Debian Bug report logs - #875334
FTBFS with Java 9: javax.xml.bind

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

From: Chris West <debian@fau.xxx>

To: submit@bugs.debian.org

Subject: FTBFS with Java 9: javax.xml.bind

Date: Sun, 10 Sep 2017 19:52:59 +0100

Source: biojava4-live
Version: 4.2.7+dfsg
Severity: normal
User: debian-java@lists.debian.org
Usertags: default-java9

This package fails to build with default-jdk pointing to openjdk-9-jdk.
Please fix it, so that we can start the transition to Java 9.
The wiki has some common problems and their solutions:
https://wiki.debian.org/Java/Java9Pitfalls

javax.xml.bind has been removed from the default classpath. Please see the
section on the wiki for further details, and hopefully eventually a
solution.

Build log:

    [mkdir] Created dir: /build/biojava4-live-4.2.7+dfsg/buildtest/biojava4-aa-prop/classes
    [javac] /build/biojava4-live-4.2.7+dfsg/biojava-aa-prop/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
    [javac] Compiling 9 source files to /build/biojava4-live-4.2.7+dfsg/buildtest/biojava4-aa-prop/classes
    [javac] /build/biojava4-live-4.2.7+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java:29: error: package javax.xml.bind is not visible
    [javac] import javax.xml.bind.JAXBException;
    [javac]                 ^
    [javac]   (package javax.xml.bind is declared in module java.xml.bind, which is not in the module graph)
    [javac] /build/biojava4-live-4.2.7+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java:47: error: cannot find symbol
    [javac] 	public void shortExample2() throws FileNotFoundException, JAXBException{
    [javac] 	                                                          ^


Cheers,
Chris.

Message #10 received at 875334@bugs.debian.org (full text, mbox, reply):

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

To: Chris West <debian@fau.xxx>, 875334@bugs.debian.org

Subject: Re: [Debian-med-packaging] Bug#875334: FTBFS with Java 9: javax.xml.bind

Date: Mon, 11 Sep 2017 10:26:48 +0200

Needs inclusion of java module java.se.ee in javac commands.


Only tests are impacted (and runtime but as it is a library it is user
responsability to add runtime modules)


On 09/10/2017 08:52 PM, Chris West wrote:
> Source: biojava4-live
> Version: 4.2.7+dfsg
> Severity: normal
> User: debian-java@lists.debian.org
> Usertags: default-java9
>
> This package fails to build with default-jdk pointing to openjdk-9-jdk.
> Please fix it, so that we can start the transition to Java 9.
> The wiki has some common problems and their solutions:
> https://wiki.debian.org/Java/Java9Pitfalls
>
> javax.xml.bind has been removed from the default classpath. Please see the
> section on the wiki for further details, and hopefully eventually a
> solution.
>
> Build log:
>
>     [mkdir] Created dir: /build/biojava4-live-4.2.7+dfsg/buildtest/biojava4-aa-prop/classes
>     [javac] /build/biojava4-live-4.2.7+dfsg/biojava-aa-prop/build.xml:86: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
>     [javac] Compiling 9 source files to /build/biojava4-live-4.2.7+dfsg/buildtest/biojava4-aa-prop/classes
>     [javac] /build/biojava4-live-4.2.7+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java:29: error: package javax.xml.bind is not visible
>     [javac] import javax.xml.bind.JAXBException;
>     [javac]                 ^
>     [javac]   (package javax.xml.bind is declared in module java.xml.bind, which is not in the module graph)
>     [javac] /build/biojava4-live-4.2.7+dfsg/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java:47: error: cannot find symbol
>     [javac] 	public void shortExample2() throws FileNotFoundException, JAXBException{
>     [javac] 	                                                          ^
>
>
> Cheers,
> Chris.
>
> _______________________________________________
> Debian-med-packaging mailing list
> Debian-med-packaging@lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 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 875334-close@bugs.debian.org (full text, mbox, reply):

From: Olivier Sallou <osallou@debian.org>

To: 875334-close@bugs.debian.org

Subject: Bug#875334: fixed in biojava4-live 4.2.7+dfsg-2

Date: Mon, 11 Sep 2017 11:49:20 +0000

Source: biojava4-live
Source-Version: 4.2.7+dfsg-2

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 875334@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)


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

Format: 1.8
Date: Mon, 11 Sep 2017 07:45:17 +0000
Source: biojava4-live
Binary: libbiojava4.0-java libbiojava4-java libbiojava4-java-doc
Architecture: source all
Version: 4.2.7+dfsg-2
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: 875334
Changes:
 biojava4-live (4.2.7+dfsg-2) unstable; urgency=medium
 .
   * Fix openjdk 1.8/1.9 compilation/testing (Closes: #875334).
   * d/control: switch policy to 4.0.0
Checksums-Sha1:
 d74dd23c5bfb6d4f00f533f2347618b5cc1123e4 2643 biojava4-live_4.2.7+dfsg-2.dsc
 18573ddca61820d66ca36a91ea8e0b9b58202a08 14448 biojava4-live_4.2.7+dfsg-2.debian.tar.xz
 6898e4bb227b90c4ecf19518dbba5e22f96ca236 11424 biojava4-live_4.2.7+dfsg-2_amd64.buildinfo
 41d0b546bb8c4e56e941d157bd4c1fcb037e3596 2305334 libbiojava4-java-doc_4.2.7+dfsg-2_all.deb
 7ea822659e5e839a6b5bd457470f772f80d1ddb3 3758 libbiojava4-java_4.2.7+dfsg-2_all.deb
 6f04934322fa07eb642f83a2c98fc5e600bd7757 5448640 libbiojava4.0-java_4.2.7+dfsg-2_all.deb
Checksums-Sha256:
 16153453d7d8b41bec7056e882ec0c02f11ae0bf3b6a1c91681a52f45cd41310 2643 biojava4-live_4.2.7+dfsg-2.dsc
 3861bf05b30a59582214bfefd7f68972765fe4ee3ed460bdc3b6c309dbdb6542 14448 biojava4-live_4.2.7+dfsg-2.debian.tar.xz
 91257f834bc5c06f04c94eeb07af469ccdc051accdfcfcf21ee50a9b15adccca 11424 biojava4-live_4.2.7+dfsg-2_amd64.buildinfo
 b1ec03c940294ad12ab48b8ee47b69abe546eeb8ae7ceb5b050f1dc0305a37f2 2305334 libbiojava4-java-doc_4.2.7+dfsg-2_all.deb
 a93124a8a4463cf77205f4cf17917897cc04df7428730d7c642c46f3b8470d4c 3758 libbiojava4-java_4.2.7+dfsg-2_all.deb
 da0f5c77c8ae7e1c283ee6250fe28b2973a5408c84161e9e17f0eedf2729d048 5448640 libbiojava4.0-java_4.2.7+dfsg-2_all.deb
Files:
 adb6e888bb83a5734ba49540138e3e49 2643 java optional biojava4-live_4.2.7+dfsg-2.dsc
 8648815e1cbc91d390175a35ba414283 14448 java optional biojava4-live_4.2.7+dfsg-2.debian.tar.xz
 f37a6333719fd471293cdf76f8ddf2bb 11424 java optional biojava4-live_4.2.7+dfsg-2_amd64.buildinfo
 57f99d0ef2e1caba6a52d7ea88440352 2305334 doc optional libbiojava4-java-doc_4.2.7+dfsg-2_all.deb
 bb4502ef08cc0a27d008c6688b29b8c0 3758 java optional libbiojava4-java_4.2.7+dfsg-2_all.deb
 514df8af76461fd88ad61a752a5fa2cd 5448640 java optional libbiojava4.0-java_4.2.7+dfsg-2_all.deb

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