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Bug 405035 - [science overlay] sci-biology/embassy-6.3.1 fails to emerge because of dependency on embassy-domainatrix-0.1.0-r5
Summary: [science overlay] sci-biology/embassy-6.3.1 fails to emerge because of depend...
Status: RESOLVED OBSOLETE
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2012-02-20 14:21 UTC by Juergen Rose
Modified: 2015-03-28 17:51 UTC (History)
0 users

See Also:
Package list:
Runtime testing required: ---


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Description Juergen Rose 2012-02-20 14:21:09 UTC
'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
Comment 1 Juergen Rose 2012-02-20 14:24:54 UTC
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.
Comment 2 Justin Lecher gentoo-dev 2012-02-20 14:32:38 UTC
# 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
Comment 3 Justin Lecher gentoo-dev 2012-02-20 14:33:45 UTC
# 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