Debian Bug report logs - #960654
src:biojava4-live: Please add support to build against libjson-simple-java >= 3

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

From: Gilles Filippini <pini@debian.org>

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

Subject: src:biojava4-live: Please add support to build against libjson-simple-java >= 3

Date: Fri, 15 May 2020 09:41:18 +0200

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

Package: src:biojava4-live
Version: 4.2.12+dfsg-2
Severity: normal
Tags: patch

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Hash: SHA512

Hi,

I'd like to transition json-simple 3.1.1 to unstable, but biojava4-live is a blocker since it builds against libjson-simple-java << 3 only.

The json-simple classes used by biojava4-live were deprecated in version 2.0.0 [1]. There were removed in versions 3.x [2].

[1] https://github.com/cliftonlabs/json-simple/blob/json-simple-2.0.0/README.txt
[2] https://github.com/cliftonlabs/json-simple/blob/json-simple-3.0.1/CHANGELOG

Please find attached a patch proposal to use the current json-simple classes. I've tested that the package builds correctly against libjson-simple-java version 2.3.0-1 from unstable and version 3.1.1-1~exp2 currently in experimental, and the build time test cases report no errors.

Thanks in advance for considering.

_g.

- -- System Information:
Debian Release: buster/sid
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 5.6.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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[biojava4-live-json-simple.debdiff (text/plain, attachment)]

Message #10 received at 960654@bugs.debian.org (full text, mbox, reply):

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

To: Gilles Filippini <pini@debian.org>, 960654@bugs.debian.org

Subject: Re: [Debian-med-packaging] Bug#960654: src:biojava4-live: Please add support to build against libjson-simple-java >= 3

Date: Fri, 15 May 2020 10:59:28 +0200

Hi,
thanks for the patch.
However, if json-simple API/ABI is broken, I think that package should
be kinda libjson-simple3-java to keep compatibility with existing
packages using old versions and allow transition of packages to new
release if needed and possible.

Anyway, gonna add your patch

Olivier

On Fri, 2020-05-15 at 09:41 +0200, Gilles Filippini wrote:
> Package: src:biojava4-live
> Version: 4.2.12+dfsg-2
> Severity: normal
> Tags: patch
> 
> Hi,
> 
> I'd like to transition json-simple 3.1.1 to unstable, but biojava4-
> live is a blocker since it builds against libjson-simple-java << 3
> only.
> 
> The json-simple classes used by biojava4-live were deprecated in
> version 2.0.0 [1]. There were removed in versions 3.x [2].
> 
> [1] 
> https://github.com/cliftonlabs/json-simple/blob/json-simple-2.0.0/README.txt
> [2] 
> https://github.com/cliftonlabs/json-simple/blob/json-simple-3.0.1/CHANGELOG
> 
> Please find attached a patch proposal to use the current json-simple
> classes. I've tested that the package builds correctly against
> libjson-simple-java version 2.3.0-1 from unstable and version 3.1.1-
> 1~exp2 currently in experimental, and the build time test cases
> report no errors.
> 
> Thanks in advance for considering.
> 
> _g.
> 
> -- System Information:
> Debian Release: buster/sid
> Architecture: amd64 (x86_64)
> Foreign Architectures: i386
> 
> Kernel: Linux 5.6.0-1-amd64 (SMP w/4 CPU cores)
> Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8),
> LANGUAGE=fr_FR.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
> LSM: AppArmor: enabled
> 
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@alioth-lists.debian.net
> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
-- 
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

Message #15 received at 960654-close@bugs.debian.org (full text, mbox, reply):

From: Debian FTP Masters <ftpmaster@ftp-master.debian.org>

To: 960654-close@bugs.debian.org

Subject: Bug#960654: fixed in biojava4-live 4.2.12+dfsg-3

Date: Fri, 15 May 2020 09:49:00 +0000

Source: biojava4-live
Source-Version: 4.2.12+dfsg-3
Done: Olivier Sallou <osallou@debian.org>

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 960654@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Olivier Sallou <osallou@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)


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Hash: SHA256

Format: 1.8
Date: Fri, 15 May 2020 09:04:30 +0000
Source: biojava4-live
Binary: libbiojava4-java libbiojava4-java-doc libbiojava4.0-java
Architecture: source all
Version: 4.2.12+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Olivier Sallou <osallou@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: 960654
Changes:
 biojava4-live (4.2.12+dfsg-3) unstable; urgency=medium
 .
   [ Michael R. Crusoe ]
   * Don't hardcode openjdk-11 path in debian/rules
 .
   [ Gilles Filippini <pini@debian.org> ]
   * Tentative fix to build against json-simple 3 Closes: #960654
Checksums-Sha1:
 037ba95d844bbe6b86ec71ea827f78edb6adc7b5 2728 biojava4-live_4.2.12+dfsg-3.dsc
 f220bc573e5f59fe39cc8fd394a2e3960ef01dfc 15712 biojava4-live_4.2.12+dfsg-3.debian.tar.xz
 1d16c99ff2d2ceb776debc05d806a54f4c23997c 12969 biojava4-live_4.2.12+dfsg-3_amd64.buildinfo
 11d7caab86017b16efb3e7e8d3ccc23b208a4a36 1979284 libbiojava4-java-doc_4.2.12+dfsg-3_all.deb
 527566370c0312f827ba6421356dd5442852b418 4668 libbiojava4-java_4.2.12+dfsg-3_all.deb
 98b3762abd0d4bd7e2fe4a1bbacbf80536fae91b 5452056 libbiojava4.0-java_4.2.12+dfsg-3_all.deb
Checksums-Sha256:
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 f105dd805c89b563181ad0d22f449b46b210f34aaf79162707d3bb5976415ccb 15712 biojava4-live_4.2.12+dfsg-3.debian.tar.xz
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Files:
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 b5e5069d902a1bf4aad76c2fdf2c1ef2 15712 java optional biojava4-live_4.2.12+dfsg-3.debian.tar.xz
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 8d30e63e632205dad873f6e94171616d 1979284 doc optional libbiojava4-java-doc_4.2.12+dfsg-3_all.deb
 907a95b12473982bae7a228950b0debf 4668 java optional libbiojava4-java_4.2.12+dfsg-3_all.deb
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Message #20 received at 960654@bugs.debian.org (full text, mbox, reply):

From: Gilles Filippini <pini@debian.org>

To: olivier sallou <olivier.sallou@irisa.fr>, 960654@bugs.debian.org

Subject: Re: [Debian-med-packaging] Bug#960654: src:biojava4-live: Please add support to build against libjson-simple-java >= 3

Date: Fri, 15 May 2020 12:16:42 +0200

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

Hi Olivier,

olivier sallou a écrit le 15/05/2020 à 10:59 :
> Hi,
> thanks for the patch.
> However, if json-simple API/ABI is broken, I think that package should
> be kinda libjson-simple3-java to keep compatibility with existing
> packages using old versions and allow transition of packages to new
> release if needed and possible.

Thanks for your inputs.

I asked the Java packaging team for advice on this matter and they
recommended not to change the package name. I won't keep the deprecated
API around since it was deprecated several years ago and it is not
maintained anymore by upstream.

I intend to proceed with a proper transition via the Release Team. There
are only 6 reverse dependencies. This should be manageable.

> Anyway, gonna add your patch

Thanks,

_g.

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