yet another jpkg dependency for Jalview: jswingreader

Jalview Developers
1

Hi Vincent.

I hope your move went smoothly!

This is a heads up about the fact that I'm very nearly ready to release the next version of Jalview - version 2.7.

Unfortunately, (since it makes your life slightly harder), Jalview 2.7 has a new (and again, slightly obscure) Java library dependency - Jswingreader, which I have been unable to locate amongst the existing jars packaged for debian.

As far as I can tell, packaging should be straightforward. It's released under an Apache license, and compilation requires only one dependency, mail.jar, which provides classes in javax.mail (and com.sun.mail), and is already available on debian.

Would you be able to submit an Intent To Package for jswingreader ? Hopefully, it should be an easy one...
Jim.

2

Hi Jim !

I hope your move went smoothly!

  Rather long, as there was quite a lot of work to do upon arrival,
but we finally have settled down (I got the computer unpacked just a
few days ago), so I'm slowly going to resume my Debian activities,
after I catch up with the most urgent stuff...

This is a heads up about the fact that I'm very nearly ready to release the
next version of Jalview - version 2.7.

  Cool !

Unfortunately, (since it makes your life slightly harder), Jalview 2.7 has a
new (and again, slightly obscure) Java library dependency - Jswingreader,
which I have been unable to locate amongst the existing jars packaged for
debian.

  A bit less cool ;-)...

As far as I can tell, packaging should be straightforward. It's released
under an Apache license, and compilation requires only one dependency,
mail.jar, which provides classes in javax.mail (and com.sun.mail), and is
already available on debian.

  Should be fine, then thanks for checking up.

Would you be able to submit an Intent To Package for jswingreader ?
Hopefully, it should be an easy one...

  Yep, I'll do that as soon as I get my hands on a little Debian time,
hopefully some time next week.

  Cheers !

      Vincent

···

On Thu, Sep 22, 2011 at 4:14 PM, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:

3

Hello everyone,

Unfortunately, (since it makes your life slightly harder), Jalview 2.7
has a new (and again, slightly obscure) Java library dependency -
Jswingreader, which I have been unable to locate amongst the existing
jars packaged for debian.

   [...]

   So, here's a little update on the status of jalview. I have finished a preliminary package for the 2.6.1 version (that doesn't pull in this dependency).

   It looks good to me, but as I haven't had the occasion to use jalview for quite a while now [1], I may be missing important things.

   The package can be downloaded there:

http://people.debian.org/~fourmond/jalview-tempo/jalview_2.6.1.dfsg~almost-1_all.deb

   It needs packages which are not in debian yet, but only in the Java team repository:

deb http://pkg-java.alioth.debian.org unstable/all/

   Please test this package, and tell me what is wrong ;-)...

   For the record, the packaging can be found there:

svn://svn.debian.org/svn/pkg-java/trunk/jalview
http://svn.debian.org/viewsvn/pkg-java/trunk/jalview

   My plans are the following:

   * upload this package to debian almost as-is
   * wait for Jim to provide the source code for vamsas (hint, hint ;-)...)
   * then, move to main and package 2.7 at the same time

   There is only one small detail left (barring problems with the current package): I need a statement from the copyright holders of the vamsas-client.jar file saying that using, copying, distributing and linking against this file are allowed. Just stating it is GPL (I seem to remember it is the case ?) won't be OK, as Debian will not have the sources, and hence will not have the possibility to comply with the GPL requirements.

   Cheers !

  Vincent

[1] When I submitted my ITP of jalview, I was working with enzymes. I then moved to another lab where I worked essentially on inorganic catalysts, for which the need for jalview was inexistant (which partly explains why it took me so long...). Now, I'm back to the previous lab for good, and I'll be using jalview much more often ;-)...

···

On 22/09/11 16:14, Jim Procter wrote:

--
Vincent Fourmond, Doctor in Physics
http://vince-debian.blogspot.com/

4

Thanks so much for getting around to this, Vincent!

http://people.debian.org/~fourmond/jalview-tempo/jalview_2.6.1.dfsg~almost-1_all.deb

    It needs packages which are not in debian yet, but only in the Java
team repository:

deb http://pkg-java.alioth.debian.org unstable/all/

    Please test this package, and tell me what is wrong ;-)...

will do. IIRC the only major flaw that might appear is the behaviour of Jalview when linked with the vanilla castor library, which could result in problems when storing and retrieving jalview and/or VAMSAS projects.

    For the record, the packaging can be found there:

svn://svn.debian.org/svn/pkg-java/trunk/jalview
http://svn.debian.org/viewsvn/pkg-java/trunk/jalview

    My plans are the following:

    * upload this package to debian almost as-is
    * wait for Jim to provide the source code for vamsas (hint, hint ;-)...)
    * then, move to main and package 2.7 at the same time

    There is only one small detail left (barring problems with the
current package): I need a statement from the copyright holders of the
vamsas-client.jar file saying that using, copying, distributing and
linking against this file are allowed. Just stating it is GPL (I seem to
remember it is the case ?) won't be OK, as Debian will not have the
sources, and hence will not have the possibility to comply with the GPL
requirements.

Vamsas is actually LGPL - but that doesn't much difference, particularly in my own mind, since it was my fault that Jalview was released before I released v3 of vamsas. Therefore, the simplest option here is for me to make the source release of vamsas within the next couple of weeks (either directly on sourceforge, or via jalview's own git repo). I just have to do some code formatting (again ... ho hum).

Regarding future steps, if you can at all manage it, it would be really good if you could take a look at Jswingreader dependency as soon as possible. Version 2.7 is significantly more reliable than 2.6.x (in particular, the alignment/structure association stuff was very buggy in last year's version, which is probably quite relevant for your work!), and I'm planning on a more rapid release cycle over the next 6 months (at least 2 releases on 2.7).

Jim.

···

On 30/09/2011 00:26, Vincent Fourmond wrote:

5

Hello,

Please test this package, and tell me what is wrong ;-)...

will do. IIRC the only major flaw that might appear is the behaviour of
Jalview when linked with the vanilla castor library, which could result
in problems when storing and retrieving jalview and/or VAMSAS projects.

   Hmmm - what is wrong with the vanilia castor library ? And what is changed in the one you distribute ? If that's a bug in castor, this may be fixed easily.

For the record, the packaging can be found there:

svn://svn.debian.org/svn/pkg-java/trunk/jalview
http://svn.debian.org/viewsvn/pkg-java/trunk/jalview

My plans are the following:

* upload this package to debian almost as-is
* wait for Jim to provide the source code for vamsas (hint, hint ;-)...)
* then, move to main and package 2.7 at the same time

There is only one small detail left (barring problems with the
current package): I need a statement from the copyright holders of the
vamsas-client.jar file saying that using, copying, distributing and
linking against this file are allowed. Just stating it is GPL (I seem to
remember it is the case ?) won't be OK, as Debian will not have the
sources, and hence will not have the possibility to comply with the GPL
requirements.

Vamsas is actually LGPL - but that doesn't much difference, particularly
in my own mind, since it was my fault that Jalview was released before I
released v3 of vamsas. Therefore, the simplest option here is for me to
make the source release of vamsas within the next couple of weeks
(either directly on sourceforge, or via jalview's own git repo). I just
have to do some code formatting (again ... ho hum).

   If the git repository is publicly accessible, then just hand over the address, and I'll handle the rest. I don't need an official release, just somewhere where I could get the code. Why do you want to perform code formatting ? If you just publish the repository, formatting can wait for an official release.

   I guess packging vamsas and then moving directly to 2.7 and to main is a good idea. I'll have a look at jswingreader.

   Cheers,

  Vincent, confident that we are getting reasonably close now...

···

On 30/09/11 11:16, Jim Procter wrote: