'emerge sci-libs/gts' fails with: ... >>> Installing (2 of 7) sci-libs/gts-20100321-r2 * checking 81 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/smooth * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-chemistry/apbs-1.3-r1 * /usr/bin/smooth * * Package 'sci-libs/gts-20100321-r2' 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-libs/gts-20100321-r2, Log file:
Any news?
mmh I don't have this file. could you please past the output of qlist apbs and emerge --info apbs?
root@moose:/root(3)# qlist -Iv apbs sci-chemistry/apbs-1.3-r1 I assume, that it is installed as a dependency of pymol: root@moose:/root(2)# equery d apbs * These packages depend on apbs: sci-chemistry/pdb2pqr-1.7.0-r1 (pdb2pka ? sci-chemistry/apbs[python,-mpi]) sci-chemistry/pymol-1.4.1 (apbs ? sci-chemistry/apbs) root@moose:/root(7)# emerge --info apbs Portage 2.1.10.34 (default/linux/amd64/10.0/desktop, gcc-4.5.3, glibc-2.13-r4, 3.1.0-gentoo-r1 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.1.0-gentoo-r1-x86_64-Intel-R-_Core-TM-2_Quad_CPU_Q9650_@_3.00GHz-with-gentoo-2.1 Timestamp of tree: Mon, 14 Nov 2011 09:00:01 +0000 app-shells/bash: 4.2_p10 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.7.2-r3::sage-on-gentoo, 3.2.2 dev-util/cmake: 2.8.6-r3 dev-util/pkgconfig: 0.26 sys-apps/baselayout: 2.1 sys-apps/openrc: 0.9.4 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-r1 sys-devel/binutils: 2.21.1-r1 sys-devel/gcc: 4.5.3-r1 sys-devel/gcc-config: 1.5-r2 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r3 sys-kernel/linux-headers: 2.6.39 (virtual/os-headers) sys-libs/glibc: 2.13-r4 Repositories: gentoo science x11 arcon qting-edge bicatali zugaina sage-on-gentoo java-overlay sunrise x-portage x-cpan g-octave ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA PUEL dlj-1.1 skype-eula googleearth AdobeFlash-10.1 cadsoft Oracle-BCLA-JavaSE" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.0/conf /usr/share/openvpn/easy-rsa /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.3/ext-active/ /etc/php/apache2-php5.4/ext-active/ /etc/php/cgi-php5.3/ext-active/ /etc/php/cgi-php5.4/ext-active/ /etc/php/cli-php5.3/ext-active/ /etc/php/cli-php5.4/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 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="assume-digests binpkg-logs distlocks ebuild-locks fixlafiles news parallel-fetch protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="de fr" MAKEOPTS="-j5" 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/science /var/lib/layman/x11 /var/lib/layman/arcon /var/lib/layman/qting-edge /var/lib/layman/bicatali /var/lib/layman/zugaina /var/lib/layman/sage-on-gentoo /var/lib/layman/java-overlay /var/lib/layman/sunrise /usr/local/portage /var/lib/cpan /var/lib/g-octave" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="64bit R X Xaw3d a52 aac abiword acl acpi admin afs alsa amd64 ao apache2 applet archive arpack asf aspell assistant atlas audacious audiofile automap automount bash-completion beagle berkdb blas blast bluetooth boo boost branding bzip2 cairo cdda cddb cdf cdio cdparanoia cdr cg cgi chm cli consolekit corba cracklib crypt css cuda 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 encode epiphany evo examples exif expat extensions extra extras fam fame ffmpeg fftw firefox fits flac fltk fontconfig foomaticdb fortran fortran95 fpx fts3 fuse galago garmin gcj gd gdal gdbm gdu gedit geoip geolocation geos gfortran gif gimp ginac git glade glib glpk gml gmp gmtsuppl gnome gnome-keyring gnome-print gnuplot gnutls gphoto2 gpm grammar graphics graphtft graphviz grass gs gsl gsm gstreamer gtk gudev guile harness hddtemp hdf hdf5 hdri http httpd hvm hwdb iconv icq icu id3 ide imagemagick imap innodb inotify ipod ipv6 irda ithreads jabber jadetex java java6 jbig john jpeg jpeg2k kdrive kerberos kpathsea kqemu kvm ladspa lame lapack latex latex3 lcms ldap lensfun libffi libgda libnotify libsamplerate lirc lm_sensors lua lzo mad mail maildir mapnik math matroska mkl mmx mmxext mng modules mono moonlight motif mozilla mp3 mp4 mpeg mpi mplayer mtp mudflap multilib musicbrainz mysql mysqli nautilus ncurses neXt netcdf netpbm network networking networkmanager nfs nls nntp nptl nptlonly nsplugin ntfs ntp numpy nvidia obex objc ocaml ocr octave odbc ogdi ogg ole openexr opengl openmp overview pae pam pango pcre pda pdf perl plotutils plugins png podcast policykit portaudio posix postgres postscript ppds pppd preview-latex proj projectx pstricks pulseaudio python python-bindings q16 q32 qemu qhull qt3support qt4 quicktime readline reiserfs reports rle romio rpc rrdcgi rrdtool sage samba sasl science sdk sdl secure-delete semantic-desktop server session sip slang slp smbclient smp sms sndfile snmp soup sox speex spell sql sqlite sse sse2 sse4 ssl ssse3 startup-notification stlport subtitles subversion suexec svg svm swig sysfs szip t1lib tcl tcpd tex tex4ht texmacs tgif theora threads thunderbird tidy tiff tk tools truetype udev unicode usb userlocales utempter v4l2 vaapi video virtualbox vorbis wav webdav webdav-serf webkit wifi wmf wxwidgets x264 xattr xcb xemacs xext xft xine xml xmlreader xmlrpc xorg xpm xulrunner xv xvid xvmc yaml 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" CALLIGRA_FEATURES="kexi words flow plan stage tables krita karbon braindump" CAMERAS="canon" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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" 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 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18" USERLAND="GNU" VIDEO_CARDS="nv nouveau 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 ================================================================= Package Settings ================================================================= sci-chemistry/apbs-1.3-r1 was built with the following: USE="arpack doc (multilib) openmp python tools -fetk -mpi"
Accually I simply needed qlsit apbs to see the files. But it is triggered by USE=tools. I will see what I can do
Created attachment 292543 [details] The result of 'root@moose:/root(10)# qlist apbs > qlist.log'
Almost one month later, any news?
+ 13 Dec 2011; Justin Lecher <jlec@gentoo.org> apbs-1.2.1b-r4.ebuild, + apbs-1.3.ebuild, apbs-1.3-r1.ebuild: + Block sci-libs/gts with USE=tools because of file collision on + /usr/bin/smooth, #387689 +
Hi Justin, is there any chance that it will be possible to install freecad, which requires sci-libs/gts and mgltools-molkit, which sci-chemistry/pdb2pqr which depends on apbs together? Regards Juergen
(In reply to comment #8) > Hi Justin, > > is there any chance that it will be possible to install freecad, which requires > sci-libs/gts and mgltools-molkit, which sci-chemistry/pdb2pqr which depends on > apbs together? > > Regards Juergen Sure, simply install apbs with USE=-tools.
Hi Justin, thanks for the hint with "USE=-tools", it worked with apbs-1.3-r1, even if I would prefer to create the binaries, which are generated with "USE=tools" and to rename the smooth binary from apbs to something like smooth_apbs. But now with apbs-1.3-r2 "USE=-tools" does not prevent the creation of usr/bin/smooth: root@moose:/root(10)# emerge -vuND world These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild U ] sci-chemistry/apbs-1.3-r2 [1.3-r1] USE="arpack doc examples%* openmp python -fetk -mpi -static-libs% -tools" 0 kB [ebuild U ] dev-vcs/monotone-1.0-r3 [1.0-r1] USE="doc ipv6 nls -test" 0 kB [ebuild U ] net-firewall/fwbuilder-5.0.1.3592 [4.2.2.3541] 0 kB ... >>> Working in BUILD_DIR: "/var/tmp/portage/sci-chemistry/apbs-1.3-r2/work/apbs-1.3-source" >>> Completed installing apbs-1.3-r2 into /var/tmp/portage/sci-chemistry/apbs-1.3-r2/image/ strip: x86_64-pc-linux-gnu-strip --strip-unneeded -R .comment -R .GCC.command.line usr/bin/apbs usr/bin/born usr/bin/mergedx2 usr/bin/coulomb usr/bin/value usr/bin/tensor2dx usr/bin/dx2uhbd usr/bin/multivalue usr/bin/mergedx usr/bin/del2dx usr/bin/driver usr/bin/dx2mol usr/bin/dxmath usr/bin/uhbd_asc2bin usr/bin/mgmesh usr/bin/benchmark usr/bin/smooth usr/bin/similarity ... >>> Installing (1 of 3) sci-chemistry/apbs-1.3-r2 * checking 261 files for package collisions * This package will overwrite one or more files that may belong to other ... * Detected file collision(s): * * /usr/bin/smooth * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-libs/gts-20100321-r2 * /usr/bin/smooth ... >>> Failed to install sci-chemistry/apbs-1.3-r2, Log file:
oh, now it has additionally USE=python trigering the installation. So USE="-python -tools"
okay renaming apbs binaries now.
