Re: How to proceed with EMBOSS packaging (Was: About having EMBOSS 6.4.0 in Wheezy or not.)
Hi Charles,
On Wed, Jun 20, 2012 at 01:34:18PM +0900, Charles Plessy wrote:
>
> For the quilt patches, please revert the switch to format 3.0 (quilt), as the
> upstream patches are not always compatible with this format (but they are
> compatible with quilt). I would really prefer keep the original upstream patch
> instead of reformatting, as it is easier to make sure that we are using the
> latest one.
Reverted.
> > I also do have some additional question how to handle some
> > lintian issues:
> >
> > 1. E: emboss-lib: embedded-library usr/lib/emboss/lib/libepcre.so.7.0.9: pcre3
>
> This is a slightly modified copy of the PCRE library. We can not use the one
> from Debian. I prefer to keep the lintian tag visible so that the issue stays
> in our radar.
I agree that hiding this problem via lintian-overrides probably is not
the best solution. However, on the other hand, the overrides file
provides a nice way to document exactly what you wrote above. So we
might tradeoff between "'hiding' and documenting" and make lintian
reporting it all the time. BTW, in the end of git-buildpackage it ends
with "error" which is possibly caused by the lintian error (I can not
see any other explanation because the packages are builded nicely - I
would love to see this problem vanish.)
> > 2. W: jemboss: codeless-jar usr/share/EMBOSS/jemboss/resources/acdstore.jar
> > as well as
> > W: jemboss: classpath-contains-relative-path usr/share/EMBOSS/jemboss/lib/jemboss.jar: lib/jakarta-regexp-1.2.jar, lib/jalviewApplet.jar
> >
> > This looks suspicious - perhaps I need to contact our Java experts
> > about this.
>
> I can not help for this. But if that warning was already present before, and
> if JEmboss works apparently well, I would recommend to ignore it.
$ lintian jemboss_6.3.1-6_all.deb
W: jemboss: script-with-language-extension usr/bin/runJemboss.csh
W: jemboss: classpath-contains-relative-path usr/share/EMBOSS/jemboss/lib/jemboss.jar: lib/jakarta-regexp-1.2.jar, lib/jalviewApplet.jar
W: jemboss: codeless-jar usr/share/EMBOSS/jemboss/resources/acdstore.jar
W: jemboss: codeless-jar usr/share/EMBOSS/jemboss/resources/resources.jar
W: jemboss: binary-without-manpage usr/bin/runJemboss.csh
W: jemboss: csh-considered-harmful usr/bin/runJemboss.csh
W: jemboss: script-not-executable usr/share/EMBOSS/jemboss/utils/install-jemboss-server.sh
W: jemboss: script-not-executable usr/share/EMBOSS/jemboss/utils/keys.sh
W: jemboss: script-not-executable usr/share/EMBOSS/jemboss/utils/makeFileManagerJNLP.sh
W: jemboss: script-not-executable usr/share/EMBOSS/jemboss/utils/makeJNLP.sh
W: jemboss: script-not-executable usr/share/EMBOSS/jemboss/utils/makeJar.csh
$ lintian jemboss_6.4.0-1_all.deb
W: jemboss: script-with-language-extension usr/bin/runJemboss.csh
W: jemboss: classpath-contains-relative-path usr/share/EMBOSS/jemboss/lib/jemboss.jar: lib/jakarta-regexp-1.2.jar, lib/jalviewApplet.jar
W: jemboss: codeless-jar usr/share/EMBOSS/jemboss/resources/acdstore.jar
W: jemboss: codeless-jar usr/share/EMBOSS/jemboss/resources/resources.jar
W: jemboss: binary-without-manpage usr/bin/runJemboss.csh
W: jemboss: csh-considered-harmful usr/bin/runJemboss.csh
W: jemboss: csh-considered-harmful usr/share/EMBOSS/jemboss/utils/makeJar.csh
So we have definitely less lintian warnings in the later package. However,
I think we are in severe trouble with "binary without source" issues and
I wonder how the EMBOSS yource code yould have passed ftpmaster.
find . -name "*.jar"
./jemboss/lib/xerces.jar
./jemboss/lib/jalviewApplet.jar
./jemboss/lib/axis/jaxrpc.jar
./jemboss/lib/axis/wsdl4j.jar
./jemboss/lib/axis/axis.jar
./jemboss/lib/axis/log4j-1.2.8.jar
./jemboss/lib/axis/commons-logging.jar
./jemboss/lib/axis/saaj.jar
./jemboss/lib/axis/servlet.jar
./jemboss/lib/axis/commons-discovery.jar
./jemboss/lib/axis/axis-ant.jar
./jemboss/lib/jemboss.jar
./jemboss/lib/jakarta-regexp-1.2.jar
./jemboss/lib/mail.jar
./jemboss/lib/activation.jar
./jemboss/lib/JembossPrintAlignment.jar
./jemboss/contrib/jaligner/src/jaligner_src.jar
./jemboss/contrib/jaligner/jaligner.jar
./jemboss/resources/resources.jar
For some of these JAR files we have Debian packages but definitely not
for all of these. So this package is not DFSG free. I would see two
solutions to this:
1. Moving the complete EMBOSS suite to non-free
2. Creating a 6.4.0~dfsg tarball by dropping the complete jemboss
dir and in addition having a jemboss-6.4.0 source package which
should be moved to non-free as a first quick shot. Then we
could sort out the jar dependencies step by step
I'm in favour of the second solution because it would be a shame to have
EMBOSS as a whole in non-free.
> > 3. W: emboss: menu-command-not-in-package usr/share/menu/emboss:8 usr/bin/x-terminal-emulator
> > ...
> >
> > Are you *really* sure that it is necessary to call x-terminal-emulator?
> > My guess is that the reason for this is the way you want the screen
> > to remain via
> > "...;echo press any key to continue"
> > If this assumption is right we probably should add an override because
> > the lintian output is that bloated to possibly oversee some relevant
> > things.
> >
> > On the other hand: Do users really call these tools via menu?
> > Wouldn't it be better to drop the menu support at all and rather
> > teach users using command line?
>
> Let's remove these menu entries for command-line programs.
Done.
Kind regards
Andreas.
--
http://fam-tille.de
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