Re: king debian pkg (2.21.120420-2, 2.21.120420+dfsg-1) questions

[Andreas Tille <andreas@fam-tille.de>]

[Since i read from your mail that you would be willing to post to
 the mailing list I simply CC the list that is fine for this topic.]

Hi Michael,

On Tue, Jul 21, 2015 at 07:52:05AM -0400, Michael Prisant wrote:
> Hi Andreas,
> 
> Thanks for your prompt and cordial reply (and continuing to actively
> maintain the packaging King).

You are welcome.  Its a pleasure to serve users promptly. :-)

> I am new to the Debian distribution so I am
> not exactly sure which mailing list to post to!  Perhaps you could steer me
> in the right direction --

The Debian Med project that is working for all biological and medical
free software inside Debian has two mailing list.  One is more developer
oriented and actually is injected as the "Maintainer" of the king
package:

$ apt-cache show king | grep ^Maintainer
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>

While this list would be definitely a proper place for your mail I think
it makes perfectly sense if you would send it to the more user oriented
list - probably you even want to subscribe this list:

   https://lists.debian.org/debian-med/

(it is CCed in this mail)

> these are not really bugs but request for
> changes/additions.

In Debian terminology this kind of feature requests are usually dealt
with in the bug tracking system.  You can select the so called severity
levels "wishlist" or even "minor".  Your requests are totally right at
this place.
 
> I am quite unfamiliar with the deb packaging system (other than invocation
> as a eg user aptitude install etc) So I don't know how to even begin -- ie
> obtain and unpack the current testing source deb package if such a thing
> exist.

Just to let you know:  Its is quite simple by doing

    apt-get source king

:-)

> I think if I might impose on you to help me directly as to where to
> obtain the source deb package and how to unpack it, it would help me make
> more productive contributions to the mailing list.  In particular, I have
> in the past hacked a spec file for preparing a fedora/redhat rpm package
> for private use. So if I could be steered to the corresponding
> files/toolsets in the Deb world I can probably hack and propose changes --
> I think that I would prefer to forward the proposed changes to you and the
> community for patch creation and interaction with the VCS.

That would be perfect.  We have a so called team policy that explains
how to work with the Debian Med VCS:

   https://lists.debian.org/debian-med/

> On the plus
> side, I can probably enlist very experienced King users to help test
> whether its full range of features are working in the packaged versions.

This help would be really appreciated.  So far your response to the king
package is the first to this package at all which was "only" a
precondition to some other package.  I wished we would have way more
responses like this!

> From our point of view the following changes/additions/clarifications would
> be most helpful:
> 
> Installation of probe and suitename:  These are individual executable
> programs included in the developer linux tarball but not in the deb
> package. They are built from C source (separate tarballs) currently
> available on the developer website.  They should probably be packaged
> separately and indeed have standalone use apart from King.  I have been
> able to download and compile both programs on a intel platform -- probe
> required a very simple change to its makefile; suitename seemed to compile
> and run by just using the correct makefile

OK, could you give the exact URL and perhaps provide a script that
downloads these files (if there is no single tarball available).
 
> The plugin directory (and top level King jar):  The plugin subdir in the
> linux tarball from the kinemage website but not in the deb package. It
> contains a number of jar files  I am not really sure whether in your
> packaging process has "remade" the java programs using ant.  I am not even
> sure whether or not the plugins have been packaged in the King jar file
> just on the basis of reading the King documentation.

If you obtain the king source package as shown above you get the tarball
the packaging is based upon.  In the unpackaged tarball you find a file
debian/copyright.  Under Files-Excluded it lists all files that were
excluded from the original download file.  These were basically *.jar
and *.class files since we need to rebuild them, the lib directory with
external jars which are considered as "binary without source" by Debian
and may not be distributed as well as some of the *.pdf files if their
source was missing (also "binary without source").

It would be nice if you could check this and specify what is missing
and what we could provide from the existing files.

> My experience in Java
> coding and build process is minimal.

Mine as well - unfortunately.  Java causes me the most trouble in the
Debian packaging work...

> We are just seeing some missing
> functionality in the deb package (but not the developer linux or binary
> tarball) and speculate that this may be part of the problem.

Lets work together to solve this problem. :-)

> Accelerated hardware support:  This support apparently provided by JOGL is
> another real concern for full use of the packaged program.  The developer
> binary tarball packages its own JRE!

JOGL is a known problem!  You might like to read the log of this bug report:

    https://bugs.debian.org/706922

Quoting for example from there:

  So it may be that graphics rendering is fast enough in openjdk-6 and -7
  that KiNG's use of JOGL is obsolete anyway?

  If the libjogl-java dependency is dropped, king should be installable on
  kfreebsd and then so would qiime.  And libjogl2-java transition can go
  ahead.

I have applied the following patch to the king source:

  https://anonscm.debian.org/viewvc/debian-med/trunk/packages/king/trunk/debian/patches/use_jogl2.patch?view=markup

(see in the end).  I have serious doubt that this works properly (see
above for my Java incompetence) and the total lack of response from king
authors - they seem to have stopped working on king - probably leads to
the fact that king does not run as performant as you might expect.  Any
help to solve this is welcome.
 
> Thanks for being receptive to my private email -- I generally feel quite
> uncomfortable posting straight away to the mailing list and not entirely
> comfortable in general.  Thanks again for your help, patience, and
> packaging of King!

I hope my push to the mailing list is in your interest.  Mails like this
are perfectly welcome there and totally appropriate.  As I said we would
waste the chance of help of others if we would hide behind private
communication.  So lets keep on discussing in public please.

Kind regards

     Andreas.

> On Tue, Jul 21, 2015 at 2:40 AM, Andreas Tille <andreas@fam-tille.de> wrote:
> 
> > Hi Michael,
> >
> > On Mon, Jul 20, 2015 at 04:58:27PM -0400, Michael Prisant wrote:
> > > I hope that I am ot breaching etiquette too much by contacting you
> > directly
> > > by email instead of posting to the mailing list.
> >
> > It is not so much about etiquette but rather wasting the chance of
> > letting more people contribute.  Since I do not know whether you are
> > fine if I switch ro the mailing list I wonder whether you could repost
> > to the list.
> >
> > To give a short answer in advance:  I'm pretty sure that the
> > shortcomings of the packaging are mainly because of my own missing
> > knowledge of king.  I packaged it just as a predependency of qiime and
> > it worked so far.  Your input to enhance the package is really welcome
> > and I would invite you to send patches to make it at best fit for your
> > purpose.  If you do not feel competent for patches we might try to
> > work together in the packaging VCS to get the best possible result.
> >
> > Hope to see you back on the mailing list
> >
> >     Andreas.
> >
> > BTW: You could also use `reportbug king` and repor tevery single
> > issue on its own.  Having things in the bug tracker has additional
> > advantages because things become more visible.
> >
> > > First, thank you for your debian packaging of king -- this is an
> > extremely
> > > important program for biomolecular visualization in our lab and your
> > > packaging of this program has greatly facilitated its use for our lab
> > > workstations with debian/ubuntu/mint distributions
> > >
> > > Second, some questions/requests.
> > >
> > > 1) Nonpackaged components in developer tarball:  Specifically what are
> > the
> > > reasons for omission of the probe, suitename executables and plugin
> > subdir
> > > of jar files included in the developer tarball but not have not the deb
> > > pkg. These components are actually quite important in many of the
> > > documented use examples on the kinemage web site.  How would you
> > recommend
> > > a quick and dirty addition to a repackaged deb for private and/or testing
> > > use?  What would you and the packagers need (from the developers or
> > others)
> > > to include these omitted components as part of the debian package?
> > >
> > > 2) Direct versus shell script wrapper execution of king:  The tarball
> > > version uses a shell script for execution of king.  The script allows for
> > > use of a private version of the jre in the tarball -- not really
> > necessary
> > > anymore from our point of view as it is handled by distribution
> > dependency
> > > on other java packages. But on the other is the option specified by: java
> > > --Xmx1024m -jar king.jar properly handled by direct shell execution of
> > the
> > > jar file?
> > >
> > > 3) Jogl optimizations:  Are these included in the deb packaged version --
> > > not really sure.
> > >
> > > Thanks for your help and deb packaging of King!
> > >
> > > MIchael
> > >
> > > Michael G. Prisant
> > >
> > > PS What I am seeing for (i) deb package contents; (ii) changelog on my
> > > install (MInt 17.2) and (iii) list of kinemage tarball download directory
> > > (with jre removed)
> > >
> > > (i) deb package content
> > >
> > > $ dpkg --search king | grep ^king
> > > king: /usr/share/pixmaps/king.xpm
> > > king: /usr/bin/king
> > > king: /usr/share/java/king.jar
> > > king: /usr/share/menu/king
> > > king: /usr/share/doc/king/format-kinemage.pdf
> > > king: /usr/share/doc-base/king
> > > king: /usr/share/doc/king/extratools-manual.pdf
> > > king: /usr/share/doc/king/copyright
> > > king: /usr/share/doc/king/king-manual.html
> > > king: /usr/share/doc-base/hacking-king
> > > king: /usr/share/doc-base/king-html
> > > king: /usr/share/doc/king
> > > king: /usr/share/doc/king/hacking-king.pdf
> > > king: /usr/share/lintian/overrides/king
> > > king: /usr/share/doc/king/README.html
> > > king: /usr/share/doc/king/kinemage-format.html
> > > king: /usr/share/doc/king/king-manual.pdf
> > > king: /usr/share/man/man1/king.1.gz
> > > king: /usr/share/doc/king/chiropraxis-manual.pdf
> > > king: /usr/share/doc/king/changelog.Debian.gz
> > > king: /usr/share/doc/king/dot_king_prefs.txt.gz
> > > king: /usr/share/java/king-2.21.120420.jar
> > >
> > >
> > > (ii) changelog on my install (MInt 17.2 system)
> > >
> > > $ zcat /usr/share/doc/king/changelog.Debian.gz
> > >
> > > king (2.21.120420-2) unstable; urgency=low
> > >
> > >   [ Niels Thykier ]
> > >   * Fix FTBFS with Java7
> > >     Closes: #678654
> > >
> > >  -- Andreas Tille <tille@debian.org>  Mon, 25 Jun 2012 09:40:44 +0200
> > >
> > > king (2.21.120420-1) unstable; urgency=low
> > >
> > >   * New upstream version
> > >   * debian/get-orig-source: This version includes molikin so the separate
> > >     fetching of this source is not needed any more.
> > >   * debian/README.source:
> > >      - drop remark about missing parts of source code
> > >      - explain handling of ndft files
> > >   * debian/king.{docs,jlibs}: Do not specify version number in
> > destination
> > >     distribution directory explicitly
> > >   * debhelper 9 (control+compat)
> > >   * debian/king.lintian-overrides: Adapted version number of binary
> > >
> > >  -- Andreas Tille <tille@debian.org>  Mon, 21 May 2012 14:45:14 +0200
> > >
> > > ( <Michael.Prisant@gmail.com>iii) list of kinemage tarball download
> > > directory (with jre removed)
> > >
> > > ~/Desktop/linux.king.nojre $ ls -R
> > > .:
> > > doc        king      LICENSE.html  probe        suitename
> > > itext.jar  king.jar  plugins       README.html
> > >
> > > ./doc:
> > > chiropraxis-manual.pdf  extratools-manual.pdf  kinemage-format.html
> > > COPYING.LIB             format-kinemage.pdf    king-manual.pdf
> > > dot_king_prefs.txt      hacking-king.pdf       LICENSE-SUN
> > >
> > > ./plugins:
> > > beanking.jar  chiropraxis.jar  extratools.jar  molikin.jar  rdcvis.jar
> >
> > --
> > http://fam-tille.de
> >

-- 
http://fam-tille.de