Debian Bug report logs - #846581
src:biojava4-live: New version available

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: src:biojava4-live: New version available

Date: Fri, 02 Dec 2016 11:55:47 +0100

Package: src:biojava4-live
Severity: normal

Hi Olivier,

we are lagging behind the official BioJava4 series.  Do you intend to
upload the latest upstream release or are there any reasons to stick to
the Debian packaged version?  I think it would be the best to distribute
the latest upstream in Stretch.

Kind regards

      Andreas.

-- System Information:
Debian Release: 8.6
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Message #10 received at 846581@bugs.debian.org (full text, mbox, reply):

From: olivier sallou <osallou@debian.org>

To: 846581@bugs.debian.org

Subject: missing deps

Date: Mon, 05 Dec 2016 08:47:39 +0000

[Message part 1 (text/plain, inline)]

forester dep cannot be found anymore, upstream modified his download
directory.
Created a bug in github to find this dependency to build new release
(biojava4)

[Message part 2 (text/html, inline)]

Message #15 received at 846581@bugs.debian.org (full text, mbox, reply):

From: olivier sallou <osallou@debian.org>

To: 846581@bugs.debian.org

Subject: Re: missing deps

Date: Mon, 05 Dec 2016 18:33:21 +0000

[Message part 1 (text/plain, inline)]

Sources are now in maven repo, i gonna update patches for new upload

Le lun. 5 déc. 2016 09:47, olivier sallou <osallou@debian.org> a écrit :

> forester dep cannot be found anymore, upstream modified his download
> directory.
> Created a bug in github to find this dependency to build new release
> (biojava4)
>

[Message part 2 (text/html, inline)]

Message #20 received at 846581@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@fam-tille.de>

To: 846581@bugs.debian.org, Olivier Sallou <olivier.sallou@irisa.fr>

Subject: Moved biojava4-live from SVN to Git

Date: Fri, 23 Dec 2016 23:40:18 +0100

Hi,

since there is another minor new upstream version of Biojava4-live and I
think orig tarballs that are not identical to upstream downloads should 
be in Git I moved the packaging from SVN to Git[1].

I think I adapted the patches properly but unfortunately the current
state in Git does not build.  Olivier, could you probably fix the build?

Kind regards

       Andreas.

[1] https://anonscm.debian.org/git/debian-med/biojava4-live.git

-- 
http://fam-tille.de

Message #25 received at 846581@bugs.debian.org (full text, mbox, reply):

From: Olivier Sallou <olivier.sallou@irisa.fr>

To: Andreas Tille <andreas@fam-tille.de>

Cc: 846581@bugs.debian.org

Subject: Re : Moved biojava4-live from SVN to Git

Date: Sat, 24 Dec 2016 16:35:30 +0100 (CET)

----- Andreas Tille <andreas@fam-tille.de> a écrit :
> Hi,
> 
> since there is another minor new upstream version of Biojava4-live and I
> think orig tarballs that are not identical to upstream downloads should 
> be in Git I moved the packaging from SVN to Git[1].
> 
> I think I adapted the patches properly but unfortunately the current
> state in Git does not build.  Olivier, could you probably fix the build?

I will check this next week

Olivier
> 
> Kind regards
> 
>        Andreas.
> 
> [1] https://anonscm.debian.org/git/debian-med/biojava4-live.git
> 
> -- 
> http://fam-tille.de

Message #30 received at 846581@bugs.debian.org (full text, mbox, reply):

From: olivier sallou <osallou@debian.org>

To: "846581@bugs.debian.org" <846581@bugs.debian.org>, "debian-med@lists.debian.org" <debian-med@lists.debian.org>, Andreas Tille <tille@debian.org>

Subject: biojava4-live build update issue

Date: Mon, 26 Dec 2016 16:28:11 +0000

[Message part 1 (text/plain, inline)]

hi Andreas,
I had a look at your build issues after switching to git and new code is
based on a more recent jmol version (14.6.2) than before. Previous was on
1.3.0.14.
Fortunatly  debian jmol release is 14.6.4.
so jmol needs to be udpated to latest and d/control must require jmol >=
14.6.4. I updated d/control

New dependency libvecmath-java was also required, added to d/control and
d/build.xml

Now build looks fine, should I go to upload and did you want to do
something else ?

Olivier

[Message part 2 (text/html, inline)]

Message #35 received at 846581-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 846581-close@bugs.debian.org

Subject: Bug#846581: fixed in biojava4-live 4.2.5+dfsg-1

Date: Tue, 27 Dec 2016 10:18:37 +0000

Source: biojava4-live
Source-Version: 4.2.5+dfsg-1

We believe that the bug you reported is fixed in the latest version of
biojava4-live, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 846581@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (supplier of updated biojava4-live package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmaster@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Fri, 23 Dec 2016 22:23:11 +0100
Source: biojava4-live
Binary: libbiojava4.0-java libbiojava4-java libbiojava4-java-doc
Architecture: source all
Version: 4.2.5+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 libbiojava4-java - Java API to biological data and applications (default version)
 libbiojava4-java-doc - [Biology] Documentation for BioJava
 libbiojava4.0-java - Java API to biological data and applications (version 4)
Closes: 846581
Changes:
 biojava4-live (4.2.5+dfsg-1) unstable; urgency=medium
 .
   * Team upload.
   * New upstream version
     Closes: #846581
   * Moved packaging from SVN to Git
Checksums-Sha1:
 5633a1a383d4e6020c1a72aff9f1627d5246d1b2 2630 biojava4-live_4.2.5+dfsg-1.dsc
 18db617e25c8505a219283851114f4fe121d48eb 17762195 biojava4-live_4.2.5+dfsg.orig.tar.gz
 8aa28362f06b98ccbb90efd21d23265cb629e219 14140 biojava4-live_4.2.5+dfsg-1.debian.tar.xz
 ba7af38df751186837a98e483804a09a8f185a01 11028 biojava4-live_4.2.5+dfsg-1_amd64.buildinfo
 bf3ce6b6815501880822f455e3a520b26ca773f9 1666248 libbiojava4-java-doc_4.2.5+dfsg-1_all.deb
 4cbfde8b9226ba9876fd41d702bd9731e2d8a174 3666 libbiojava4-java_4.2.5+dfsg-1_all.deb
 bb3e40e4f4a32e9e3c00bd4877b3958812be79a8 5462806 libbiojava4.0-java_4.2.5+dfsg-1_all.deb
Checksums-Sha256:
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 ea86e7a5806c779e0570fb190b33e93bdd5aed7832cf55a78070ed8d6f9074e4 17762195 biojava4-live_4.2.5+dfsg.orig.tar.gz
 91203133fa14c00d4f3b70fefecdc79d048a56a00086b720a31d2a75f25f3fc7 14140 biojava4-live_4.2.5+dfsg-1.debian.tar.xz
 af3bd932fcedef9a8fb297e71c143efc8c47b77eddcca2e3ec5c94bf61fac679 11028 biojava4-live_4.2.5+dfsg-1_amd64.buildinfo
 950d99772c4f0b0ac059dc77137feb116664fccd0055a90654e9e8eed96694f9 1666248 libbiojava4-java-doc_4.2.5+dfsg-1_all.deb
 0ebb1e0ac0c1035982b131fbbc4e85c26e20ede7873127cfca664ca5a6bcc4c6 3666 libbiojava4-java_4.2.5+dfsg-1_all.deb
 2c0f776323b3a64828542fb45aa5df0a4112667e118f8b8d40fe74d64b7c1ce6 5462806 libbiojava4.0-java_4.2.5+dfsg-1_all.deb
Files:
 eae942818450af55c9ce6e777c8b7d18 2630 java optional biojava4-live_4.2.5+dfsg-1.dsc
 b673e914b8775b99a9f8b81c34880242 17762195 java optional biojava4-live_4.2.5+dfsg.orig.tar.gz
 401e903e5de3b3e82f0f5d6345341713 14140 java optional biojava4-live_4.2.5+dfsg-1.debian.tar.xz
 02d88ed71f59ecca3c03581018961ad4 11028 java optional biojava4-live_4.2.5+dfsg-1_amd64.buildinfo
 22081011de919a686c09a993bea1538d 1666248 doc optional libbiojava4-java-doc_4.2.5+dfsg-1_all.deb
 65723d92a78f9a09454b973d9d454be4 3666 java optional libbiojava4-java_4.2.5+dfsg-1_all.deb
 aedd0578aca14521fe4fa6432d9b5e3b 5462806 java optional libbiojava4.0-java_4.2.5+dfsg-1_all.deb

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