Hi Andreas, and other Debian developers,
I saw that CDK 2.3 is now in unstable! Great news! Many thanks for your
time during the BioHackathon, and others for their effort to make this
happen. Very much appreciated.
Egon
On Tue, Nov 19, 2019 at 6:40 PM Andreas Tille wrote:
> Hi,
>
>
Awesome! Plz let me know if I can answer any questions around dependencies,
or impact of missing dependencies.
Egon
On Wed, Nov 20, 2019 at 9:35 PM Andrius Merkys wrote:
> Hi Andreas,
>
> On Wed, 20 Nov 2019, 22:19 Andreas Tille, wrote:
>
>> I have no idea what restrictions
Hi all,
are there plans within Debian for the upcoming Java security changes,
which make many unsigned and self-signed applets blocked somewhere in
2014?
Are there options for Debian to become a trusted signer of applets?
Egon
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Hi Niels, Onkar,
On Sun, Aug 5, 2012 at 10:02 AM, Egon Willighagen
wrote:
> I will have a look the JavaDoc cleaning thing now...
I quickly figured out that that would take me more effort, to properly
hook that in the Debian build systems...
I did have a look at compiling 1.4.12 which resul
h some 10 other Debian
developers for a lunch.
We briefly spoke about the CDK package, and I'm happy to see that
Cinfony 1.1 is in testing, which means that libcdk-java should be
upgraded without much trouble... I will have a look the JavaDoc
cleaning thing now...
Egon
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encies will not pose an issue
> then. :)
Except that the python-cinfony package needs updating too, and that
may imply having to updated rdkit and openbabel as well... (nothing
wrong with that, of course! :)
Egon
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nuine reverse dependency.
Stupid of me to forget about Cinfony!
Cinfony 1.1 should work fine with CDK 1.4.x:
http://baoilleach.blogspot.com/2011/12/cinfony-11-released.html
That post tells about a compile against 1.4.5, but as said, within
1.4.x there are no API changes (or very minor ones).
ink of any... I cannot find right now where to find that rev
dep info...
Egon
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Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog:
On Wed, Jun 1, 2011 at 5:31 PM, Egon Willighagen
wrote:
> On Wed, Jun 1, 2011 at 8:32 AM, Onkar Shinde wrote:
>> Latest changelog for reference.
>> cdk (1:1.2.10-1) unstable; urgency=low
>> - Remove modules which do not contain any class files when built - inchi,
&g
st one needs
jni-inchi packaged.
I'll check later if these have RFPs yet.
Egon
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Institutet för miljömedicin
Karolinska Institutet (http://ki.se/imm)
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Blog
which branch to use to generate git patches and I
> will send them. Trunk or any 1.2.x specific branch?
cdk-1.2.x branch.
https://github.com/cdk/cdk/tree/cdk-1.2.x
Egon
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Karolinska Institutet (http://ki.se/imm)
Home
On Mon, Apr 18, 2011 at 10:26 AM, Onkar Shinde wrote:
> On Mon, Apr 18, 2011 at 12:39 PM, Egon Willighagen
> wrote:
>> Can you please file patch 21 and 22 'upstream'? Preferably as Git
>> patches, but the raw Debian patches are fine with me too:
>>
>>
will need to check them first...)
Moreover, 1.2.8 has been release, which should be simple to update
for. It has only bug fixes, but important ones.
Egon
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Karolinska Institutet (http://ki.se/imm)
Homepage: http://egonw.gi
Hi all,
On Tue, Feb 16, 2010 at 11:13 AM, Egon Willighagen
wrote:
> On Tue, Feb 16, 2010 at 11:47 AM, Niels Thykier wrote:
>> We would need to package all of its dependencies, so a list of
>> bioclipse's dependencies would be nice. Bonus if you go further and
>>
someone looked at it in the past, and not sure how much API
changes there are compared to 0.6...
Any advice?
Egon
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Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
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PubList: http://
i-bin/bugzilla/show_bug.cgi?id=1871
Egon
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.g. the MySQL driver, are you?),
and a adapter-jar?
> This has been one of the most time-consuming
> tasks with getting eclipse done - hardly any of eclipse's dependencies
> had OSGi metadata.
So, metadata must be injected into the third party libs too? So, for
the elixis exampl
ve that this is a bug on jabref package.
Quite so.
The suggested alternative was the buggy Debian .deb or nothing... then
I rather see peope use the JabRef.jar instead...
What is the bug number? I'd like to cc on it...
Egon
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Proteochemometrics / Bioclipse Gr
I have been out of the Debian
Java loop for quite a long time now, and cc-ed the list, hoping they
can provide further information.
Kind regards,
Egon Willighagen
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Homepage: http://egonw.git
ving solr there would suggest that Debian packaging of solr
> has halted. I would prefer Vincent's suggestion. What do others think?
Removing from a VCS does not really delete it, and it the best way to
ensure people do not accidentally make additional commits.
Egon
--
Pos
you cope with that? Use a patched version of sun-java6-jdk
> installed in a local archive?
See Daniel's blog:
http://www.wgdd.de/?p=36
Egon
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ath.org/mediation/FreeSwingTestApps
or if it's only AWT:
http://developer.classpath.org/mediation/FreeAWTTestApps
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mple, it is reasonable to expect IT to be ported
to the same platforms as gcj currently has? What are the plans of the
gcj (/Classpath) community with respect to coverage of the J5/6
language? That is, what advantages does IT have over gcj (and vice
versa), now and in, say, 6 months?
> tested, few of them were working properly in Etch with gcjappletviewer.
> > :(
Petter, please add entries here:
http://developer.classpath.org/mediation/Applets
Thanx,
Egon
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with a subjec
f you explain how
they can reproduce the problem yourself.
BTW, I'll try to reproduce your tutorial next weekend.
Egon
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GPG: 1024D/D6336BA6
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xamples ../jri/run
> > ../inst/jri/)
>
> This looks like a change without a difference.
:)
I reverted that one, since removing the $(JFLAGS) made the examples
compilable, but put the example dir at the wrong position :)
Egon
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1:52:30.0 +0200
+++ rJava/src/Makevars.in 2006-10-22 12:39:36.0 +0200
@@ -14,5 +14,5 @@
jri:
$(MAKE) -C ../jri/
[EMAIL PROTECTED] -p ../inst/jri
-
@(cp -r ../jri/src/JRI.jar ../jri/*jri.* ../jri/run ../jri/examples
../inst/jri/)
+
@(cp -r ../jri/
cal(now)) :
unable to load shared
library '/usr/local/lib/R/site-library/rJava/libs/rJava.so':
libjvm.so: cannot open shared object file: No such file or directory
Error in library(rJava) : .First.lib failed for 'rJava'
Not sure what else I can/should try now. Ideas?
Egon
On Saturday 01 November 2003 20:08, Etienne Gagnon wrote:
> E.L. Willighagen (Egon) wrote:
> > The big question seems to come done to:
> >
> > "What part of Java is library and what part is language?"
> >
> > It seems to me that at least the syntax *and*
Thus as long as you don't use anything else then java.lang classes, you can
use kaffe to run *any* Java byte code, independent which license...
(If agreed on the fact that GPL does not cover running software... which is
mostly agreed on... e.g. running MS Office in Linux)
Egon
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implemented but it might just do what you need...
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an use a sponsor...
> > I haven't discussed the question of whether it is correct for a program
> > that can be compiled with free software but not run with free software
> > to go into main.
>
> It is not.
Agreed. BTW, the debian build deamons won't be able to make it anyway... which
is required to enter main, or not?
Egon
an use a sponsor...
> > I haven't discussed the question of whether it is correct for a program
> > that can be compiled with free software but not run with free software
> > to go into main.
>
> It is not.
Agreed. BTW, the debian build deamons won't be able to make
On Thursday 07 August 2003 12:54, Paolo Ariano wrote:
> Il gio, 2003-08-07 alle 11:43, Egon Willighagen ha scritto:
> > I would suggest to apt-get source of some Java application and check how
> > that does it... e.g. Jmol on mentors.debian.net, which is not in Debian
> > itse
binary Debian packages for the kdelibs, kdebase, etc... ?
kind regards,
Egon
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On Friday 08 August 2003 15:31, Matt Zimmerman wrote:
> On Fri, Aug 08, 2003 at 03:26:34PM +0200, Egon Willighagen wrote:
> > Right... and I understood from Hein's email that the sablevm package
> > does this upon upgrade...
> >
> > Is that a bug?
>
> If sabl
On Friday 08 August 2003 15:15, Matt Zimmerman wrote:
> On Fri, Aug 08, 2003 at 02:54:56PM +0200, Egon Willighagen wrote:
> > On Friday 08 August 2003 14:26, Hein Meling wrote:
> > > Every time I do an update, and there is a new version of sablevm (I
> > > think), the
2sdk1.4 as the default.
>
> Anyone know why this keeps happening?
The auto mode selects a JVM based on highest priority...
The solution seems to be to just increase the priority of the j2sdk1.4
such that it is higher than that of the SableVM...
Egon
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binary Debian packages for the kdelibs, kdebase, etc... ?
kind regards,
Egon
On Friday 08 August 2003 15:31, Matt Zimmerman wrote:
> On Fri, Aug 08, 2003 at 03:26:34PM +0200, Egon Willighagen wrote:
> > Right... and I understood from Hein's email that the sablevm package
> > does this upon upgrade...
> >
> > Is that a bug?
>
> If sabl
On Friday 08 August 2003 15:15, Matt Zimmerman wrote:
> On Fri, Aug 08, 2003 at 02:54:56PM +0200, Egon Willighagen wrote:
> > On Friday 08 August 2003 14:26, Hein Meling wrote:
> > > Every time I do an update, and there is a new version of sablevm (I
> > > think), the
2sdk1.4 as the default.
>
> Anyone know why this keeps happening?
The auto mode selects a JVM based on highest priority...
The solution seems to be to just increase the priority of the j2sdk1.4
such that it is higher than that of the SableVM...
Egon
On Thursday 07 August 2003 12:54, Paolo Ariano wrote:
> Il gio, 2003-08-07 alle 11:43, Egon Willighagen ha scritto:
> > I would suggest to apt-get source of some Java application and check how
> > that does it... e.g. Jmol on mentors.debian.net, which is not in Debian
> > itse
..
To all, what package would be best to download as an example of how to
package Java applications as Debian package?
Egon
..
To all, what package would be best to download as an example of how to
package Java applications as Debian package?
Egon
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ready exists!) instead of autoconf/ automake/ make?
It does: http://ant.apache.org/manual/CoreTasks/javac.html
Supported are these compilers in the javac task (1.5.3 at least):
classic, modern, jikes, jvc, kjc, gcj, and sj.
Egon
ready exists!) instead of autoconf/ automake/ make?
It does: http://ant.apache.org/manual/CoreTasks/javac.html
Supported are these compilers in the javac task (1.5.3 at least):
classic, modern, jikes, jvc, kjc, gcj, and sj.
Egon
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r packages into main than
> > discussing this any longer.
>
> Sorry not sooner reply. I maint junit and it's my responsibility.
Egon
r packages into main than
> > discussing this any longer.
>
> Sorry not sooner reply. I maint junit and it's my responsibility.
Egon
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d, is that it is not clearly used. However, I would like to mention
that I would prioritize the similarity with non-Java libraries higher...
Egon
d, is that it is not clearly used. However, I would like to mention
that I would prioritize the similarity with non-Java libraries higher...
Egon
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ding the Debian package to:
http://mentors.debian.net/
which is organized by Debian mentors and contains packages for which
sponsors are searched...
The website features a full apt-get-able resource...
Egon
ding the Debian package to:
http://mentors.debian.net/
which is organized by Debian mentors and contains packages for which
sponsors are searched...
The website features a full apt-get-able resource...
Egon
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a shot at
> > integrating it into kaffe, which has an Xlib based AWT, if the license
> > permits it (kaffe is GPL).
>
> What about SWT? I've used it under both gij and from gcj-compiled code for
> some simple tests.
Where are those? Are the online, or even packaged?
Egon
o into /usr/share/doc/...
BTW, is creating two packages really as easy as suggested, i.e. just making a
second subdir in the created /debian dir structure?
Egon
drop me a mail. Thank you very much!
See the Debian GNU/Linux Java FAQ. The j2re1.4 package is the Debian package
from Blackdown, and you can get that at blackdown.org.
regards,
Egon
Right. I do a similar things for Jmol, see:
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/jmol/Jmol/packaging/debian/Makefile?rev=1.11&content-type=text/vnd.viewcvs-markup
with the setup target.
Egon
there
are *no* changes to record.
> There could still be packaging-only changes in the future, which would
> only increase the revision number (omitted for the main releases).
Ofcourse.
kind regards,
Egon
Hi all,
does Debian have a Java library to make animated images?
Any ideas are much appreciated.
regards,
Egon
Debian and Java"
> Then "debianjava.pdf"
>
> You may have to make some adjustments.
> Feedback welcomed.
Would you mind of I would copy parts of it into the Debian GNU/Linux Java
Guide? (What license is the PDF?)
Egon
be satisfied.
That's an interesting one... How would one do that?
Wouldn't it be easier to have an installer package then? Like there is
for Sun's JDK 1.1?
kind regards,
Egon
the version in CVS.
Egon
On Thursday 10 April 2003 04:53, Michael Hackett wrote:
> On Wed, 9 Apr 2003 08:50:15 +0200
> Egon Willighagen <[EMAIL PROTECTED]> wrote:
> > - or maybe even a CD image as an add on for Debian (including the
> > Blackdown stuff)
> > - a Build-Java-software-on-Debian-
On Wednesday 09 April 2003 22:01, Mark Howard wrote:
> On Wed, 2003-04-09 at 07:50, Egon Willighagen wrote:
> > Are there other people interested in setting up a Debian/Alioth project
> > that should centralize the various Debian/Java efforts? This project
> > would involve
ting FDL documentation)
- a project to determine/write down what is 'missing' in this Debian/Java
(leading to implementations solving those ommissions)
- a repository of java debian packages that are not yet in Debian
Ideas? Suggestions?
Personally, I like the CD image with a Java Addon for Debian most.
Egon
like one more to be able
> to apply it.
Five-ed (excluding posting not send to this list ;)
Egon
te-alternatives --config java' (etc)
to create /usr/bin/java (etc)...
This mechanism thus allows for other JVM's to be installed as well,
while keeping /usr/bin/java general...
Egon
like one more to be able
> to apply it.
Five-ed (excluding posting not send to this list ;)
Egon
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te-alternatives --config java' (etc)
to create /usr/bin/java (etc)...
This mechanism thus allows for other JVM's to be installed as well,
while keeping /usr/bin/java general...
Egon
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e appropriate to have a separate package for those
> intending to extend ant as opposed to use it as-is.
But anyway, what about libx packages? Those are libraries too. Where is the
API documentation of those packages? It seems exactly like that...
Egon
e appropriate to have a separate package for those
> intending to extend ant as opposed to use it as-is.
But anyway, what about libx packages? Those are libraries too. Where is the
API documentation of those packages? It seems exactly like that...
Egon
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't want to remove j2sdk1.3 as it removes a load of other packages.
Yes, in general I would like to have them both installed too... for testing
compilation etc...
I guess they should not conflict, and use the alternatives method, right?
regards,
Egon
't want to remove j2sdk1.3 as it removes a load of other packages.
Yes, in general I would like to have them both installed too... for testing
compilation etc...
I guess they should not conflict, and use the alternatives method, right?
regards,
Egon
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On Sunday 20 October 2002 11:37, Arash Bijanzadeh wrote:
> On Sunday 20 October 2002 12:48, Egon Willighagen wrote:
> > On Sunday 20 October 2002 08:38, Arash Bijanzadeh wrote:
> > > Can I use kdevelop for my java project? Any one have experience with
> > > this?
>
On Sunday 20 October 2002 08:38, Arash Bijanzadeh wrote:
> Can I use kdevelop for my java project? Any one have experience with this?
Yes, but you cannot make KDE/Java programs at this moment, because the
kdebindings for Java are not yet available for Debian...
Egon
point to some info on how to get them?
Looking forward to any ideas/suggestions/etc,
kind regards,
Egon Willighagen
PS. If I get it to run, I'll write an article about KDE/Java development with
Gideon in LinuxFocus. It is really great software!
point to some info on how to get them?
Looking forward to any ideas/suggestions/etc,
kind regards,
Egon Willighagen
PS. If I get it to run, I'll write an article about KDE/Java development with
Gideon in LinuxFocus. It is really great software!
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look at the source code of the JCPCDK module
on SourceForge:
http://sourceforge.net/cvs/?group_id=10084
Look at the JChemPaint.java on how to load the resources, and build.xml (Ant)
on how we add them to the jar...
regards,
Egon
look at the source code of the JCPCDK module
on SourceForge:
http://sourceforge.net/cvs/?group_id=10084
Look at the JChemPaint.java on how to load the resources, and build.xml (Ant)
on how we add them to the jar...
regards,
Egon
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this could that work?
Then why not have a Debian GNU/Linux with just source packages (actually,
there is such a project i think)? Makes it a lot easier for us too...
Anyway, I tend to disagree... You want a binary distro, so you might question
if Emacs is doing the right think...
Egon
--
that this could that work?
Then why not have a Debian GNU/Linux with just source packages (actually,
there is such a project i think)? Makes it a lot easier for us too...
Anyway, I tend to disagree... You want a binary distro, so you might question
if Emacs is doing the right think...
Egon
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like stuff compiled from C.
Thus libfoo and not libfoo-gcj-java...
However, if libfoo is taken already you have trouble; then you would have a
name clash and libfoo-gcj might not be too bad...
Egon
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On Sunday 12 May 2002 21:32, Ola Lundqvist wrote:
> On Sun, May 12, 2002 at 09:13:35PM +0200, Egon Willighagen wrote:
> > On Sunday 12 May 2002 21:11, Egon Willighagen wrote:
> > > Only if your binary package can run with free virtual machines (like
> > > kaffe, libgcj,
On Sunday 12 May 2002 21:11, Egon Willighagen wrote:
> Only if your binary package can run with free virtual machines (like kaffe,
> libgcj, ORP and KissMe), it may go into main. Otherwise, it must go into
> non-free, or in contrib if your package itself is free.
Better:
Only if yo
own's JVM to kaffe? Do I need to
recompile or can kaffe run classes?
And the same for gcj? Is there an easy way to port a Ant based compilation
to some Makefile like stuff for compiling with gcj? Is there a good tutorial
on it somewhere?
Egon
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uld be like stuff compiled from C.
Thus libfoo and not libfoo-gcj-java...
However, if libfoo is taken already you have trouble; then you would have a
name clash and libfoo-gcj might not be too bad...
Egon
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On Sunday 12 May 2002 21:32, Ola Lundqvist wrote:
> On Sun, May 12, 2002 at 09:13:35PM +0200, Egon Willighagen wrote:
> > On Sunday 12 May 2002 21:11, Egon Willighagen wrote:
> > > Only if your binary package can run with free virtual machines (like
> > > kaffe, libgcj,
On Sunday 12 May 2002 21:11, Egon Willighagen wrote:
> Only if your binary package can run with free virtual machines (like kaffe,
> libgcj, ORP and KissMe), it may go into main. Otherwise, it must go into
> non-free, or in contrib if your package itself is free.
Better:
Only if yo
ckdown's JVM to kaffe? Do I need to
recompile or can kaffe run classes?
And the same for gcj? Is there an easy way to port a Ant based compilation
to some Makefile like stuff for compiling with gcj? Is there a good tutorial
on it somewhere?
Egon
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t about a one/two years ago...
and am rather interested in tested your packages... I have apache installed as
well...
Egon
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t about a one/two years ago...
and am rather interested in tested your packages... I have apache installed as
well...
Egon
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Hi all,
to get J2SDK for linux running on my machine, i had to make a symbolic link:
/usr/lib# ln -s libstdc++-libc6.1-2.so.3 libstdc++-libc6.1-1.so.2
Is there a more elegant way?
regards,
Egon
Hi all,
to get J2SDK for linux running on my machine, i had to make a symbolic link:
/usr/lib# ln -s libstdc++-libc6.1-2.so.3 libstdc++-libc6.1-1.so.2
Is there a more elegant way?
regards,
Egon
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; also on the cc (or just keep it on the list unless the experts
> say they are bored with it.)
Did you have a look at the Java Policy? It is available in the
java-common package... Or, alternatively, from
http://people.debian.org/~bortz//Java/policy.html
To the rest on this list: is this the latest up-to-date version?
Egon
> also on the cc (or just keep it on the list unless the experts
> say they are bored with it.)
Did you have a look at the Java Policy? It is available in the
java-common package... Or, alternatively, from
http://people.debian.org/~bortz//Java/policy.html
To the rest on this list:
> On Tue, Oct 23, 2001 at 11:04:47AM +0200, Egon Willighagen wrote:
> > Is it "legal" to have (I am thinking Java here):
> >
> > - A GPL-ed program that uses
> > a LPGL-ed libraries that uses
> > a "Apache Public License"-ed library
> &
this a legal argument?
Please enlighten me.
kind regards,
Egon
1. http://cdk.sf.net/
2. http://packages.debian.org/unstable/libs/libxerces-java.html
3. http://packages.debian.org/unstable/libs/liblog4j.html
this a legal argument?
Please enlighten me.
kind regards,
Egon
1. http://cdk.sf.net/
2. http://packages.debian.org/unstable/libs/libxerces-java.html
3. http://packages.debian.org/unstable/libs/liblog4j.html
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k.sf.net), and use GCJ to compile it... This should stress
test both the CDK libs *and* the (Debian) Java Policy...
> I would be *very* excited to see this!
>
> Kevin
Egon
k.sf.net), and use GCJ to compile it... This should stress
test both the CDK libs *and* the (Debian) Java Policy...
> I would be *very* excited to see this!
>
> Kevin
Egon
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