CVS log for pkgsrc/biology/hmmer/distinfo

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biology/hmmer: fix build on NetBSD/powerpc.

When building with -maltivec (as we do here, when on NetBSD/powerpc),
__APPLE_ALTIVEC__ gets defined, but you still need to include
<altivec.h>, at least on NetBSD.

biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes

biology: Remove SHA1 hashes for distfiles

Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.

Update to 3.0
Add LICENSE
Add more distfile mirrors

Upstream changelog please visit:
http://selab.janelia.org/software/hmmer3/3.0/RELEASE-NOTES

Fix patch-aa sum.

Add RMD160 digests in addition to the SHA1 ones.

Update hmmer to 2.3.2.  Patch provided by David Price in PR pkg/28483.
While here, enable pkgviews installation.

Changes:
-:- hmmsearch intermittently failed on Swissprot searches, on some
    platforms (reports on AMD/Linux; Mac OS/X). (#h25)
-:- hmmpfam memory allocation strategy did not guarantee RAMLIMIT,
    and could explode to very large allocations when searching
    with large sequences. (#h26)
-:- technical improvements in handing dsq's (digitized sequences);
    "bug" has no visible effects, except when compiling on
    different platforms. (#h27)
-:- typo fix in P7Forward() recursion; typo may have had minor
    effect on calculated scores. (#h28)
-:- hmmalign now includes --outformat and --oneline option for
    specifying different output alignment formats than the default
    Stockholm.

Remove unnecessary -p following MKDIR commands.

Make hmmer honor $MKDIR for cross-platform install.
Addresses pr#26650 from Georg Schwarz.

Initial import of hmmer,  one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

HMMER is an implementation of profile HMM methods for sensitive database 
searches using multiple sequence alignments as queries. HMMER takes 
multiple sequence alignement as input and builds statistical model 
called "Hidden Markov Model" which can be used as a query into a 
sequence database to find and/or align additional homologues of the 
sequence family.

Initial revision