'emerge embassy' complains about: root@moose:/root(32)# emerge -pvuND embassy These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild UD ] sci-biology/emboss-6.1.0-r1::gentoo [6.3.1_p4-r1::x-portage] USE="X png -minimal (-mysql%*) (-pdf%*) (-postgres%*) (-static-libs%)" 21,454 kB [ebuild N ] sci-biology/embassy-domainatrix-0.1.0-r4 USE="X png" 391 kB [ebuild N ] sci-biology/embassy-topo-1.0.0-r6 USE="X png" 370 kB [ebuild N ] sci-biology/embassy-memenew-4.0.0 USE="X png" 482 kB [ebuild N ] sci-biology/embassy-iprscan-4.3.1-r1 USE="X png" 336 kB [ebuild N ] sci-biology/embassy-esim4-1.0.0-r6 USE="X png" 396 kB [ebuild N ] sci-biology/embassy-domalign-0.1.0-r4 USE="X png" 425 kB [ebuild N ] sci-biology/embassy-mira-2.8.2-r1 USE="X png" 334 kB [ebuild N ] sci-biology/embassy-mse-1.0.0-r7 USE="X png" 415 kB [ebuild N ] sci-biology/embassy-domsearch-0.1.0-r4 USE="X png" 434 kB [ebuild N ] sci-biology/embassy-signature-0.1.0-r4 USE="X png" 542 kB [ebuild N ] sci-biology/embassy-vienna-1.7.2-r1 USE="X png" 621 kB [ebuild N ] sci-biology/embassy-phylipnew-3.68 USE="X png" 1,589 kB [ebuild N ] sci-biology/embassy-hmmer-2.3.2-r3 USE="X png" 530 kB [ebuild N ] sci-biology/embassy-emnu-1.05-r6 USE="X png" 357 kB [ebuild N ] sci-biology/embassy-structure-0.1.0-r4 USE="X png" 508 kB [ebuild N ] sci-biology/embassy-cbstools-1.0.0-r1 USE="X png" 349 kB [ebuild U ] sci-biology/rebase-1202 [1111] USE="emboss -minimal" 25,202 kB [ebuild N ] sci-biology/embassy-6.1.0 0 kB [ebuild U ] net-libs/gnutls-2.12.16 [2.10.5] USE="cxx doc examples guile lzo nettle%* nls zlib -bindist -pkcs11% -static-libs% -test" 0 kB Total: 20 packages (2 upgrades, 1 downgrade, 17 new), Size of downloads: 54,725 kB WARNING: One or more updates have been skipped due to a dependency conflict: ... !!! The following update has been skipped due to unsatisfied dependencies: sci-biology/embassy:0 emerge: there are no ebuilds to satisfy "=sci-biology/embassy-domainatrix-0.1.0-r5". (dependency required by "sci-biology/embassy-6.3.1" [ebuild]) But there is only embassy-domainatrix-0.1.0-r6: root@moose:/root(33)# eix embassy-domainatrix * sci-biology/embassy-domainatrix Available versions: 0.1.0-r3 (~)0.1.0-r4 (~)0.1.0-r6[1] {X mysql pdf png postgres static-libs} Homepage: http://emboss.sourceforge.net/ Description: Protein domain analysis add-on package for EMBOSS
There are more issues with embassy-6.3.1 form science overlay, see comment 7 of https://bugs.gentoo.org/show_bug.cgi?id=335603.
# Justin Lecher <jlec@gentoo.org> (20 Feb 2012) # They are broken in one or the other way # Need to be bumped to emboss-6.4.0 sci-biology/emboss::science sci-biology/embassy::science sci-biology/embassy-cbstools::science sci-biology/embassy-domainatrix::science sci-biology/embassy-domalign::science sci-biology/embassy-domsearch::science sci-biology/embassy-emnu::science sci-biology/embassy-esim4::science sci-biology/embassy-hmmer::science sci-biology/embassy-iprscan::science sci-biology/embassy-mse::science sci-biology/embassy-phylipnew::science sci-biology/embassy-signature::science sci-biology/embassy-structure::science sci-biology/embassy-topo::science sci-biology/embassy-vienna::science
