CVS log for pkgsrc/biology/hmmer/Makefile

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Keyword substitution: kv
Default branch: MAIN

various: Typos in MAINTAINER addresses

various: Reset MAINTAINER

Email fails, and someone still at the same domain confirmed they are no
longer there.

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.

update homepage and master site

Convert all occurrences (353 by my count) of

	MASTER_SITES= 	site1 \
			site2

style continuation lines to be simple repeated

	MASTER_SITES+= site1
	MASTER_SITES+= site2

lines. As previewed on tech-pkg. With thanks to rillig for fixing pkglint
accordingly.

Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.

Update to 3.0
Add LICENSE
Add more distfile mirrors

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

"user-destdir" is default these days

user-destdir support

fetch from gentoo mirror.

update homepage and master site. new master needs active ftp. it doesn't work with EPSV. commented out.

Whitespace cleanup, courtesy of pkglint.
Patch provided by Sergey Svishchev in private mail.

Fixed pkglint warnings. The warnings are mostly quoting issues, for
example MAKE_ENV+=FOO=${BAR} is changed to MAKE_ENV+=FOO=${BAR:Q}. Some
other changes are outlined in

    http://mail-index.netbsd.org/tech-pkg/2005/12/02/0034.html

Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.

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.

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

Convert to buildlink3 and correct a spelling error in DESCR.

Move WRKSRC definition away from the first paragraph in a Makefile.

Add trailing slash to HOMEPAGE to placate pkglint.

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