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

[Andreas Tille]

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.

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
> 
> -- 
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>    `-   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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