.9-final-0, default/linux/amd64/13.0/desktop/kde, gcc-4.9.2, glibc-2.20-r2, 3.19.4-hardened x86_64)
=================================================================
System uname: Linux-3.19.4-hardened-x86_64-Intel-R-_Core-TM-_i7-3770_CPU_@_3.40GHz-with-gentoo-2.2
KiB Mem:    16164756 total,    936720 free
KiB Swap:          0 total,         0 free
Timestamp of repository gentoo: Sat, 18 Apr 2015 12:00:01 +0000
sh bash 4.3_p33-r2
ld GNU ld (Gentoo 2.25 p1.0) 2.25
app-shells/bash:          4.3_p33-r2::gentoo
dev-java/java-config:     2.2.0::gentoo
dev-lang/perl:            5.20.2::gentoo
dev-lang/python:          2.7.9-r2::gentoo, 3.3.5-r1::gentoo
dev-util/cmake:           3.2.1::gentoo
sys-apps/baselayout:      2.2::gentoo
sys-apps/openrc:          0.13.11::gentoo
sys-apps/sandbox:         2.6-r1::gentoo
sys-devel/autoconf:       2.13::gentoo, 2.69-r1::gentoo
sys-devel/automake:       1.9.6-r4::gentoo, 1.10.3-r1::gentoo, 1.11.6-r1::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo
sys-devel/binutils:       2.25::gentoo
sys-devel/gcc:            4.8.4::gentoo, 4.9.2::gentoo
sys-devel/gcc-config:     1.8::gentoo
sys-devel/libtool:        2.4.6-r1::gentoo
sys-devel/make:           4.1-r1::gentoo
sys-kernel/linux-headers: 4.0::gentoo (virtual/os-headers)
sys-libs/glibc:           2.20-r2::gentoo
Repositories:

gentoo
    location: /usr/portage
    sync-type: rsync
    sync-uri: rsync://rsync.gentoo.org/gentoo-portage
    priority: -1000

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

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 /etc/entropy /opt/openfire/resources/security/ /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/qpsmtpd/plugins /var/lib/hsqldb /var/spool/torque"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/games/angband/edit/ /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.5/ext-active/ /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.5/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.5/ext-active/ /etc/php/cli-php5.6/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"
DISTDIR="/var/tmp/distfiles"
EMERGE_DEFAULT_OPTS="--nospinner --tree --quiet-build --jobs 1"
FCFLAGS="-O2 -pipe"
FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync"
FFLAGS="-O2 -pipe"
GENTOO_MIRRORS="http://ftp.uni-erlangen.de/pub/mirrors/gentoo rsync://mirror.netcologne.de/gentoo/ ftp://sunsite.informatik.rwth-aachen.de/pub/Linux/gor.bytemark.co.uk/gentoo/ rsync://ftp.snt.utwente.nl/gentoo"
LANG="en_US.utf8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
MAKEOPTS="-j1"
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"
PORTAGE_TMPDIR="/var/tmp"
USE="X a52 aac acl acpi aes-ni alsa amd64 apache2 avx avx2 berkdb bluetooth branding bzip2 cairo cdda cdr cli consolekit corefonts cracklib crypt cups cxx dbus declarative designer dnssec dot dri drmkms dts dvd dvdr ecc emboss encode exif extraengine fam ffmpeg firefox flac fontconfig fortran fpm gd gdbm gif glamor gpm gtk gudev gui iconv icu isag jadetex jpeg kde kipi kvm lapack lcms libkms libnotify libvirtd logrotate mad mbox minizip mmx mmxext mng modules mp3 mp4 mpeg multilib mysql ncurses nls nptl ogg opengl openmp openssl pam pango pax_kernel pcre pcre16 pdf phonon plasma png policykit ppds pwquality python qemu qt3support qt4 readline scrpyt sdl session spell spice sqlite sse sse2 sse4 sse4_1 sse4_2 ssh-askpass ssl ssse3 startup-notification svg tcpd theora thinkpad threads tiff tk tls truetype udev udisks uml unicode upower usb usbredir uxa v4l v4l2 video vorbis wxwidgets x264 xa xcb xcomposite xinerama xkb xml xmp xscreensaver xslt xv xvfb xvid xvmc 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" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_GB" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_3" RUBY_TARGETS="ruby19 ruby20" USERLAND="GNU" VIDEO_CARDS="fbdev glint intel mach64 mga nouveau nv r128 radeon savage sis tdfx trident vesa via vmware 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"
Unset:  CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON

[Comment 1 Thomas Kahle (RETIRED) 2015-04-20 18:18:05 UTC]

Hi amynka, does lib3ds need to install /usr/bin/cube or could it be renamed?  In principle topcom could move.  'cube' there is just a little helper tool, but it is user facing, that is the manual mentions its name as 'cube'.

[Comment 2 Thomas Kahle (RETIRED) 2015-04-26 10:58:36 UTC]

I went forward and changed the files installed by topcom:

+*topcom-0.17.4-r1 (26 Apr 2015)
+
+  26 Apr 2015; Thomas Kahle <[e-mail]> +topcom-0.17.4-r1.ebuild,
+  -files/topcom-0.16.2-no-internal-libs.patch, -topcom-0.16.2.ebuild,
+  -topcom-0.17.4.ebuild:
+  Fix collision (bug 547030), remove old.

[Comment 3 Amy Liffey 2015-04-30 11:21:03 UTC]

Sorry, Well I must say that I am maintainer for lib3ds but I use only lib3ds-1.3.0-r1 for 3d printing the other one is from games herd. Unfortunately in my version there is no cube.. So I cant tell.. 

Amy