[Debian-med-packaging] Bug#768710: Bug#768710: biojava3-live: FTBFS in jessie: dh_install: libbiojava3-java-doc missing files (doc/biojava/*), aborting

[Olivier Sallou]

On 11/18/2014 06:56 AM, Andreas Tille wrote:
> Hi Gregor,
>
> I'm in (semi)-Vac since the weekend and will go on VAC tomorrow.  Feel
> free to NMU (or "team" upload).  It seems Olivier who is usually very
> responsive has some time constraints.
Hi,
I gonna add the patch and upload the fix today.

Thanks for your help

Olivier
>
> Thanks for your help
>
>        Andreas.
>
> On Mon, Nov 17, 2014 at 09:12:30PM +0100, gregor herrmann wrote:
>> Control: tag -1 + confirmed patch
>>
>> On Sun, 09 Nov 2014 08:07:04 +0100, Lucas Nussbaum wrote:
>>
>>> Source: biojava3-live
>>> Version: 3.1.0+dfsg-1
>>> Severity: serious
>>> Tags: jessie sid
>>> User: debian-qa at lists.debian.org
>>> Usertags: qa-ftbfs-20141108 qa-ftbfs
>>> Justification: FTBFS in jessie on amd64
>>  
>>>> javadocs:
>>>>   [javadoc] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ontology/utils/Annotatable.java:77: error: unmappable character for encoding ASCII
>>>>   [javadoc]  * @author  Kalle N???slund (docs)
>>>>   [javadoc]                    ^
>>>>   [javadoc] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ontology/utils/Annotatable.java:77: error: unmappable character for encoding ASCII
>>>>   [javadoc]  * @author  Kalle N???slund (docs)
>>>>   [javadoc]                     ^
>>>>   [javadoc] /«BUILDDIR»/biojava3-live-3.1.0+dfsg/biojavadoc/src/main/java/org/biojava3/ontology/utils/Annotatable.java:77: error: unmappable character for encoding ASCII
>>>>   [javadoc]  * @author  Kalle N???slund (docs)
>>>>   [javadoc]                      ^
>> The package doesn't build in my sid chroot (because of some rdep
>> glitch [0]) but I've tested the attached patch in a jessie chroot.
>>
>> (There are other ways to tell javadoc about the file encodings but
>> that was my first try and it works.)
>>
>>
>>
>> Cheers,
>> gregor
>>
>>
>> [0]
>> Errors were encountered while processing:
>>  icedtea-netx:amd64
>> E: Sub-process /usr/bin/dpkg returned an error code (1)
>> Failed to perform requested operation on package.  Trying to recover:
>> Setting up icedtea-netx:amd64 (1.5.1-1) ...
>> update-alternatives: warning: forcing reinstallation of alternative /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/itweb-settings because link group itweb-settings is broken
>> update-alternatives: warning: not replacing /usr/share/man/man1/itweb-settings.1.gz with a link
>> update-alternatives: warning: forcing reinstallation of alternative /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/itweb-settings because link group itweb-settings is broken
>> update-alternatives: warning: not replacing /usr/share/man/man1/itweb-settings.1.gz with a link
>> update-alternatives: error: alternative path /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/javaws doesn't exist
>> dpkg: error processing package icedtea-netx:amd64 (--configure):
>>  subprocess installed post-installation script returned error exit status 2
>> Errors were encountered while processing:
>>  icedtea-netx:amd64
>>
>> -- 
>>  .''`.  Homepage: http://info.comodo.priv.at/ - OpenPGP key 0xBB3A68018649AA06
>>  : :' : Debian GNU/Linux user, admin, and developer  -  http://www.debian.org/
>>  `. `'  Member of VIBE!AT & SPI, fellow of the Free Software Foundation Europe
>>    `-   NP: The Beatles: Good Morning Good Morning
>> Index: debian/build.xml
>> ===================================================================
>> --- debian/build.xml	(revision 18487)
>> +++ debian/build.xml	(working copy)
>> @@ -61,7 +61,7 @@
>>  	<target name="javadocs">
>>                  <mkdir dir="${docs.dir}"/>
>>  		<mkdir dir="${docs.lib.dir}"/>
>> -		<javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*">
>> +		<javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*" encoding="UTF-8">
>>  			<link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
>>  		</javadoc>
>>  	</target>
>> Index: debian/changelog
>> ===================================================================
>> --- debian/changelog	(revision 18487)
>> +++ debian/changelog	(working copy)
>> @@ -1,3 +1,14 @@
>> +biojava3-live (3.1.0+dfsg-1.1) UNRELEASED; urgency=medium
>> +
>> +  * Non-maintainer upload.
>> +  * Fix "FTBFS in jessie: dh_install: libbiojava3-java-doc missing files
>> +    (doc/biojava/*), aborting":
>> +    debian/build.xml: tell javadoc that source files are encoded as UTF-8;
>> +    otherwise it bails out, and dh_install finds nothing to install.
>> +    (Closes: #768710)
>> +
>> + -- gregor herrmann <gregoa at debian.org>  Mon, 17 Nov 2014 20:36:16 +0100
>> +
>>  biojava3-live (3.1.0+dfsg-1) unstable; urgency=medium
>>  
>>    * New upstream release 
>
>
>
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>

-- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

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