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CVS log for pkgsrc/biology/mummer/Makefile

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Default branch: MAIN


Revision 1.33: download - view: text, markup, annotated - select for diffs
Thu Aug 22 17:05:59 2024 UTC (2 months, 3 weeks ago) by gdt
Branches: MAIN
CVS tags: pkgsrc-2024Q3-base, pkgsrc-2024Q3, HEAD
Diff to: previous 1.32: preferred, colored
Changes since revision 1.32: +2 -2 lines
various: Typos in MAINTAINER addresses

Revision 1.32: download - view: text, markup, annotated - select for diffs
Thu Aug 22 17:01:17 2024 UTC (2 months, 3 weeks ago) by gdt
Branches: MAIN
Diff to: previous 1.31: preferred, colored
Changes since revision 1.31: +2 -2 lines
various: Reset MAINTAINER

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

Revision 1.31: download - view: text, markup, annotated - select for diffs
Tue Jun 28 11:31:01 2022 UTC (2 years, 4 months ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2024Q2-base, pkgsrc-2024Q2, pkgsrc-2024Q1-base, pkgsrc-2024Q1, pkgsrc-2023Q4-base, pkgsrc-2023Q4, pkgsrc-2023Q3-base, pkgsrc-2023Q3, pkgsrc-2023Q2-base, pkgsrc-2023Q2, pkgsrc-2023Q1-base, pkgsrc-2023Q1, pkgsrc-2022Q4-base, pkgsrc-2022Q4, pkgsrc-2022Q3-base, pkgsrc-2022Q3
Diff to: previous 1.30: preferred, colored
Changes since revision 1.30: +2 -2 lines
*: recursive bump for perl 5.36

Revision 1.30: download - view: text, markup, annotated - select for diffs
Mon May 24 19:49:11 2021 UTC (3 years, 5 months ago) by wiz
Branches: MAIN
CVS tags: 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
Diff to: previous 1.29: preferred, colored
Changes since revision 1.29: +2 -2 lines
*: recursive bump for perl 5.34

Revision 1.29: download - view: text, markup, annotated - select for diffs
Mon Aug 31 18:06:39 2020 UTC (4 years, 2 months ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2021Q1-base, pkgsrc-2021Q1, pkgsrc-2020Q4-base, pkgsrc-2020Q4, pkgsrc-2020Q3-base, pkgsrc-2020Q3
Diff to: previous 1.28: preferred, colored
Changes since revision 1.28: +2 -2 lines
*: bump PKGREVISION for perl-5.32.

Revision 1.28: download - view: text, markup, annotated - select for diffs
Sun Jan 26 05:26:15 2020 UTC (4 years, 9 months ago) by rillig
Branches: MAIN
CVS tags: pkgsrc-2020Q2-base, pkgsrc-2020Q2, pkgsrc-2020Q1-base, pkgsrc-2020Q1
Diff to: previous 1.27: preferred, colored
Changes since revision 1.27: +2 -2 lines
all: migrate some SourceForge homepage URLs back from https to http

https://mail-index.netbsd.org/pkgsrc-changes/2020/01/18/msg205146.html

In the above commit, the homepage URLs were migrated from http to https,
assuming that SourceForge would use the same host names for both http and
https connections. This assumption was wrong. Their documentation at
https://sourceforge.net/p/forge/documentation/Custom%20VHOSTs/ states
that the https URLs use the domain sourceforge.io instead.

To make the homepages from the above commit reachable again, pkglint has
been extended to check for reachable homepages. This check is only
enabled when the --network command line option is given.

Each of the homepages that referred to https://$project.sourceforge.net
before was migrated to https://$project.sourceforge.io (27), and if that
was not reachable, to the fallback URL http://$project.sourceforge.net
(163).

Revision 1.27: download - view: text, markup, annotated - select for diffs
Sat Jan 18 23:30:09 2020 UTC (4 years, 9 months ago) by rillig
Branches: MAIN
Diff to: previous 1.26: preferred, colored
Changes since revision 1.26: +2 -2 lines
all: migrate several HOMEPAGEs to https

pkglint --only "https instead of http" -r -F

With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.

This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.

Revision 1.26: download - view: text, markup, annotated - select for diffs
Sun Aug 11 13:18:00 2019 UTC (5 years, 3 months ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3
Diff to: previous 1.25: preferred, colored
Changes since revision 1.25: +2 -2 lines
Bump PKGREVISIONs for perl 5.30.0

Revision 1.25: download - view: text, markup, annotated - select for diffs
Wed Aug 22 09:42:59 2018 UTC (6 years, 2 months ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4, pkgsrc-2018Q3-base, pkgsrc-2018Q3
Diff to: previous 1.24: preferred, colored
Changes since revision 1.24: +2 -2 lines
Recursive bump for perl5-5.28.0

Revision 1.24: download - view: text, markup, annotated - select for diffs
Sat Jul 9 06:37:51 2016 UTC (8 years, 4 months ago) by wiz
Branches: MAIN
CVS tags: 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, pkgsrc-2016Q4-base, pkgsrc-2016Q4, pkgsrc-2016Q3-base, pkgsrc-2016Q3
Diff to: previous 1.23: preferred, colored
Changes since revision 1.23: +2 -2 lines
Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.

Revision 1.23: download - view: text, markup, annotated - select for diffs
Fri Jun 12 10:48:26 2015 UTC (9 years, 5 months ago) by wiz
Branches: MAIN
CVS tags: 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
Diff to: previous 1.22: preferred, colored
Changes since revision 1.22: +2 -2 lines
Recursive PKGREVISION bump for all packages mentioning 'perl',
having a PKGNAME of p5-*, or depending such a package,
for perl-5.22.0.

Revision 1.22: download - view: text, markup, annotated - select for diffs
Thu May 29 23:35:17 2014 UTC (10 years, 5 months ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2015Q1-base, pkgsrc-2015Q1, pkgsrc-2014Q4-base, pkgsrc-2014Q4, pkgsrc-2014Q3-base, pkgsrc-2014Q3, pkgsrc-2014Q2-base, pkgsrc-2014Q2
Diff to: previous 1.21: preferred, colored
Changes since revision 1.21: +2 -2 lines
Bump for perl-5.20.0.
Do it for all packages that
* mention perl, or
* have a directory name starting with p5-*, or
* depend on a package starting with p5-
like last time, for 5.18, where this didn't lead to complaints.
Let me know if you have any this time.

Revision 1.21: download - view: text, markup, annotated - select for diffs
Fri May 31 12:39:39 2013 UTC (11 years, 5 months ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2014Q1-base, pkgsrc-2014Q1, pkgsrc-2013Q4-base, pkgsrc-2013Q4, pkgsrc-2013Q3-base, pkgsrc-2013Q3, pkgsrc-2013Q2-base, pkgsrc-2013Q2
Diff to: previous 1.20: preferred, colored
Changes since revision 1.20: +2 -2 lines
Bump all packages for perl-5.18, that
a) refer 'perl' in their Makefile, or
b) have a directory name of p5-*, or
c) have any dependency on any p5-* package

Like last time, where this caused no complaints.

Revision 1.20: download - view: text, markup, annotated - select for diffs
Wed Oct 3 21:53:59 2012 UTC (12 years, 1 month ago) by wiz
Branches: MAIN
CVS tags: pkgsrc-2013Q1-base, pkgsrc-2013Q1, pkgsrc-2012Q4-base, pkgsrc-2012Q4
Diff to: previous 1.19: preferred, colored
Changes since revision 1.19: +2 -1 lines
Bump all packages that use perl, or depend on a p5-* package, or
are called p5-*.

I hope that's all of them.

Revision 1.19: download - view: text, markup, annotated - select for diffs
Tue Sep 11 20:32:13 2012 UTC (12 years, 2 months ago) by asau
Branches: MAIN
CVS tags: pkgsrc-2012Q3-base, pkgsrc-2012Q3
Diff to: previous 1.18: preferred, colored
Changes since revision 1.18: +1 -3 lines
"user-destdir" is default these days

Revision 1.18: download - view: text, markup, annotated - select for diffs
Sat Oct 11 22:01:13 2008 UTC (16 years, 1 month ago) by schwarz
Branches: 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, pkgsrc-2009Q2-base, pkgsrc-2009Q2, pkgsrc-2009Q1-base, pkgsrc-2009Q1, pkgsrc-2008Q4-base, pkgsrc-2008Q4
Diff to: previous 1.17: preferred, colored
Changes since revision 1.17: +4 -4 lines
updated to MUMmer3.20

Revision 1.17: download - view: text, markup, annotated - select for diffs
Sun May 25 21:42:20 2008 UTC (16 years, 5 months ago) by joerg
Branches: MAIN
CVS tags: pkgsrc-2008Q3-base, pkgsrc-2008Q3, pkgsrc-2008Q2-base, pkgsrc-2008Q2, cwrapper, cube-native-xorg-base, cube-native-xorg
Diff to: previous 1.16: preferred, colored
Changes since revision 1.16: +2 -2 lines
Explicitly add pax dependency in those Makefiles that use it (or have
patches to add it). Drop pax from the default USE_TOOLS list.
Make bsdtar the default for those places that wanted gtar to extract
long links etc, as bsdtar can be built of the tree.

Revision 1.16: download - view: text, markup, annotated - select for diffs
Mon Mar 3 01:10:06 2008 UTC (16 years, 8 months ago) by jlam
Branches: MAIN
CVS tags: pkgsrc-2008Q1-base, pkgsrc-2008Q1
Diff to: previous 1.15: preferred, colored
Changes since revision 1.15: +8 -5 lines
Mechanical changes to add full DESTDIR support to packages that install
their files via a custom do-install target.

Revision 1.15: download - view: text, markup, annotated - select for diffs
Thu Jan 18 19:13:10 2007 UTC (17 years, 9 months ago) by rillig
Branches: MAIN
CVS tags: pkgsrc-2007Q4-base, pkgsrc-2007Q4, pkgsrc-2007Q3-base, pkgsrc-2007Q3, pkgsrc-2007Q2-base, pkgsrc-2007Q2, pkgsrc-2007Q1-base, pkgsrc-2007Q1
Diff to: previous 1.14: preferred, colored
Changes since revision 1.14: +11 -53 lines
Updated mummer to 3.19.

Changes since 3.18:
- More documentation.

Revision 1.14: download - view: text, markup, annotated - select for diffs
Wed Dec 6 16:52:20 2006 UTC (17 years, 11 months ago) by joerg
Branches: MAIN
CVS tags: pkgsrc-2006Q4-base, pkgsrc-2006Q4
Diff to: previous 1.13: preferred, colored
Changes since revision 1.13: +3 -2 lines
Fix path to csh in scripts. Bump revision.

Revision 1.13: download - view: text, markup, annotated - select for diffs
Wed Jun 21 19:02:03 2006 UTC (18 years, 4 months ago) by minskim
Branches: MAIN
CVS tags: pkgsrc-2006Q3-base, pkgsrc-2006Q3, pkgsrc-2006Q2-base, pkgsrc-2006Q2
Diff to: previous 1.12: preferred, colored
Changes since revision 1.12: +3 -3 lines
Add csh:run to USE_TOOLS because this package installs csh scripts.
Bump PKGREVISION.

Revision 1.12: download - view: text, markup, annotated - select for diffs
Sun Feb 5 23:08:20 2006 UTC (18 years, 9 months ago) by joerg
Branches: MAIN
CVS tags: pkgsrc-2006Q1-base, pkgsrc-2006Q1
Diff to: previous 1.11: preferred, colored
Changes since revision 1.11: +2 -1 lines
Recursive revision bump / recommended bump for gettext ABI change.

Revision 1.11: download - view: text, markup, annotated - select for diffs
Sun Jan 29 19:31:43 2006 UTC (18 years, 9 months ago) by schwarz
Branches: MAIN
Diff to: previous 1.10: preferred, colored
Changes since revision 1.10: +42 -14 lines

Updated biology/mummer to release 3.18. Changes include:
- MUMmer now resides at Sourceforge
- new tools such as delta-filter
- more extensive html documentation and examples
- bug fixes

Revision 1.10: download - view: text, markup, annotated - select for diffs
Mon Dec 5 20:49:51 2005 UTC (18 years, 11 months ago) by rillig
Branches: MAIN
CVS tags: pkgsrc-2005Q4-base, pkgsrc-2005Q4
Diff to: previous 1.9: preferred, colored
Changes since revision 1.9: +3 -3 lines
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 1.9: download - view: text, markup, annotated - select for diffs
Sat Jul 16 19:10:38 2005 UTC (19 years, 4 months ago) by jlam
Branches: MAIN
CVS tags: pkgsrc-2005Q3-base, pkgsrc-2005Q3
Diff to: previous 1.8: preferred, colored
Changes since revision 1.8: +2 -3 lines
Remove some unnecessarily strong dependencies on perl that resulted
from including perl5/buildlink3.mk.  These packages just need the Perl
interpreter, and can just add "perl" to USE_TOOLS instead.

Revision 1.8: download - view: text, markup, annotated - select for diffs
Sun Jun 19 01:13:23 2005 UTC (19 years, 4 months ago) by kristerw
Branches: MAIN
CVS tags: pkgsrc-2005Q2-base, pkgsrc-2005Q2
Diff to: previous 1.7: preferred, colored
Changes since revision 1.7: +3 -1 lines
Prevent paths to the build directories from being included in the package.
Bump PKGREVISION.

Revision 1.7: download - view: text, markup, annotated - select for diffs
Thu Jun 16 06:57:40 2005 UTC (19 years, 5 months ago) by jlam
Branches: MAIN
Diff to: previous 1.6: preferred, colored
Changes since revision 1.6: +2 -1 lines
Create directories before installing files into them.

Revision 1.6: download - view: text, markup, annotated - select for diffs
Sun May 22 20:07:40 2005 UTC (19 years, 5 months ago) by jlam
Branches: MAIN
Diff to: previous 1.5: preferred, colored
Changes since revision 1.5: +2 -2 lines
Remove USE_GNU_TOOLS and replace with the correct USE_TOOLS definitions:

	USE_GNU_TOOLS	-> USE_TOOLS
	awk		-> gawk
	m4		-> gm4
	make		-> gmake
	sed		-> gsed
	yacc		-> bison

Revision 1.5: download - view: text, markup, annotated - select for diffs
Mon Apr 11 21:45:01 2005 UTC (19 years, 7 months ago) by tv
Branches: MAIN
Diff to: previous 1.4: preferred, colored
Changes since revision 1.4: +1 -2 lines
Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.

Revision 1.4: download - view: text, markup, annotated - select for diffs
Sun Dec 5 15:24:54 2004 UTC (19 years, 11 months ago) by cube
Branches: MAIN
CVS tags: pkgsrc-2005Q1-base, pkgsrc-2005Q1, pkgsrc-2004Q4-base, pkgsrc-2004Q4
Diff to: previous 1.3: preferred, colored
Changes since revision 1.3: +4 -4 lines
Update to version 3.15.  From David Price in PR#28305.

3.05 - Added -k option to show-coords to only display the best frame for
       overlapping PROmer alignments. Added --[no]optimize option to nucmer
       and promer to allow alignment score optimization to be turned off, i.e
       allow alignments to extend to the ends of sequences rather than
       backtracking to optimize the alignment score. Updated docs.
3.06 - Added -F and -h option to mummer. Changed -mumcand option to
       -mumreference, but left deprecated -mumcand option available. Added
       -maxmatch option to mummer, and changed default behavior of all
       applicable programs to -mumreference (nucmer, promer and mummer).
       Added -w (screen width) option to show-aligns. Updated documentation
       with all of these changes.
3.07 - Added the 'mapview' plotting utility and appropriate documentation.
       Fixed origin wrap shadowing bug in show-tiling when using the -c option.
       NUCmer and PROmer now convert to absolute paths to avoid ambiguity.
3.08 - Added MUMmer examples web docs which gives brief walkthroughs
3.10 - Now Mac OSX compatible. Added -R option to show-tiling.
3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed
       the issue with mummerplot being to faint.
3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed
       a bug in nucmer and promer. Fixed rounding issue in show-coords.
       Updated citations.
3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation.
       Fixed bug in show-tiling -R
3.14 - Fixed gcc3 compilation bug
3.15 - Fixed --nooptimize in nuc/promer.

Revision 1.3: download - view: text, markup, annotated - select for diffs
Sun Apr 11 04:07:05 2004 UTC (20 years, 7 months ago) by snj
Branches: MAIN
CVS tags: pkgsrc-2004Q3-base, pkgsrc-2004Q3, pkgsrc-2004Q2-base, pkgsrc-2004Q2
Diff to: previous 1.2: preferred, colored
Changes since revision 1.2: +3 -3 lines
Convert to buildlink3.

Revision 1.2: download - view: text, markup, annotated - select for diffs
Tue Jan 20 12:08:40 2004 UTC (20 years, 9 months ago) by agc
Branches: MAIN
CVS tags: pkgsrc-2004Q1-base, pkgsrc-2004Q1
Diff to: previous 1.1: preferred, colored
Changes since revision 1.1: +2 -2 lines
Move WRKSRC definition away from the first paragraph in a Makefile.

Revision 1.1.1.1 (vendor branch): download - view: text, markup, annotated - select for diffs
Sat Sep 27 22:24:56 2003 UTC (21 years, 1 month ago) by jschauma
Branches: TNF
CVS tags: pkgsrc-base, pkgsrc-2003Q4-base, pkgsrc-2003Q4
Diff to: previous 1.1: preferred, colored
Changes since revision 1.1: +0 -0 lines
Initial import of mummer, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

Mummer is a system for aligning whole genome sequences. Using an efficient
data structure called a suffix tree, the system is able rapidly to align
sequences containing millions of nucleotides whether in complete or draft
form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s
of contigs from a shotgun sequencing project with ease, and will align them to
another set of contigs or a genome using the NUCmer program included with the
system. 

Revision 1.1: download - view: text, markup, annotated - select for diffs
Sat Sep 27 22:24:56 2003 UTC (21 years, 1 month ago) by jschauma
Branches: MAIN
Initial revision

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