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18 commits

Author SHA1 Message Date
wiz
8292204475 *: recursive bump for perl 5.36 2022-06-28 11:30:51 +00:00
nia
4dd52433ec biology: Replace RMD160 checksums with BLAKE2s checksums 
All checksums have been double-checked against existing RMD160 and
SHA512 hashes
 2021-10-26 10:03:36 +00:00
nia
169fb9f0f3 biology: Remove SHA1 hashes for distfiles 2021-10-07 13:19:36 +00:00
wiz
6eae1297d5 *: recursive bump for perl 5.34 2021-05-24 19:49:01 +00:00
wiz
00da7815c0 *: bump PKGREVISION for perl-5.32. 2020-08-31 18:06:29 +00:00
rillig
84f2203288 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).
 2020-01-26 05:26:08 +00:00
rillig
ffe83de7b1 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.
 2020-01-18 23:30:05 +00:00
rillig
d93bec131e biology: align variable assignments 
pkglint -Wall -F --only aligned --only indent -r
 2019-11-02 22:09:00 +00:00
wiz
84e123ddd2 Bump PKGREVISIONs for perl 5.30.0 2019-08-11 13:17:48 +00:00
wiz
9bd737fe76 Recursive bump for perl5-5.28.0 2018-08-22 09:42:51 +00:00
he
a81a9abae7 Re-add patch to bring timeval definition and select prototype into scope. 
Bump PKGREVISION.
 2017-12-27 23:44:01 +00:00
bacon
f78486b904 biology/bwa: Update to 0.7.17 
Numerous bug fixes, enhancements, and new command-line options

ok wiz@
 2017-12-17 14:30:36 +00:00
joerg
eeb5c912e8 Add missing include. 2017-02-14 21:34:34 +00:00
wiz
2b0a009d0e Bump PKGREVISION for perl-5.24.0 for everything mentioning perl. 2016-07-09 06:37:46 +00:00
wiedi
6a6bdae524 Fix int types and network libs on SunOS 2015-12-12 16:56:04 +00:00
dholland
9e4d91002d Unconditionally uses <emmintrin.h>, so restrict to x86. 2015-11-07 20:20:54 +00:00
agc
bca6c81b27 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.
 2015-11-02 18:42:20 +00:00
leot
ff3972c8c8 Import biology/bwa as bwa-0.7.9a. 
Packaged in pkgsrc-wip by Jason Bacon.

BWA is a software package for mapping low-divergent sequences against a large
reference genome, such as the human genome.
 2015-10-14 17:12:52 +00:00