On Tue, 13 Jan 2009, Vincent Fourmond wrote:
About the repository, I think the best is pkg-java, as the skills
required are more on the Java side than on the Biological side - but
please correct me if I'm wrong.
Well, there is no right or wrong - finally we have to store the
packaging stuff in a publicly available repository. Via Vcs tags
we will find the location and the upcoming 'mr' tool will probably
help fetching stuff from different repositories. So I would just
*ask* on pkg-java whether they like the idea to maintain the
package there (yes, Java knowledge on Debian Med is not so wide
spread). If there is no response this is probably not the proper
place. Perhaps Steffen might like to say something more than
'why isn't anybody mentioning pkg-escience ?'
My answer to this question is simple: This group is not vocal
enough and how can I assume that there is some Java competence?
The main problem is that it has loads
of dependencies:
12:40 f...@vncent ~/tmp/jalview find -name '*.jar'
./lib/castor-1.1-cycle-xml.jar
http://www.castor.org/ (not yet packaged) ?
./lib/commons-logging.jar
libcommons-logging-java ?
./lib/commons-discovery.jar
libcommons-discovery-java ?
./lib/wsdl4j.jar
libwsdl4j-java
./lib/regex.jar
libgnu-regexp-java | libjrexx-java libjrexx-java | liboro-java | libregexp-java
?
./lib/saaj.jar
https://saaj.dev.java.net/ (not packaged yet) ?
Seems to have to do something with SOAP, perhaps there are alternative
implementations
like the packaged libaxis-java ???
./lib/jaxrpc.jar
Reading http://de.wikipedia.org/wiki/JAX-RPC the package
libxmlrpc3-common-java
might provide what we need. At least the package contains
/usr/share/java/jaxrpc.jar
./lib/mail.jar
Hmm:
$ apt-file search '/mail.jar'
jspwiki: /usr/share/jspwiki/WEB-INF/lib/mail.jar <- probably not
roxen4: /usr/share/roxen4/java/classes/mail.jar
Perhaps this might be a reasonable solution:
libgnumail-java: /usr/share/java/gnumail.jar
./lib/axis.jar
libaxis-java: /usr/share/java/axis.jar
./lib/vamsas-client.jar
http://www.vamsas.ac.uk/ ?
--> If this is a precondition for JalView Debian Med should
perhaps concentrate on this part. Unfortunately the web
page is a little bit sparse about vamsas itself - but
seems deeply connected with JalView. I will have a look
at the other free part Topali (AstexViewer seems to
be non-free)
./lib/Jmol-11.0.2.jar
We have an inofficial package of an outdated version of jmol:
http://debian.wgdd.de/temp/jmol/
Daniel, any news from Jmol?
./lib/activation.jar
libgnujaf-java: /usr/share/java/activation.jar
./lib/jhall.jar
javahelp2: /usr/share/java/jhall.jar
./lib/xercesImpl.jar
libxerces2-java: /usr/share/java/xercesImpl.jar
./lib/xml-apis.jar
libxalan2-java: /usr/share/java/xml-apis.jar
maven2: /usr/share/maven2/lib/xml-apis.jar
./lib/log4j-1.2.8.jar
liblog4j1.2-java (and others)
./utils/castor-1.1-cycle-codegen-anttask.jar
No idea - perhaps
http://castor.codehaus.org/srcgen-maven-plugin.html
ist helpful. While having no idea what maven2 might be at all I have read
this keyword on the Debian-Java list recently quite frequently.
./utils/jhindexer.jar
No idea.
./utils/castor-1.1-cycle-codegen.jar
see castor above
./utils/wsdl4j.jar
libwsdl4j-java
./utils/proguard.jar
proguard: /usr/share/java/proguard.jar
./utils/roxes-ant-tasks-1.2-2004-01-30.jar
./utils/jalopy/lib/oro-2.0.6.jar
./utils/jalopy/lib/sax-2.0.1.jar
./utils/jalopy/lib/jalopy-ant-0.6.2.jar
./utils/jalopy/lib/log4j-1.2.6.jar
./utils/jalopy/lib/jaxp-1.2.jar
./utils/jalopy/lib/aelfred-1.2.jar
./utils/jalopy/lib/jalopy-1.0b11.jar
./utils/jalopy/lib/jdom-1.0b8.jar
./utils/jhall.jar
./utils/axis-ant.jar
I'll start to sort it out this week-end. You can join in too,s
Just joined. ;-)
for
instance, to see which of those are really necessary, file ITP, block
this bug by the ITPs (CCing this bug), and package them (and their
dependencies...). I guess the best would be to use this bug
mailing-list for coordination. I think it is possible we can get rid
of the dependencies from the utils/ directory...
Lets see. I'm occupied with other tasks for this afternoon, but may
be I might provide some more info later.
Kind regards
Andreas.
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http://fam-tille.de
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