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CVS log for pkgsrc/biology/hmmer/Makefile

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Request diff between arbitrary revisions


Default branch: MAIN


Revision 1.16 / (download) - annotate - [select for diffs], Thu Jan 19 18:52:03 2017 UTC (6 years, 8 months ago) by agc
Branch: MAIN
CVS Tags: pkgsrc-2023Q2-base, pkgsrc-2023Q2, pkgsrc-2023Q1-base, pkgsrc-2023Q1, pkgsrc-2022Q4-base, pkgsrc-2022Q4, pkgsrc-2022Q3-base, pkgsrc-2022Q3, pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1, pkgsrc-2021Q4-base, pkgsrc-2021Q4, pkgsrc-2021Q3-base, pkgsrc-2021Q3, pkgsrc-2021Q2-base, pkgsrc-2021Q2, pkgsrc-2021Q1-base, pkgsrc-2021Q1, pkgsrc-2020Q4-base, pkgsrc-2020Q4, pkgsrc-2020Q3-base, pkgsrc-2020Q3, pkgsrc-2020Q2-base, pkgsrc-2020Q2, pkgsrc-2020Q1-base, pkgsrc-2020Q1, pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3, pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4, pkgsrc-2018Q3-base, pkgsrc-2018Q3, pkgsrc-2018Q2-base, pkgsrc-2018Q2, pkgsrc-2018Q1-base, pkgsrc-2018Q1, pkgsrc-2017Q4-base, pkgsrc-2017Q4, pkgsrc-2017Q3-base, pkgsrc-2017Q3, pkgsrc-2017Q2-base, pkgsrc-2017Q2, pkgsrc-2017Q1-base, pkgsrc-2017Q1, HEAD
Changes since 1.15: +4 -4 lines
Diff to previous 1.15 (colored)

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.

Revision 1.15 / (download) - annotate - [select for diffs], Thu Oct 9 14:06:00 2014 UTC (8 years, 11 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2016Q4-base, pkgsrc-2016Q4, pkgsrc-2016Q3-base, pkgsrc-2016Q3, pkgsrc-2016Q2-base, pkgsrc-2016Q2, pkgsrc-2016Q1-base, pkgsrc-2016Q1, pkgsrc-2015Q4-base, pkgsrc-2015Q4, pkgsrc-2015Q3-base, pkgsrc-2015Q3, pkgsrc-2015Q2-base, pkgsrc-2015Q2, pkgsrc-2015Q1-base, pkgsrc-2015Q1, pkgsrc-2014Q4-base, pkgsrc-2014Q4
Changes since 1.14: +1 -3 lines
Diff to previous 1.14 (colored)

Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.

Revision 1.14 / (download) - annotate - [select for diffs], Sun Jul 21 15:58:51 2013 UTC (10 years, 2 months ago) by wen
Branch: MAIN
CVS Tags: pkgsrc-2014Q3-base, pkgsrc-2014Q3, pkgsrc-2014Q2-base, pkgsrc-2014Q2, pkgsrc-2014Q1-base, pkgsrc-2014Q1, pkgsrc-2013Q4-base, pkgsrc-2013Q4, pkgsrc-2013Q3-base, pkgsrc-2013Q3
Changes since 1.13: +6 -3 lines
Diff to previous 1.13 (colored)

Update to 3.0
Add LICENSE
Add more distfile mirrors

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

Revision 1.13 / (download) - annotate - [select for diffs], Tue Sep 11 20:32:12 2012 UTC (11 years ago) by asau
Branch: MAIN
CVS Tags: pkgsrc-2013Q2-base, pkgsrc-2013Q2, pkgsrc-2013Q1-base, pkgsrc-2013Q1, pkgsrc-2012Q4-base, pkgsrc-2012Q4, pkgsrc-2012Q3-base, pkgsrc-2012Q3
Changes since 1.12: +1 -2 lines
Diff to previous 1.12 (colored)

"user-destdir" is default these days

Revision 1.12 / (download) - annotate - [select for diffs], Wed Jul 8 15:20:04 2009 UTC (14 years, 2 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2012Q2-base, pkgsrc-2012Q2, pkgsrc-2012Q1-base, pkgsrc-2012Q1, pkgsrc-2011Q4-base, pkgsrc-2011Q4, pkgsrc-2011Q3-base, pkgsrc-2011Q3, pkgsrc-2011Q2-base, pkgsrc-2011Q2, pkgsrc-2011Q1-base, pkgsrc-2011Q1, pkgsrc-2010Q4-base, pkgsrc-2010Q4, pkgsrc-2010Q3-base, pkgsrc-2010Q3, pkgsrc-2010Q2-base, pkgsrc-2010Q2, pkgsrc-2010Q1-base, pkgsrc-2010Q1, pkgsrc-2009Q4-base, pkgsrc-2009Q4, pkgsrc-2009Q3-base, pkgsrc-2009Q3
Changes since 1.11: +2 -1 lines
Diff to previous 1.11 (colored)

user-destdir support

Revision 1.11 / (download) - annotate - [select for diffs], Sat May 16 23:28:13 2009 UTC (14 years, 4 months ago) by zafer
Branch: MAIN
CVS Tags: pkgsrc-2009Q2-base, pkgsrc-2009Q2
Changes since 1.10: +2 -2 lines
Diff to previous 1.10 (colored)

fetch from gentoo mirror.

Revision 1.10 / (download) - annotate - [select for diffs], Sat May 16 23:19:19 2009 UTC (14 years, 4 months ago) by zafer
Branch: MAIN
Changes since 1.9: +3 -3 lines
Diff to previous 1.9 (colored)

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

Revision 1.9 / (download) - annotate - [select for diffs], Thu Feb 22 19:26:09 2007 UTC (16 years, 7 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2009Q1-base, pkgsrc-2009Q1, pkgsrc-2008Q4-base, pkgsrc-2008Q4, pkgsrc-2008Q3-base, pkgsrc-2008Q3, pkgsrc-2008Q2-base, pkgsrc-2008Q2, pkgsrc-2008Q1-base, pkgsrc-2008Q1, pkgsrc-2007Q4-base, pkgsrc-2007Q4, pkgsrc-2007Q3-base, pkgsrc-2007Q3, pkgsrc-2007Q2-base, pkgsrc-2007Q2, pkgsrc-2007Q1-base, pkgsrc-2007Q1, cwrapper, cube-native-xorg-base, cube-native-xorg
Changes since 1.8: +2 -2 lines
Diff to previous 1.8 (colored)

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

Revision 1.8 / (download) - annotate - [select for diffs], Mon Dec 5 20:49:51 2005 UTC (17 years, 9 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2006Q4-base, pkgsrc-2006Q4, pkgsrc-2006Q3-base, pkgsrc-2006Q3, pkgsrc-2006Q2-base, pkgsrc-2006Q2, pkgsrc-2006Q1-base, pkgsrc-2006Q1, pkgsrc-2005Q4-base, pkgsrc-2005Q4
Changes since 1.7: +2 -2 lines
Diff to previous 1.7 (colored)

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

Revision 1.7 / (download) - annotate - [select for diffs], Mon Apr 11 21:45:01 2005 UTC (18 years, 5 months ago) by tv
Branch: MAIN
CVS Tags: pkgsrc-2005Q3-base, pkgsrc-2005Q3, pkgsrc-2005Q2-base, pkgsrc-2005Q2
Changes since 1.6: +1 -2 lines
Diff to previous 1.6 (colored)

Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.

Revision 1.6 / (download) - annotate - [select for diffs], Wed Dec 1 04:01:09 2004 UTC (18 years, 9 months ago) by minskim
Branch: MAIN
CVS Tags: pkgsrc-2005Q1-base, pkgsrc-2005Q1, pkgsrc-2004Q4-base, pkgsrc-2004Q4
Changes since 1.5: +5 -4 lines
Diff to previous 1.5 (colored)

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.

Revision 1.5 / (download) - annotate - [select for diffs], Mon Aug 16 02:47:49 2004 UTC (19 years, 1 month ago) by ben
Branch: MAIN
CVS Tags: pkgsrc-2004Q3-base, pkgsrc-2004Q3
Changes since 1.4: +3 -1 lines
Diff to previous 1.4 (colored)

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

Revision 1.4 / (download) - annotate - [select for diffs], Sun Apr 11 04:06:09 2004 UTC (19 years, 5 months ago) by snj
Branch: MAIN
CVS Tags: pkgsrc-2004Q2-base, pkgsrc-2004Q2
Changes since 1.3: +2 -2 lines
Diff to previous 1.3 (colored)

Convert to buildlink3 and correct a spelling error in DESCR.

Revision 1.3 / (download) - annotate - [select for diffs], Tue Jan 20 12:08:40 2004 UTC (19 years, 8 months ago) by agc
Branch: MAIN
CVS Tags: pkgsrc-2004Q1-base, pkgsrc-2004Q1
Changes since 1.2: +2 -2 lines
Diff to previous 1.2 (colored)

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

Revision 1.2 / (download) - annotate - [select for diffs], Fri Sep 26 05:21:04 2003 UTC (20 years ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2003Q4-base, pkgsrc-2003Q4
Changes since 1.1: +2 -2 lines
Diff to previous 1.1 (colored)

Add trailing slash to HOMEPAGE to placate pkglint.

Revision 1.1.1.1 / (download) - annotate - [select for diffs] (vendor branch), Fri Sep 26 03:52:47 2003 UTC (20 years ago) by jschauma
Branch: TNF
CVS Tags: pkgsrc-base
Changes since 1.1: +0 -0 lines
Diff to previous 1.1 (colored)

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.

Revision 1.1 / (download) - annotate - [select for diffs], Fri Sep 26 03:52:47 2003 UTC (20 years ago) by jschauma
Branch: MAIN

Initial revision

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