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Bug 328911 - sci-biology/embassy-hmmer-2.3.2 wants to downgrade sci-biology/hmmer
Summary: sci-biology/embassy-hmmer-2.3.2 wants to downgrade sci-biology/hmmer
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High normal
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords:
Depends on:
Blocks: 414997
  Show dependency tree
 
Reported: 2010-07-19 06:23 UTC by Christian Faulhammer (RETIRED)
Modified: 2016-10-09 15:15 UTC (History)
2 users (show)

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


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Description Christian Faulhammer (RETIRED) gentoo-dev 2010-07-19 06:23:13 UTC
3.0 just want stable and is not compatible with the current stable embassy-hmmer.
Comment 1 Martin Mokrejš 2011-02-22 15:19:47 UTC
I just learned 3.0 is a testing release. Some binaries disappeared and some functionality is still not available: http://hmmer.janelia.org/software/archive . I posted upstream with the following email right now:

<quote>
  I have just realized I need hmmer-2.3 because some application
uses hmmpfam. So far I had hmmer-3.0 installed. Would you mind
changing the libhmmer.a to libhmmer3.a in the hmmer-3.x branch
and also append the '3' to the name of the binaries so that one
could install both version together? Please let me know what is
possible to for you.
</quote>

Unless they can be installed concurrently I propose masking 3.0 even for `~' arches.
Comment 2 Andrey Kislyuk (RETIRED) gentoo-dev 2011-02-22 15:40:06 UTC
It's not a testing release, and we won't mask it. Feel free to supply a patch to slot HMMER 2 and 3 properly, though. An eselect module might be necessary.
Comment 3 Pacho Ramos gentoo-dev 2012-06-16 05:52:53 UTC
hmmer should either be slotted or hardmasked as explained in bug 414997
Comment 4 Martin Mokrejš 2015-11-19 22:29:58 UTC
Yes, they should use SLOT.

Quoting from http://hmmer.org/download.html

<quote>
The 1992-1998 HMMER1 lineage was closer to the original Krogh/Haussler conception of profile HMMs. It includes a feature that is missing in HMMER2 and HMMER3: the hmmt program for training HMMs from initially unaligned sequences (and hence creating multiple alignments). The final stable release of HMMER1 was 1.8.5 (Feb 2006). The 1998-2003 HMMER2 lineage introduced the "Plan 7" profile HMM architecture (which HMMER3 still largely shares), and was the long-time foundation for Pfam and other protein domain databases. It still included glocal and global alignment modes that HMMER3 lacks, because HMMER3 currently implements only fully local/local alignment; HMMER2 lacks DNA-DNA comparison that was present in HMMER1, and has returned in HMMER3.1. The final stable release of HMMER2 was 2.3.2 (Oct 2003).
</quote>


I just put hmmer-3.1_beta2.ebuild to science overlay but cannot help with SLOTs. Seems current Pfam-A.hmm files cannot be indexed using hmmpress from 3.0 package. The error message was "... does not appear to be in a recognized HMM format".
Comment 5 David Seifert gentoo-dev 2016-10-09 15:15:48 UTC
hmmer-2.3.2 is now SLOTed properly (which required renaming the hmm* binaries and man pages).

commit 895b3abfbdacf52dbd7a0e817eb7ebf101ce55a7
Author: David Seifert <soap@gentoo.org>
Date:   Sun Oct 9 16:52:52 2016 +0200

    sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2
    
    Gentoo-bug: 328911, 586960
    * EAPI=6
    * Introduce SLOT=2 and rename binaries and
      static libraries