Bug 690042 – sci-biology/GBrowse should try to remove dependency on dev-perl/Net-SMTP-SSL

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Kent Fredric (IRC: kent\n) (RETIRED) 2019-07-17 05:21:33 UTC]

Net-SMTP-SSL is now redundant as SSL support is implemented in Net-SMTP.

This removal should ideally be handled by upstream.

But upstream haven't seen activity since 2012, and the links on thier site still talk about search.cpan.org still being a thing, ... and GBrowse is no longer discoverable on CPAN.

So I guess one option is to retire this package entirely.

Nothing appears to depend on it, maybe its time to put this out to pasture?

[Comment 1 Martin Mokrejš 2019-07-21 17:39:49 UTC]

I agree that Gbrowse is not actively maintained:

<quote>
From: Scott Cain <[e-mail]>
Date: Tue, 11 Sep 2018 13:23:44 -0700
...

Are you setting up a genome browser for a new project?  If so, I'd suggest that you look into JBrowse (http://jbrowse.org), which is a GMOD project but is significantly more modern and well maintained.  While we are still around to help and answer questions for GBrowse, it does not receive version updates.  With JBrowse, your item 1 is easy to achieve, and with a little javascripting, item 2 could be done as well.

If, on the other hand, this is an existing project and you'd like to modify how GBrowse works, I'd still suggest looking at JBrowse, but certainly understand why you'd be reluctant.  I'm not sure how to do item 1 on your list, though I imagine it would be possible with some javascript and css hacks.

...

_______________________________________________
Gmod-gbrowse mailing list
[e-mail]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
</quote>



So, the easiest is really to drop it from Gentoo. @weaver and me spent so much time in this ebuild (and several approaches) but Andrey is retired and I am not interested in studying the perl stuff.

[Comment 2 Larry the Git Cow 2022-03-19 15:39:13 UTC]

The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3ef36b7c1ea596ab58fdf49c866e41f3e949f2b3

commit 3ef36b7c1ea596ab58fdf49c866e41f3e949f2b3
Author:     David Seifert <[e-mail]>
AuthorDate: 2022-03-19 15:39:03 +0000
Commit:     David Seifert <[e-mail]>
CommitDate: 2022-03-19 15:39:03 +0000

    profiles: last-rite sci-biology/GBrowse
    
    Bug: https://bugs.gentoo.org/402849
    Bug: https://bugs.gentoo.org/513594
    Bug: https://bugs.gentoo.org/690042
    Bug: https://bugs.gentoo.org/828702
    Signed-off-by: David Seifert <[e-mail]>

 profiles/package.mask | 6 ++++++
 1 file changed, 6 insertions(+)

[Comment 3 Larry the Git Cow 2022-04-17 20:27:33 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f71d2fd07f0ec1a96b6772fa4412e6ece900c6e2

commit f71d2fd07f0ec1a96b6772fa4412e6ece900c6e2
Author:     Jakov Smolić <[e-mail]>
AuthorDate: 2022-04-17 20:26:33 +0000
Commit:     Jakov Smolić <[e-mail]>
CommitDate: 2022-04-17 20:26:33 +0000

    sci-biology/GBrowse: treeclean
    
    Closes: https://bugs.gentoo.org/828702
    Closes: https://bugs.gentoo.org/690042
    Closes: https://bugs.gentoo.org/513594
    Closes: https://bugs.gentoo.org/402849
    Signed-off-by: Jakov Smolić <[e-mail]>

 profiles/package.mask                              |  6 --
 sci-biology/GBrowse/GBrowse-2.48-r1.ebuild         | 71 ---------------------
 sci-biology/GBrowse/Manifest                       |  1 -
 .../GBrowse/files/GBrowseInstall.pm-2.39.patch     | 72 ----------------------
 sci-biology/GBrowse/metadata.xml                   | 11 ----
 5 files changed, 161 deletions(-)