Bug 356211 – [science overlay] sci-biology/gbrowse fails to update to version 2.26 if gbrowse-2.03 is installed

• Product: Gentoo Linux
• Status: RESOLVED WONTFIX

[Description Juergen Rose 2011-02-23 13:23:13 UTC]

'emerge -uvDN gbrowse' fails with:
...

>>> Installing (1 of 5) sci-biology/gbrowse-2.26
 * checking 514 files for package collisions
 * 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). Once again, please do NOT file
 * a bug report unless you have completely understood the above message.
 * 
 * Detected file collision(s):
 * 
 *      /usr/bin/gbrowse_syn_load_alignment_database.pl
 *      /usr/bin/gbrowse_syn_load_alignments_msa.pl
 *      /usr/bin/gbrowse_clean.pl
 *      /usr/bin/wiggle2gff3.pl
 *      /usr/bin/gbrowse_set_admin_passwd.pl
 *      /usr/bin/gbrowse_slave
 *      /usr/bin/make_das_conf.pl
 *      /usr/share/man/man1/wiggle2gff3.pl.1.bz2
 *      /usr/share/man/man1/make_das_conf.pl.1.bz2
 *      /usr/share/man/man1/gbrowse_clean.pl.1.bz2
 *      /var/www/gbrowse2/databases/admin_uploads/README
 *      /var/www/gbrowse2/databases/gbrowse_syn/alignments/rice.aln.gz
 *      /var/www/gbrowse2/databases/gbrowse_syn/rice/rice.gff3
 *      /var/www/gbrowse2/databases/gbrowse_syn/wild_rice/wild_rice.gff3
 *      /var/www/gbrowse2/databases/ideograms/human_cytobands.gff
 *      /var/www/gbrowse2/databases/ideograms/mouse_cytobands.gff
 *      /var/www/gbrowse2/databases/ideograms/rat_cytobands.gff
 *      /var/www/gbrowse2/databases/pop_demo/pop_demo.gff3
 *      /var/www/gbrowse2/databases/yeast_chr1+2/yeast_chr1+2.gff3
 *      /var/www/gbrowse2/databases/yeast_scaffolds/chr1.fa
 *      /var/www/gbrowse2/databases/yeast_scaffolds/chr2.fa
 *      /var/www/gbrowse2/databases/yeast_scaffolds/chromosomes.gff3
 *      /var/www/localhost/htdocs/gbrowse/i

 * 
 * Searching all installed packages for file collisions...
 * 
 * Press Ctrl-C to Stop
 * 
 * sci-biology/gbrowse-2.03
 *      /usr/bin/gbrowse_clean.pl
 *      /usr/bin/gbrowse_set_admin_passwd.pl
 *      /usr/bin/gbrowse_slave
 *      /usr/bin/gbrowse_syn_load_alignment_database.pl
 *      /usr/bin/gbrowse_syn_load_alignments_msa.pl
 *      /usr/bin/make_das_conf.pl
 *      /usr/bin/wiggle2gff3.pl
 *      /usr/share/man/man1/gbrowse_clean.pl.1.bz2
 *      /usr/share/man/man1/make_das_conf.pl.1.bz2
 *      /usr/share/man/man1/wiggle2gff3.pl.1.bz2
 *      /var/www/gbrowse2/databases/admin_uploads/README
 *      /var/www/gbrowse2/databases/gbrowse_syn/alignments/rice.aln.gz
 *      /var/www/gbrowse2/databases/gbrowse_syn/rice/rice.gff3
 *      /var/www/gbrowse2/databases/gbrowse_syn/wild_rice/wild_rice.gff3
 *      /var/www/gbrowse2/databases/ideograms/human_cytobands.gff
 *      /var/www/gbrowse2/databases/ideograms/mouse_cytobands.gff
 *      /var/www/gbrowse2/databases/ideograms/rat_cytobands.gff
 *      /var/www/gbrowse2/databases/pop_demo/pop_demo.gff3
 *      /var/www/gbrowse2/databases/yeast_chr1+2/yeast_chr1+2.gff3
 *      /var/www/gbrowse2/databases/yeast_scaffolds/chr1.fa
 * 
 * Package 'sci-biology/gbrowse-2.26' NOT merged due to file collisions.
 * If necessary, refer to your elog messages for the whole content of the
 * above message.

>>> Failed to install sci-biology/gbrowse-2.26, Log file:

Deleting gbrowse and reinstalling gbrowse works except the error described in Bug 354961


Reproducible: Always




root@cheetah:/root(6)# emerge --info =gbrowse-2.26
Portage 2.1.9.41 (!../home_cheetah/ftp/pub/portage/profiles/default/linux/x86/10.0/desktop, gcc-4.5.2, glibc-2.13-r1, 2.6.37-gentoo i686)
=================================================================
                        System Settings
=================================================================
System uname: Linux-2.6.37-gentoo-i686-AMD_Athlon-tm-_XP_1800+-with-gentoo-2.0.1
Timestamp of tree: Wed, 23 Feb 2011 03:00:01 +0000
ccache version 3.1.4 [disabled]
app-shells/bash:     4.1_p9
dev-java/java-config: 2.1.11-r3
dev-lang/python:     2.7.1-r1, 3.1.3-r1
dev-util/ccache:     3.1.4
dev-util/cmake:      2.8.4
sys-apps/baselayout: 2.0.1-r1
sys-apps/openrc:     0.7.0
sys-apps/sandbox:    2.5
sys-devel/autoconf:  2.13, 2.68
sys-devel/automake:  1.9.6-r3, 1.10.3, 1.11.1
sys-devel/binutils:  2.21
sys-devel/gcc:       4.5.2
sys-devel/gcc-config: 1.4.1
sys-devel/libtool:   2.4-r1
sys-devel/make:      3.82
virtual/os-headers:  2.6.36.1 (sys-kernel/linux-headers)
ACCEPT_KEYWORDS="x86 ~x86"
ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft"
CBUILD="i686-pc-linux-gnu"
CFLAGS="-O2 -march=athlon-xp -fomit-frame-pointer"
CHOST="i686-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/openvpn/easy-rsa /var/lib/hsqldb"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/eselect/compiler /etc/eselect/postgresql /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.2/ext-active/ /etc/php/apache2-php5.3/ext-active/ /etc/php/cgi-php5.2/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cli-php5.2/ext-active/ /etc/php/cli-php5.3/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="-O2 -march=athlon-xp -fomit-frame-pointer"
DISTDIR="/usr/portage/distfiles"
FEATURES="assume-digests binpkg-logs distlocks fixlafiles fixpackages news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch"
FFLAGS="-O2 -march=athlon-xp -fomit-frame-pointer"
GENTOO_MIRRORS="http://distfiles.gentoo.org"
LANG="en_US.UTF-8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed"
LINGUAS="de fr"
MAKEOPTS="-j1"
PKGDIR="/usr/portage/packages"
PORTAGE_CONFIGROOT="/"
PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages"
PORTAGE_TMPDIR="/var/tmp"
PORTDIR="/usr/portage"
PORTDIR_OVERLAY="/var/lib/layman/java-overlay /var/lib/layman/x11 /var/lib/layman/sunrise /var/lib/layman/science /var/lib/layman/pro-audio /var/lib/layman/n4g /usr/local/portage /var/lib/cpan /var/lib/g-octave"
SYNC="rsync://rsync.gentoo.org/gentoo-portage"
USE="3dnow 3dnowext R X Xaw3d a52 aac abiword acl acpi admin afs alsa ao apache2 applet archive arpack asf aspell assistant audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cardbus cdda cddb cdf cdio cdparanoia cdr cgi chm cli consolekit corba cracklib crypt css cups curl cxx daap db dbase dbi dbm dbus declarative designer devhelp device-mapper dga dia djvu doc dri ds2490 ds9097 ds9097u dts dv dvb dvd dvdr dvi dynamicplugin eds elf emacs emboss emf empathy encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fpx fts3 fuse galago garmin gd gdal gdbm gdu gedit geoip geolocation geos gif gimp ginac git glade glib gml gmp gmtsuppl gnokii gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk guile hal harness hddtemp hdf hdf5 hdri hlapi http httpd iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java5 java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mailwrapper mapnik math matroska matrox mikmod mkl mmx mmxext mng modules mono moonlight motif mozdevelop mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numarray numeric obex objc ocaml octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio pymol python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool samba sasl science sdl secure-delete semantic-desktop server session sip slang slp smbclient sms sndfile snmp soup sox speex spell sql sqlite sse ssl startup-notification stlport subtitles subversion suexec svg swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs theora threads thunderbird tidy tiff tk tntc tools truetype udev unicode usb userlocales utempter v4l2 virtualbox vorbis wav webdav webdav-serf webkit win32codecs wmf wxwidgets x264 x86 xattr xcb xemacs xext xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc zlib zvbi" ALSA_CARDS="intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mmap_emul mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic auth_digest authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgid dav dav_fs dav_lock dbd deflate dir disk_cache env expires ext_filter file_cache filter headers ident imagemap include info log_config logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_http rewrite setenvif so speling status unique_id userdir usertrack vhost_alias" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" DVB_CARDS="tda10045 tda10046lifeview" 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 ubx" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de fr" LIRC_DEVICES="hauppauge" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy gsf harness ide identity j2ee java mobility nb php profiler ruby websvccommon xml" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 ppc ppc64 x86_64" QEMU_USER_TARGETS="arm i386 x86_64" RUBY_TARGETS="ruby18 jruby" USERLAND="GNU" VIDEO_CARDS="mga matrox vesa" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS

[Comment 1 Nowa Ammerlaan 2021-05-05 17:21:49 UTC]

WONTFIX because package has been removed