>>> Source compiled. >>> Test phase [not enabled]: sci-biology/muscle-3.7 >>> Install muscle-3.7 into /var/tmp/portage/sci-biology/muscle-3.7/image/ category sci-biology >>> Completed installing muscle-3.7 into /var/tmp/portage/sci-biology/muscle-3.7/image/ >>> Installing (1 of 1) sci-biology/muscle-3.7 * 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/muscle * * Searching all installed packages for file collisions... * * Press Ctrl-C to Stop * * sci-libs/libmuscle-3.7-r1 * /usr/bin/muscle * * Package 'sci-biology/muscle-3.7' 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/muscle-3.7, Log file: >>> '/var/tmp/portage/sci-biology/muscle-3.7/temp/build.log' # equery files libmuscle * Searching for libmuscle ... * Contents of sci-libs/libmuscle-3.7-r1: /usr /usr/bin /usr/bin/muscle /usr/include /usr/include/libMUSCLE-3.7 /usr/include/libMUSCLE-3.7/libMUSCLE /usr/include/libMUSCLE-3.7/libMUSCLE/alpha.h /usr/include/libMUSCLE-3.7/libMUSCLE/clust.h /usr/include/libMUSCLE-3.7/libMUSCLE/cluster.h /usr/include/libMUSCLE-3.7/libMUSCLE/clustset.h /usr/include/libMUSCLE-3.7/libMUSCLE/clustsetdf.h /usr/include/libMUSCLE-3.7/libMUSCLE/clustsetmsa.h /usr/include/libMUSCLE-3.7/libMUSCLE/diaglist.h /usr/include/libMUSCLE-3.7/libMUSCLE/distcalc.h /usr/include/libMUSCLE-3.7/libMUSCLE/distfunc.h /usr/include/libMUSCLE-3.7/libMUSCLE/dpregionlist.h /usr/include/libMUSCLE-3.7/libMUSCLE/dpreglist.h /usr/include/libMUSCLE-3.7/libMUSCLE/edgelist.h /usr/include/libMUSCLE-3.7/libMUSCLE/enumopts.h /usr/include/libMUSCLE-3.7/libMUSCLE/enums.h /usr/include/libMUSCLE-3.7/libMUSCLE/estring.h /usr/include/libMUSCLE-3.7/libMUSCLE/gapscoredimer.h /usr/include/libMUSCLE-3.7/libMUSCLE/gonnet.h /usr/include/libMUSCLE-3.7/libMUSCLE/intmath.h /usr/include/libMUSCLE-3.7/libMUSCLE/msa.h /usr/include/libMUSCLE-3.7/libMUSCLE/msadist.h /usr/include/libMUSCLE-3.7/libMUSCLE/muscle.h /usr/include/libMUSCLE-3.7/libMUSCLE/objscore.h /usr/include/libMUSCLE-3.7/libMUSCLE/params.h /usr/include/libMUSCLE-3.7/libMUSCLE/profile.h /usr/include/libMUSCLE-3.7/libMUSCLE/pwpath.h /usr/include/libMUSCLE-3.7/libMUSCLE/refine.h /usr/include/libMUSCLE-3.7/libMUSCLE/scorehistory.h /usr/include/libMUSCLE-3.7/libMUSCLE/seq.h /usr/include/libMUSCLE-3.7/libMUSCLE/seqvect.h /usr/include/libMUSCLE-3.7/libMUSCLE/textfile.h /usr/include/libMUSCLE-3.7/libMUSCLE/threadstorage.h /usr/include/libMUSCLE-3.7/libMUSCLE/timing.h /usr/include/libMUSCLE-3.7/libMUSCLE/tree.h /usr/include/libMUSCLE-3.7/libMUSCLE/types.h /usr/include/libMUSCLE-3.7/libMUSCLE/unixio.h /usr/lib64 /usr/lib64/libMUSCLE-3.7.a /usr/lib64/libMUSCLE-3.7.la /usr/lib64/libMUSCLE-3.7.so -> libMUSCLE-3.7.so.1.0.0 /usr/lib64/libMUSCLE-3.7.so.1 -> libMUSCLE-3.7.so.1.0.0 /usr/lib64/libMUSCLE-3.7.so.1.0.0 /usr/lib64/pkgconfig /usr/lib64/pkgconfig/libMUSCLE-3.7.pc # On a different host (even arch) I have: # equery files muscle * Searching for muscle ... * Contents of sci-biology/muscle-3.7: /usr /usr/bin /usr/bin/muscle #
sci-lib/libmuscle and sci-biology/muscle are more or less the same programs, but developed independently. libmuscle is forked from muscle-3.7 by the mauve developers and contains some improvements/bugfixes according to them. There is also an experimental version of muscle-4.0 (released July 2009). I guess programs using muscle don't really bother what version they are using (at least seaview doesn't seem to matter according to the ebuild).
+*muscle-3.8.31 (24 Jun 2010) + + 24 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/3.8.31-make.patch, + muscle-3.6.ebuild, muscle-3.7.ebuild, +muscle-3.8.31.ebuild: + Version BUmp, blocking sci-libs/libmuscle, #308707 +
