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Bug 335603 - sci-biology/embassy-6.3.1 version bump request
Summary: sci-biology/embassy-6.3.1 version bump request
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal enhancement (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on: 358035 358037
Blocks:
  Show dependency tree
 
Reported: 2010-09-01 21:47 UTC by Joel Berendzen
Modified: 2015-03-28 17:47 UTC (History)
0 users

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


Attachments
An embassy-6.3.1.ebuild which solves the issue. (embassy-6.3.1.ebuild,1.08 KB, text/plain)
2011-12-24 13:14 UTC, Juergen Rose
Details

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Description Joel Berendzen 2010-09-01 21:47:03 UTC
6.3.1 is out; latest in portage is 6.1.0.  It would be nice to update this, though I realize it's a sizeable undertaking.

I hope the hmmer 3.0 conflict can also be resolved.

Reproducible: Always
Comment 1 Justin Lecher (RETIRED) gentoo-dev 2011-03-09 12:02:31 UTC
+*emboss-6.3.1 (09 Mar 2011)
+
+  09 Mar 2011; Justin Lecher <jlec@gentoo.org>
+  +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2,
+  emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild,
+  +emboss-6.3.1.ebuild, metadata.xml:
+  Version Bump #335603, Unbundled libs, removed old, fix clash with
+  /usr/bin/digest, #330507
+
Comment 2 Justin Lecher (RETIRED) gentoo-dev 2011-03-10 19:09:05 UTC
I placed a complete rewritte in the sci overlay. Please test.
Comment 3 Joel Berendzen 2011-03-11 22:40:14 UTC
(In reply to comment #2)
> I placed a complete rewritte in the sci overlay. Please test.

Works for me, thanks.
Comment 4 Justin Lecher (RETIRED) gentoo-dev 2011-03-12 09:03:18 UTC
Please leave the bug open until I moved it to the tree. Thanks for testing.
Comment 5 Juergen Rose 2011-12-11 17:41:54 UTC
[science-overlay] sci-biology/embassy-6.3.1 fails to emerge due missing embassy-cbstools-1.0.0-r2 ebuild:

root@caiman:/root(10)# emerge -uvDN embassy

These are the packages that would be merged, in order:

Calculating dependencies... done!

Total: 0 packages, Size of downloads: 0 kB

!!! The following update has been skipped due to unsatisfied dependencies:

sci-biology/embassy:0

emerge: there are no ebuilds to satisfy "=sci-biology/embassy-cbstools-1.0.0-r2".
(dependency required by "sci-biology/embassy-6.3.1" [ebuild])


 * sci-biology/embassy
Comment 6 Juergen Rose 2011-12-21 11:00:28 UTC
Any news?
Comment 7 Juergen Rose 2011-12-24 13:14:55 UTC
Created attachment 296851 [details]
An embassy-6.3.1.ebuild  which solves the issue.

The attached embassy-6.3.1.ebuild and adding SRC_URIs to all embassy-* packages
solved the issue for me.
Comment 8 Justin Lecher (RETIRED) gentoo-dev 2012-02-20 14:32:24 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 9 Juergen Rose 2014-07-18 10:19:40 UTC
(In reply to Justin Lecher from comment #8)
> # 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

Any news? 

The download link at http://emboss.sourceforge.net/download/ :
ftp://emboss.open-bio.org/pub/EMBOSS/
emboss.open-bio.org (208.94.50.58) seems to be down for several days?

root@impala:/root(23)# ping -c 3 emboss.open-bio.org
PING emboss.open-bio.org (208.94.50.58) 56(84) bytes of data.

--- emboss.open-bio.org ping statistics ---
3 packets transmitted, 0 received, 100% packet loss, time 1999ms
Comment 10 Justin Lecher (RETIRED) gentoo-dev 2014-07-18 11:38:02 UTC
(In reply to Juergen Rose from comment #9)
> 
> Any news? 
> 
no, nobody is working on it.
Comment 11 Justin Lecher (RETIRED) gentoo-dev 2015-03-28 17:47:06 UTC
*embassy-6.6.0 (28 Mar 2015)

  28 Mar 2015; Justin Lecher <jlec@gentoo.org> +embassy-6.6.0.ebuild,
  metadata.xml:
  Import latest changes from science overlay, thanks Ted Tanberry for the work;
  fixes #335603