[Debian-med-packaging] Bug#963430: Any volunteer to spent some time on the new version of artemis (Was: Bug#963430: artemis: FTBFS: /bin/sh: 1: /usr/share/java/j2ssh-core.jar: Permission denied)

[Andreas Tille]

Hi,

we are lagging several upstream versions behind due to new dependencies
and other build issues.  I wonder whether somebody might volunteer to
update artemis.  It would be great to get the latest version at least
before the freeze starts.  While this takes some time I guess having
latest artemis is time consuming as well - thus I'm asking here.

Any takers?  Despite I'm the only remaining Uploader this exceeds my
current time capacity.

Kind regards

      Andreas.

On Sun, Jun 21, 2020 at 10:26:05PM +0200, Lucas Nussbaum wrote:
> Source: artemis
> Version: 17.0.1+dfsg-2
> Severity: serious
> Justification: FTBFS on amd64
> Tags: bullseye sid ftbfs
> Usertags: ftbfs-20200620 ftbfs-bullseye
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build
> on amd64.
> 
> Relevant part (hopefully):
> >  debian/rules build
> > dh build --with javahelper
> >    dh_update_autotools_config
> >    dh_autoreconf
> >    dh_auto_configure
> >    jh_linkjars
> >    debian/rules override_dh_auto_build
> > make[1]: Entering directory '/<<PKGBUILDDIR>>'
> > dh_auto_build -- jar
> > 	make -j4 "INSTALL=install --strip-program=true" jar
> > make[2]: Entering directory '/<<PKGBUILDDIR>>'
> > CLASSPATH=/usr/share/java/biojava.jar /usr/share/java/j2ssh-core.jar /usr/share/java/ibatis.jar /usr/share/java/log4j-1.2.jar /usr/share/java/postgresql-jdbc3.jar /usr/share/java/picard.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-net.jar /usr/share/java/commons-lang3.jar /usr/share/java/batik-all.jar /usr/share/java/batik-awt-util.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/batik-xml.jar /usr/share/EMBOSS/jemboss/lib/jemboss.jar /<<PKGBUILDDIR>>: javac -source 1.8 -target 1.8   uk/ac/sanger/artemis/Action.java
> > CLASSPATH=/usr/share/java/biojava.jar /usr/share/java/j2ssh-core.jar /usr/share/java/ibatis.jar /usr/share/java/log4j-1.2.jar /usr/share/java/postgresql-jdbc3.jar /usr/share/java/picard.jar /usr/share/java/htsjdk.jar /usr/share/java/commons-net.jar /usr/share/java/commons-lang3.jar /usr/share/java/batik-all.jar /usr/share/java/batik-awt-util.jar /usr/share/java/batik-dom.jar /usr/share/java/batik-ext.jar /usr/share/java/batik-svggen.jar /usr/share/java/batik-util.jar /usr/share/java/batik-xml.jar /usr/share/EMBOSS/jemboss/lib/jemboss.jar /<<PKGBUILDDIR>>: javac -source 1.8 -target 1.8   uk/ac/sanger/artemis/ActionController.java
> > /bin/sh: 1: /usr/share/java/j2ssh-core.jar: Permission denied
> > make[2]: *** [Makefile:48: uk/ac/sanger/artemis/Action.class] Error 126
> 
> The full build log is available from:
>    http://qa-logs.debian.net/2020/06/20/artemis_17.0.1+dfsg-2_unstable.log
> 
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
> 
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
> 
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