Bug 228758 - biology/tRNAscan-SE: update to 2.0.0
Summary: biology/tRNAscan-SE: update to 2.0.0
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Only Me
Assignee: Jason W. Bacon
URL:
Keywords:
Depends on: 228776
Blocks:
  Show dependency treegraph
 
Reported: 2018-06-05 08:54 UTC by Motomichi Matsuzaki
Modified: 2019-08-08 01:29 UTC (History)
2 users (show)

See Also:


Attachments
svn diff (9.63 KB, patch)
2018-06-05 08:54 UTC, Motomichi Matsuzaki
no flags Details | Diff
svn diff (10.43 KB, patch)
2018-06-05 09:52 UTC, Motomichi Matsuzaki
no flags Details | Diff
svn diff (to 2.0.0) (22.98 KB, patch)
2018-06-06 15:00 UTC, Motomichi Matsuzaki
no flags Details | Diff

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Description Motomichi Matsuzaki 2018-06-05 08:54:28 UTC
Created attachment 194013 [details]
svn diff

updating biology/tRNAscan-SE from 1.23 to 1.3.1, requiring PORTEPOCH bump.

* new MASTER_SITES, with changing WWW line in pkg-descr
* removing files/patch-sqio.c

NOTE: the MASTER_SITES contains the recent version 2.0.0.
There seem many changes including build system, dependencies, etc. and
I have no time for examining these changes.
Comment 1 Motomichi Matsuzaki 2018-06-05 09:52:34 UTC
Created attachment 194016 [details]
svn diff

oops!
* Installing perl modules into ${SITE_PERL}
* Add LICENSE
Comment 2 Kirill Ponomarev freebsd_committer 2018-06-06 00:12:00 UTC
I'd suggest to update it to the latest 2.0.0, it would be awesome if you'd find time and contribute
Comment 3 Motomichi Matsuzaki 2018-06-06 15:00:54 UTC
Created attachment 194046 [details]
svn diff (to 2.0.0)

(In reply to Kirill Ponomarev from comment #2)

Here you are!

Changes:
* updating to 2.0.0 (without bumping PORTEPOCH)
* taking over MAINTAINER
* new COMMENT
* add RUN_DEPENDS on upcoming biology/infernal (bug #228776)

This version uses autotools, so patches/knobs are rewritten from scratch.

The original Makefile installs some files to strange places,
so the location is modified to fit with FreeBSD hier(7) as follows:
* configuration file: $(bindir) to $(sysconfdir)
* header files: $(includedir) to not installed since unnecessary
* static data files: $(libdir) to $(pkgdatadir)
* perl modules: $(libdir) to $(pkgdatadir)

Tested by: poudriere testport (amd64/i386 11.1)
Comment 4 Motomichi Matsuzaki 2018-06-06 15:05:21 UTC
Deleted files:
       files/patch-Makefile
       files/patch-sqio.c

Added files:
       files/patch-Makefile.am
       files/patch-configure.ac
       files/patch-tRNAscan-SE.src
       pkg-plist
Comment 5 commit-hook freebsd_committer 2018-06-06 15:21:57 UTC
A commit references this bug:

Author: krion
Date: Wed Jun  6 15:20:58 UTC 2018
New revision: 471852
URL: https://svnweb.freebsd.org/changeset/ports/471852

Log:
  Update to 2.0.0 and pass maintainership to committer.

  PR:		228758
  Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>

Changes:
  head/biology/tRNAscan-SE/Makefile
  head/biology/tRNAscan-SE/distinfo
  head/biology/tRNAscan-SE/files/patch-Makefile
  head/biology/tRNAscan-SE/files/patch-Makefile.am
  head/biology/tRNAscan-SE/files/patch-configure.ac
  head/biology/tRNAscan-SE/files/patch-sqio.c
  head/biology/tRNAscan-SE/files/patch-tRNAscan-SE.src
  head/biology/tRNAscan-SE/pkg-descr
Comment 6 Motomichi Matsuzaki 2018-07-12 02:15:27 UTC
pkg-plist, which is present in the svn diff, is lacking in the repository.
Comment 7 commit-hook freebsd_committer 2018-09-28 00:13:31 UTC
A commit references this bug:

Author: wen
Date: Fri Sep 28 00:12:49 UTC 2018
New revision: 480837
URL: https://svnweb.freebsd.org/changeset/ports/480837

Log:
  - Unbreak by adding missing pkg-plist

  PR:		228758
  Submitted by:	mzaki@niid.go.jp(maintainer)

Changes:
  head/biology/tRNAscan-SE/Makefile
  head/biology/tRNAscan-SE/pkg-plist
Comment 8 Jason W. Bacon freebsd_committer 2018-11-11 22:27:10 UTC
Hold on, I think wen@ just forgot to close this after commit.