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Revision 1.31 / (download) - annotate - [select for diffs], Tue Jun 28 11:31:01 2022 UTC (21 months, 3 weeks ago) by wiz
Branch: MAIN
CVS Tags: 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,
HEAD
Changes since 1.30: +2 -2
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Diff to previous 1.30 (colored)
*: recursive bump for perl 5.36
Revision 1.30 / (download) - annotate - [select for diffs], Mon May 24 19:49:11 2021 UTC (2 years, 10 months ago) by wiz
Branch: 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
Changes since 1.29: +2 -2
lines
Diff to previous 1.29 (colored)
*: recursive bump for perl 5.34
Revision 1.29 / (download) - annotate - [select for diffs], Mon Aug 31 18:06:39 2020 UTC (3 years, 7 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2021Q1-base,
pkgsrc-2021Q1,
pkgsrc-2020Q4-base,
pkgsrc-2020Q4,
pkgsrc-2020Q3-base,
pkgsrc-2020Q3
Changes since 1.28: +2 -2
lines
Diff to previous 1.28 (colored)
*: bump PKGREVISION for perl-5.32.
Revision 1.28 / (download) - annotate - [select for diffs], Sun Jan 26 05:26:15 2020 UTC (4 years, 2 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2020Q2-base,
pkgsrc-2020Q2,
pkgsrc-2020Q1-base,
pkgsrc-2020Q1
Changes since 1.27: +2 -2
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Diff to previous 1.27 (colored)
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) - annotate - [select for diffs], Sat Jan 18 23:30:09 2020 UTC (4 years, 3 months ago) by rillig
Branch: MAIN
Changes since 1.26: +2 -2
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Diff to previous 1.26 (colored)
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) - annotate - [select for diffs], Sun Aug 11 13:18:00 2019 UTC (4 years, 8 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2019Q4-base,
pkgsrc-2019Q4,
pkgsrc-2019Q3-base,
pkgsrc-2019Q3
Changes since 1.25: +2 -2
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Diff to previous 1.25 (colored)
Bump PKGREVISIONs for perl 5.30.0
Revision 1.25 / (download) - annotate - [select for diffs], Wed Aug 22 09:42:59 2018 UTC (5 years, 7 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base,
pkgsrc-2019Q2,
pkgsrc-2019Q1-base,
pkgsrc-2019Q1,
pkgsrc-2018Q4-base,
pkgsrc-2018Q4,
pkgsrc-2018Q3-base,
pkgsrc-2018Q3
Changes since 1.24: +2 -2
lines
Diff to previous 1.24 (colored)
Recursive bump for perl5-5.28.0
Revision 1.24 / (download) - annotate - [select for diffs], Sat Jul 9 06:37:51 2016 UTC (7 years, 9 months ago) by wiz
Branch: 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
Changes since 1.23: +2 -2
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Diff to previous 1.23 (colored)
Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.
Revision 1.23 / (download) - annotate - [select for diffs], Fri Jun 12 10:48:26 2015 UTC (8 years, 10 months ago) by wiz
Branch: 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
Changes since 1.22: +2 -2
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Diff to previous 1.22 (colored)
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) - annotate - [select for diffs], Thu May 29 23:35:17 2014 UTC (9 years, 10 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2015Q1-base,
pkgsrc-2015Q1,
pkgsrc-2014Q4-base,
pkgsrc-2014Q4,
pkgsrc-2014Q3-base,
pkgsrc-2014Q3,
pkgsrc-2014Q2-base,
pkgsrc-2014Q2
Changes since 1.21: +2 -2
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Diff to previous 1.21 (colored)
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) - annotate - [select for diffs], Fri May 31 12:39:39 2013 UTC (10 years, 10 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2014Q1-base,
pkgsrc-2014Q1,
pkgsrc-2013Q4-base,
pkgsrc-2013Q4,
pkgsrc-2013Q3-base,
pkgsrc-2013Q3,
pkgsrc-2013Q2-base,
pkgsrc-2013Q2
Changes since 1.20: +2 -2
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Diff to previous 1.20 (colored)
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) - annotate - [select for diffs], Wed Oct 3 21:53:59 2012 UTC (11 years, 6 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2013Q1-base,
pkgsrc-2013Q1,
pkgsrc-2012Q4-base,
pkgsrc-2012Q4
Changes since 1.19: +2 -1
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Diff to previous 1.19 (colored)
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) - annotate - [select for diffs], Tue Sep 11 20:32:13 2012 UTC (11 years, 7 months ago) by asau
Branch: MAIN
CVS Tags: pkgsrc-2012Q3-base,
pkgsrc-2012Q3
Changes since 1.18: +1 -3
lines
Diff to previous 1.18 (colored)
"user-destdir" is default these days
Revision 1.18 / (download) - annotate - [select for diffs], Sat Oct 11 22:01:13 2008 UTC (15 years, 6 months ago) by schwarz
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,
pkgsrc-2009Q2-base,
pkgsrc-2009Q2,
pkgsrc-2009Q1-base,
pkgsrc-2009Q1,
pkgsrc-2008Q4-base,
pkgsrc-2008Q4
Changes since 1.17: +4 -4
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Diff to previous 1.17 (colored)
updated to MUMmer3.20
Revision 1.17 / (download) - annotate - [select for diffs], Sun May 25 21:42:20 2008 UTC (15 years, 10 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2008Q3-base,
pkgsrc-2008Q3,
pkgsrc-2008Q2-base,
pkgsrc-2008Q2,
cwrapper,
cube-native-xorg-base,
cube-native-xorg
Changes since 1.16: +2 -2
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Diff to previous 1.16 (colored)
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) - annotate - [select for diffs], Mon Mar 3 01:10:06 2008 UTC (16 years, 1 month ago) by jlam
Branch: MAIN
CVS Tags: pkgsrc-2008Q1-base,
pkgsrc-2008Q1
Changes since 1.15: +8 -5
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Diff to previous 1.15 (colored)
Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target.
Revision 1.15 / (download) - annotate - [select for diffs], Thu Jan 18 19:13:10 2007 UTC (17 years, 3 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2007Q4-base,
pkgsrc-2007Q4,
pkgsrc-2007Q3-base,
pkgsrc-2007Q3,
pkgsrc-2007Q2-base,
pkgsrc-2007Q2,
pkgsrc-2007Q1-base,
pkgsrc-2007Q1
Changes since 1.14: +11 -53
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Diff to previous 1.14 (colored)
Updated mummer to 3.19. Changes since 3.18: - More documentation.
Revision 1.14 / (download) - annotate - [select for diffs], Wed Dec 6 16:52:20 2006 UTC (17 years, 4 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2006Q4-base,
pkgsrc-2006Q4
Changes since 1.13: +3 -2
lines
Diff to previous 1.13 (colored)
Fix path to csh in scripts. Bump revision.
Revision 1.13 / (download) - annotate - [select for diffs], Wed Jun 21 19:02:03 2006 UTC (17 years, 10 months ago) by minskim
Branch: MAIN
CVS Tags: pkgsrc-2006Q3-base,
pkgsrc-2006Q3,
pkgsrc-2006Q2-base,
pkgsrc-2006Q2
Changes since 1.12: +3 -3
lines
Diff to previous 1.12 (colored)
Add csh:run to USE_TOOLS because this package installs csh scripts. Bump PKGREVISION.
Revision 1.12 / (download) - annotate - [select for diffs], Sun Feb 5 23:08:20 2006 UTC (18 years, 2 months ago) by joerg
Branch: MAIN
CVS Tags: pkgsrc-2006Q1-base,
pkgsrc-2006Q1
Changes since 1.11: +2 -1
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Diff to previous 1.11 (colored)
Recursive revision bump / recommended bump for gettext ABI change.
Revision 1.11 / (download) - annotate - [select for diffs], Sun Jan 29 19:31:43 2006 UTC (18 years, 2 months ago) by schwarz
Branch: MAIN
Changes since 1.10: +42 -14
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Diff to previous 1.10 (colored)
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) - annotate - [select for diffs], Mon Dec 5 20:49:51 2005 UTC (18 years, 4 months ago) by rillig
Branch: MAIN
CVS Tags: pkgsrc-2005Q4-base,
pkgsrc-2005Q4
Changes since 1.9: +3 -3
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Diff to previous 1.9 (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 1.9 / (download) - annotate - [select for diffs], Sat Jul 16 19:10:38 2005 UTC (18 years, 9 months ago) by jlam
Branch: MAIN
CVS Tags: pkgsrc-2005Q3-base,
pkgsrc-2005Q3
Changes since 1.8: +2 -3
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Diff to previous 1.8 (colored)
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) - annotate - [select for diffs], Sun Jun 19 01:13:23 2005 UTC (18 years, 10 months ago) by kristerw
Branch: MAIN
CVS Tags: pkgsrc-2005Q2-base,
pkgsrc-2005Q2
Changes since 1.7: +3 -1
lines
Diff to previous 1.7 (colored)
Prevent paths to the build directories from being included in the package. Bump PKGREVISION.
Revision 1.7 / (download) - annotate - [select for diffs], Thu Jun 16 06:57:40 2005 UTC (18 years, 10 months ago) by jlam
Branch: MAIN
Changes since 1.6: +2 -1
lines
Diff to previous 1.6 (colored)
Create directories before installing files into them.
Revision 1.6 / (download) - annotate - [select for diffs], Sun May 22 20:07:40 2005 UTC (18 years, 11 months ago) by jlam
Branch: MAIN
Changes since 1.5: +2 -2
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Diff to previous 1.5 (colored)
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) - annotate - [select for diffs], Mon Apr 11 21:45:01 2005 UTC (19 years ago) by tv
Branch: MAIN
Changes since 1.4: +1 -2
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Diff to previous 1.4 (colored)
Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.
Revision 1.4 / (download) - annotate - [select for diffs], Sun Dec 5 15:24:54 2004 UTC (19 years, 4 months ago) by cube
Branch: MAIN
CVS Tags: pkgsrc-2005Q1-base,
pkgsrc-2005Q1,
pkgsrc-2004Q4-base,
pkgsrc-2004Q4
Changes since 1.3: +4 -4
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Diff to previous 1.3 (colored)
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) - annotate - [select for diffs], Sun Apr 11 04:07:05 2004 UTC (20 years ago) by snj
Branch: MAIN
CVS Tags: pkgsrc-2004Q3-base,
pkgsrc-2004Q3,
pkgsrc-2004Q2-base,
pkgsrc-2004Q2
Changes since 1.2: +3 -3
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Diff to previous 1.2 (colored)
Convert to buildlink3.
Revision 1.2 / (download) - annotate - [select for diffs], Tue Jan 20 12:08:40 2004 UTC (20 years, 3 months ago) by agc
Branch: MAIN
CVS Tags: pkgsrc-2004Q1-base,
pkgsrc-2004Q1
Changes since 1.1: +2 -2
lines
Diff to previous 1.1 (colored)
Move WRKSRC definition away from the first paragraph in a Makefile.
Revision 1.1.1.1 / (download) - annotate - [select for diffs] (vendor branch), Sat Sep 27 22:24:56 2003 UTC (20 years, 6 months ago) by jschauma
Branch: TNF
CVS Tags: pkgsrc-base,
pkgsrc-2003Q4-base,
pkgsrc-2003Q4
Changes since 1.1: +0 -0
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Diff to previous 1.1 (colored)
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) - annotate - [select for diffs], Sat Sep 27 22:24:56 2003 UTC (20 years, 6 months ago) by jschauma
Branch: MAIN
Initial revision