From avilella at ebi.ac.uk  Thu Apr  1 08:36:47 2004
From: avilella at ebi.ac.uk (avilella)
Date: Thu Apr  1 08:42:16 2004
Subject: [DAS] Entry_points - wormbase elegans
Message-ID: <1080826607.5053.3.camel@localhost.localdomain>

Hi,

again another tricky point where the entry_points call to the elegans
dsn of wormbase is empty:

http://www.wormbase.org/db/das/elegans/entry_points

<?xml version="1.0" standalone="no"?>
<!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd">
<DASEP>
<ENTRY_POINTS href="http://www.wormbase.org/db/das/elegans/entry_points" version="1.0">
</ENTRY_POINTS>
</DASEP>

Surprisingly, I have no problem with the briggsae entry_points query:

http://www.wormbase.org/db/das/briggsae/entry_points

Does that mean that the elegans dsn is empty in wormbase?

Thanks in advance,

    Albert.

From ak at ebi.ac.uk  Thu Apr  1 09:21:37 2004
From: ak at ebi.ac.uk (Andreas Kahari)
Date: Thu Apr  1 09:26:45 2004
Subject: [DAS] Entry_points - wormbase elegans
In-Reply-To: <1080826607.5053.3.camel@localhost.localdomain>
References: <1080826607.5053.3.camel@localhost.localdomain>
Message-ID: <20040401142137.GA1251@ebi.ac.uk>

On Thu, Apr 01, 2004 at 02:36:47PM +0100, avilella wrote:
> Hi,
> 
> again another tricky point where the entry_points call to the elegans
> dsn of wormbase is empty:
> 
> http://www.wormbase.org/db/das/elegans/entry_points
> 
> <?xml version="1.0" standalone="no"?>
> <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd">
> <DASEP>
> <ENTRY_POINTS href="http://www.wormbase.org/db/das/elegans/entry_points" version="1.0">
> </ENTRY_POINTS>
> </DASEP>
> 
> Surprisingly, I have no problem with the briggsae entry_points query:
> 
> http://www.wormbase.org/db/das/briggsae/entry_points
> 
> Does that mean that the elegans dsn is empty in wormbase?
> 

No, it just means that the server didn't provide any usable data
for the entry_points command for one or another reason.

There is data in there.  See e.g.

    http://www.wormbase.org/db/das/elegans/features?segment=F28B3


The sources are possibly served off two differently implemented
adaptors/plugins/modules/servers.


Andreas

-- 
|][][| Andreas K?h?ri      EMBL, European Bioinformatics Institute
|[][]|                     Wellcome Trust Genome Campus
|][][| DAS Project Leader  Hinxton, Cambridgeshire, CB10 1SD
|[][]| Ensembl Developer   United Kingdom
From ak at ebi.ac.uk  Thu Apr  1 09:59:11 2004
From: ak at ebi.ac.uk (Andreas Kahari)
Date: Thu Apr  1 10:04:25 2004
Subject: [DAS] Entry_points - wormbase elegans
In-Reply-To: <20040401142137.GA1251@ebi.ac.uk>
References: <1080826607.5053.3.camel@localhost.localdomain>
	<20040401142137.GA1251@ebi.ac.uk>
Message-ID: <20040401145911.GA14217@ebi.ac.uk>

On Thu, Apr 01, 2004 at 03:21:37PM +0100, Andreas Kahari wrote:
> On Thu, Apr 01, 2004 at 02:36:47PM +0100, avilella wrote:
> > Hi,
> > 
> > again another tricky point where the entry_points call to the elegans
> > dsn of wormbase is empty:
> > 
> > http://www.wormbase.org/db/das/elegans/entry_points
> > 
> > <?xml version="1.0" standalone="no"?>
> > <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd">
> > <DASEP>
> > <ENTRY_POINTS href="http://www.wormbase.org/db/das/elegans/entry_points" version="1.0">
> > </ENTRY_POINTS>
> > </DASEP>
> > 
> > Surprisingly, I have no problem with the briggsae entry_points query:
> > 
> > http://www.wormbase.org/db/das/briggsae/entry_points
> > 
> > Does that mean that the elegans dsn is empty in wormbase?
> > 
> 
> No, it just means that the server didn't provide any usable data
> for the entry_points command for one or another reason.
> 
> There is data in there.  See e.g.
> 
>     http://www.wormbase.org/db/das/elegans/features?segment=F28B3
> 
> 
> The sources are possibly served off two differently implemented
> adaptors/plugins/modules/servers.

For the list:  After discussion with Albert (avilella), I've
decided that the DAS server is misbehaving and will point this
out to whoever is running it.

Does anyone on the list know who that might be?


Andreas

-- 
|=][=| Andreas K?h?ri      EMBL, European Bioinformatics Institute
|[==]|                     Wellcome Trust Genome Campus
|=][=| DAS Project Leader  Hinxton, Cambridgeshire, CB10 1SD
|[==]| Ensembl Developer   United Kingdom
From td2 at sanger.ac.uk  Thu Apr  1 14:18:58 2004
From: td2 at sanger.ac.uk (Thomas Down)
Date: Thu Apr  1 14:24:07 2004
Subject: [DAS] Dazzle 1.00 release
Message-ID: <6D3C3B22-8411-11D8-9B37-000A95C8B056@sanger.ac.uk>

I've just put out a new release of the Dazzle modular DAS server.  The 
new release features improvements to the plugin API, updates to work 
with the BioJava 1.4 release, and many minor fixes.

You can download either source or a prebuilt web-application skeleton 
from:

      http://www.biojava.org/download/dazzle/

If you have the Subversion client available, you can also check it out 
from:

      http://www.derkholm.net/svn/repos/dazzle/tags/dazzle-1.00

Installation instructions can be found at:

      http://www.biojava.org/dazzle/deploy.html

Please not that this release *will not* work with the old ensembl-das 
plugins.  I've been working on a major re-write of the biojava-ensembl 
adaptors, including support for the schema changes in Ensembl release 
20 and some substantially improved DAS plugins.  There should be a 
release sometime next week.  In the mean time, development code is 
available from the Subversion repository at:

     http://www.derkholm.net/svn/repos/biojava-ensembl/trunk

Thomas.

From ak at ebi.ac.uk  Mon Apr  5 11:48:20 2004
From: ak at ebi.ac.uk (Andreas Kahari)
Date: Mon Apr  5 11:53:23 2004
Subject: [DAS] Entry_points - wormbase elegans
In-Reply-To: <20040401145911.GA14217@ebi.ac.uk>
References: <1080826607.5053.3.camel@localhost.localdomain>
	<20040401142137.GA1251@ebi.ac.uk>
	<20040401145911.GA14217@ebi.ac.uk>
Message-ID: <20040405154820.GA32027@ebi.ac.uk>

On Thu, Apr 01, 2004 at 03:59:11PM +0100, Andreas Kahari wrote:
> On Thu, Apr 01, 2004 at 03:21:37PM +0100, Andreas Kahari wrote:
> > On Thu, Apr 01, 2004 at 02:36:47PM +0100, avilella wrote:
> > > Hi,
> > > 
> > > again another tricky point where the entry_points call to the elegans
> > > dsn of wormbase is empty:
> > > 
> > > http://www.wormbase.org/db/das/elegans/entry_points
> > > 
> > > <?xml version="1.0" standalone="no"?>
> > > <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd">
> > > <DASEP>
> > > <ENTRY_POINTS href="http://www.wormbase.org/db/das/elegans/entry_points" version="1.0">
> > > </ENTRY_POINTS>
> > > </DASEP>
> > > 
> > > Surprisingly, I have no problem with the briggsae entry_points query:
> > > 
> > > http://www.wormbase.org/db/das/briggsae/entry_points
> > > 
> > > Does that mean that the elegans dsn is empty in wormbase?

This seems to have been fixed now.


Andreas

-- 
|=  =| Andreas K?h?ri      EMBL, European Bioinformatics Institute
| == |                     Wellcome Trust Genome Campus
|=  =| DAS Project Leader  Hinxton, Cambridgeshire, CB10 1SD
| == | Ensembl Developer   United Kingdom
From avilella at ebi.ac.uk  Thu Apr  1 06:55:45 2004
From: avilella at ebi.ac.uk (avilella)
Date: Wed Apr  7 23:36:14 2004
Subject: [DAS] another little typo in spec.html
Message-ID: <1080820544.2929.13.camel@localhost.localdomain>

find patch attached,

    Albert.
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From avilella at ebi.ac.uk  Thu Apr  1 06:59:21 2004
From: avilella at ebi.ac.uk (avilella)
Date: Wed Apr  7 23:36:14 2004
Subject: [DAS] little typo in the spec.html document
Message-ID: <1080820761.2929.19.camel@localhost.localdomain>

There is a 'format format' typo.

Find diff and modified file attached,

    Albert.
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From avilella at ebi.ac.uk  Thu Apr  1 06:53:54 2004
From: avilella at ebi.ac.uk (avilella)
Date: Wed Apr  7 23:36:15 2004
Subject: [DAS] another little typo in spec.html
Message-ID: <1080820434.2929.10.camel@localhost.localdomain>

find patch attached,

    Albert.
-------------- next part --------------
--- spec.html	2003-05-23 08:45:47.000000000 +0100
+++ spec.html.modif2	2004-04-01 12:51:39.064838040 +0100
@@ -1485,7 +1485,7 @@
   <dd>The appropriate doctype and root tag is DASSTYLE.
       <p>
   <dt>&lt;STYLESHEET&gt; (required; one only) 
-  <dd>There is a single &lt;STYLESHEETgt; tag.  Its <b>version </b>
+  <dd>There is a single &lt;STYLESHEET&gt; tag.  Its <b>version </b>
       (required)
       attribute indicates the current version of the stylesheet, and
       can be used for caching purposes.
From lstein at cshl.edu  Sat Apr  3 16:43:46 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu Apr  8 07:05:29 2004
Subject: [DAS] Entry_points - wormbase elegans
In-Reply-To: <1080826607.5053.3.camel@localhost.localdomain>
References: <1080826607.5053.3.camel@localhost.localdomain>
Message-ID: <200404031643.46529.lstein@cshl.edu>

This is an April Fool's joke, right?  When I try this URL, I get:

<?xml version="1.0" standalone="no"?>
<!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd">
<DASEP>
<ENTRY_POINTS 
href="http://www.wormbase.org/db/das/elegans/entry_points" 
version="1.0">
<SEGMENT id="I" size="15080483" start="1" stop="15080483" 
class="Sequence" orientation="+" subparts="yes">I</SEGMENT>
<SEGMENT id="II" size="15279308" start="1" stop="15279308" 
class="Sequence" orientation="+" subparts="yes">II</SEGMENT>
<SEGMENT id="III" size="13783313" start="1" stop="13783313" 
class="Sequence" orientation="+" subparts="yes">III</SEGMENT>
<SEGMENT id="IV" size="17493791" start="1" stop="17493791" 
class="Sequence" orientation="+" subparts="yes">IV</SEGMENT>
<SEGMENT id="MtDNA" size="13794" start="1" stop="13794" 
class="Sequence" orientation="+" subparts="yes">MtDNA</SEGMENT>
<SEGMENT id="V" size="20922231" start="1" stop="20922231" 
class="Sequence" orientation="+" subparts="yes">V</SEGMENT>
<SEGMENT id="X" size="17718849" start="1" stop="17718849" 
class="Sequence" orientation="+" subparts="yes">X</SEGMENT>
</ENTRY_POINTS>
</DASEP>

Which is correct, I believe.

Lincoln

On Thursday 01 April 2004 08:36 am, avilella wrote:> Hi,
>
> again another tricky point where the entry_points call to the
> elegans dsn of wormbase is empty:
>
> http://www.wormbase.org/db/das/elegans/entry_points
>
> <?xml version="1.0" standalone="no"?>
> <!DOCTYPE DASEP SYSTEM "http://www.biodas.org/dtd/dasep.dtd">
> <DASEP>
> <ENTRY_POINTS
> href="http://www.wormbase.org/db/das/elegans/entry_points"
> version="1.0"> </ENTRY_POINTS>
> </DASEP>
>
> Surprisingly, I have no problem with the briggsae entry_points
> query:
>
> http://www.wormbase.org/db/das/briggsae/entry_points
>
> Does that mean that the elegans dsn is empty in wormbase?
>
> Thanks in advance,
>
>     Albert.
>
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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From jason at cgt.duhs.duke.edu  Thu Apr  8 11:01:02 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Thu Apr  8 13:31:30 2004
Subject: [DAS] Re: LDAS makefile problem
In-Reply-To: <200403051220.16472.lstein@cshl.edu>
References: <200403040756.i247ugH05723@mhost2.ucalgary.ca>
	<200403051220.16472.lstein@cshl.edu>
Message-ID: <Pine.LNX.4.50.0404080854020.9937-100000@tenero.duhs.duke.edu>

you can also solve the problem by fixing your /etc/sysconfig/i18n I
believe

Mine looks like this and perl works fine on RHL 9.
$ more /etc/sysconfig/i18n
LANG="en_US.iso885915"
SUPPORTED="en_US:en"
SYSFONT="lat0-sun16"
SYSFONTACM="iso01"

You might try this first at any rate before doing a full perl build.


-jason

On Fri, 5 Mar 2004, Lincoln Stein wrote:

> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hi,
>
> I've seen this problem with faulty Perl installations.  The easiest
> way out of this is to build Perl from source and reinstall.  It won't
> take you more than 10 minutes.
>
> Lincoln
>
> On Thursday 04 March 2004 02:56 am, hili@ucalgary.ca wrote:
> > Hi,
> >
> > I am trying to intall the LDAS on my Redhat Linux 9.0 server, but I
> > constantly have a problem with the makefile generated by
> > Makefile.PL. My Linux server has Apache 2 and Mysql server 3.23
> > installed by default. Also, it has built-in perl-DBI and
> > perl-DBD-mysql. I have installed bioperl-live using cpan shell,
> > which I had got some testing failed, but not many. When I tried
> > 'perl Makefile.PL', I gave the configuaration directory as
> > /etc/httpd/conf, the CGI script directory as /var/www/cgi-bin, and
> > load script directory as /usr/bin. Then I got warning that pod2man
> > program could be located. I made a softlink in the LDAS directory
> > to the /usr/bin/pod2man. When I tried make, I got error message
> > like this: Makefile:81: *** missing separator. Stop. What have I
> > done wrong? This is the beggining of my term project. Please help!
> >
> > Thank you.
> >
> > Irene
>
> - --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.2.1 (GNU/Linux)
>
> iD8DBQFASLbQ0CIvUP7P+AkRAi0jAJ9qWKqm6XidnRe4ktUDPbfetsxDBACfT2g1
> omqGj+eRlMhwgk1OowL/M6s=
> =56U+
> -----END PGP SIGNATURE-----
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From jason at cgt.duhs.duke.edu  Thu Apr  8 13:02:59 2004
From: jason at cgt.duhs.duke.edu (Jason Stajich)
Date: Thu Apr  8 13:31:30 2004
Subject: [DAS] Re: LDAS makefile problem
In-Reply-To: <200404081233.34130.lstein@cshl.edu>
References: <200403040756.i247ugH05723@mhost2.ucalgary.ca>
	<200403051220.16472.lstein@cshl.edu>
	<Pine.LNX.4.50.0404080854020.9937-100000@tenero.duhs.duke.edu>
	<200404081233.34130.lstein@cshl.edu>
Message-ID: <Pine.LNX.4.50.0404081258300.10600-100000@tenero.duhs.duke.edu>

Let's see if it works for Irene.  It fixed the problems Chuck was having
compiling AcePerl.  It's really a bug in perl and UTF8 handling. LANG=C
should also work.

This may also work  -
LANG="en_US"
SUPPORTED="en_US:en"
SYSFONT="lat0-sun16"
SYSFONTACM="iso01"

The problem comes when it says
LANG="en_US.UTF-8"

http://twiki.org/cgi-bin/view/Codev/UsingPerl58OnRedHat8?skin=print

http://bugzilla.redhat.com/bugzilla/show_bug.cgi?id=112339

-jason
On Thu, 8 Apr 2004, Lincoln Stein wrote:

> Is it really as simple as that?
>
> Lincoln
>
> On Thursday 08 April 2004 11:01 am, Jason Stajich wrote:
> > you can also solve the problem by fixing your /etc/sysconfig/i18n I
> > believe
> >
> > Mine looks like this and perl works fine on RHL 9.
> > $ more /etc/sysconfig/i18n
> > LANG="en_US.iso885915"
> > SUPPORTED="en_US:en"
> > SYSFONT="lat0-sun16"
> > SYSFONTACM="iso01"
> >
> > You might try this first at any rate before doing a full perl
> > build.
> >
> >
> > -jason
> >
> > On Fri, 5 Mar 2004, Lincoln Stein wrote:
> > > -----BEGIN PGP SIGNED MESSAGE-----
> > > Hash: SHA1
> > >
> > > Hi,
> > >
> > > I've seen this problem with faulty Perl installations.  The
> > > easiest way out of this is to build Perl from source and
> > > reinstall.  It won't take you more than 10 minutes.
> > >
> > > Lincoln
> > >
> > > On Thursday 04 March 2004 02:56 am, hili@ucalgary.ca wrote:
> > > > Hi,
> > > >
> > > > I am trying to intall the LDAS on my Redhat Linux 9.0 server,
> > > > but I constantly have a problem with the makefile generated by
> > > > Makefile.PL. My Linux server has Apache 2 and Mysql server 3.23
> > > > installed by default. Also, it has built-in perl-DBI and
> > > > perl-DBD-mysql. I have installed bioperl-live using cpan shell,
> > > > which I had got some testing failed, but not many. When I tried
> > > > 'perl Makefile.PL', I gave the configuaration directory as
> > > > /etc/httpd/conf, the CGI script directory as /var/www/cgi-bin,
> > > > and load script directory as /usr/bin. Then I got warning that
> > > > pod2man program could be located. I made a softlink in the LDAS
> > > > directory to the /usr/bin/pod2man. When I tried make, I got
> > > > error message like this: Makefile:81: *** missing separator.
> > > > Stop. What have I done wrong? This is the beggining of my term
> > > > project. Please help!
> > > >
> > > > Thank you.
> > > >
> > > > Irene
> > >
> > > - --
> > > Lincoln D. Stein
> > > Cold Spring Harbor Laboratory
> > > 1 Bungtown Road
> > > Cold Spring Harbor, NY 11724
> > > -----BEGIN PGP SIGNATURE-----
> > > Version: GnuPG v1.2.1 (GNU/Linux)
> > >
> > > iD8DBQFASLbQ0CIvUP7P+AkRAi0jAJ9qWKqm6XidnRe4ktUDPbfetsxDBACfT2g1
> > > omqGj+eRlMhwgk1OowL/M6s=
> > > =56U+
> > > -----END PGP SIGNATURE-----
> > > _______________________________________________
> > > DAS mailing list
> > > DAS@biodas.org
> > > http://biodas.org/mailman/listinfo/das
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu
From lstein at cshl.edu  Thu Apr  8 12:33:33 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Thu Apr  8 13:41:26 2004
Subject: [DAS] Re: LDAS makefile problem
In-Reply-To: <Pine.LNX.4.50.0404080854020.9937-100000@tenero.duhs.duke.edu>
References: <200403040756.i247ugH05723@mhost2.ucalgary.ca>
	<200403051220.16472.lstein@cshl.edu>
	<Pine.LNX.4.50.0404080854020.9937-100000@tenero.duhs.duke.edu>
Message-ID: <200404081233.34130.lstein@cshl.edu>

Is it really as simple as that?

Lincoln

On Thursday 08 April 2004 11:01 am, Jason Stajich wrote:
> you can also solve the problem by fixing your /etc/sysconfig/i18n I
> believe
>
> Mine looks like this and perl works fine on RHL 9.
> $ more /etc/sysconfig/i18n
> LANG="en_US.iso885915"
> SUPPORTED="en_US:en"
> SYSFONT="lat0-sun16"
> SYSFONTACM="iso01"
>
> You might try this first at any rate before doing a full perl
> build.
>
>
> -jason
>
> On Fri, 5 Mar 2004, Lincoln Stein wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
> > Hash: SHA1
> >
> > Hi,
> >
> > I've seen this problem with faulty Perl installations.  The
> > easiest way out of this is to build Perl from source and
> > reinstall.  It won't take you more than 10 minutes.
> >
> > Lincoln
> >
> > On Thursday 04 March 2004 02:56 am, hili@ucalgary.ca wrote:
> > > Hi,
> > >
> > > I am trying to intall the LDAS on my Redhat Linux 9.0 server,
> > > but I constantly have a problem with the makefile generated by
> > > Makefile.PL. My Linux server has Apache 2 and Mysql server 3.23
> > > installed by default. Also, it has built-in perl-DBI and
> > > perl-DBD-mysql. I have installed bioperl-live using cpan shell,
> > > which I had got some testing failed, but not many. When I tried
> > > 'perl Makefile.PL', I gave the configuaration directory as
> > > /etc/httpd/conf, the CGI script directory as /var/www/cgi-bin,
> > > and load script directory as /usr/bin. Then I got warning that
> > > pod2man program could be located. I made a softlink in the LDAS
> > > directory to the /usr/bin/pod2man. When I tried make, I got
> > > error message like this: Makefile:81: *** missing separator.
> > > Stop. What have I done wrong? This is the beggining of my term
> > > project. Please help!
> > >
> > > Thank you.
> > >
> > > Irene
> >
> > - --
> > Lincoln D. Stein
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724
> > -----BEGIN PGP SIGNATURE-----
> > Version: GnuPG v1.2.1 (GNU/Linux)
> >
> > iD8DBQFASLbQ0CIvUP7P+AkRAi0jAJ9qWKqm6XidnRe4ktUDPbfetsxDBACfT2g1
> > omqGj+eRlMhwgk1OowL/M6s=
> > =56U+
> > -----END PGP SIGNATURE-----
> > _______________________________________________
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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From lstein at cshl.edu  Fri Apr  9 16:26:15 2004
From: lstein at cshl.edu (Lincoln Stein)
Date: Sun Apr 11 06:50:50 2004
Subject: [DAS] little typo in the spec.html document
In-Reply-To: <1080739216.3527.7.camel@localhost.localdomain>
References: <1080739216.3527.7.camel@localhost.localdomain>
Message-ID: <200404091626.16066.lstein@cshl.edu>

Thanks for the two patch files.  To make it easier in the future, it 
would be helpful if you used relative pathnames in the diffs rather 
than absolute ones.

Lincoln

On Wednesday 31 March 2004 08:20 am, avilella wrote:
> There is a 'format format' typo.
>
> Find diff and modified file attached,
>
>     Albert.

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
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From dlondon at ebi.ac.uk  Wed Apr 28 06:06:37 2004
From: dlondon at ebi.ac.uk (Darin London)
Date: Wed Apr 28 06:26:18 2004
Subject: [DAS] BOSC 2nd Call For Papers
Message-ID: <Pine.LNX.4.44.0404281104180.4053-100000@parrot.ebi.ac.uk>

 {Please pass the word!}
 
 SECOND CALL FOR SPEAKERS
 
 BOSC PROGRAM & CONTACT INFO
 
 * Web: http://www.open-bio.org/bosc2004/
 * Email: bosc@open-bio.org
 * Online registration: https://www.cteusa.com/iscb3/
  
 The program committee is currently seeking abstracts for talks at BOSC 
 2004. BOSC is a great opportunity for you to tell the community about 
 your use, development, or philosophy of open source software development 
 in bioinformatics. The committee will select several submitted abstracts 
 for 25-minute talks and others for shorter "lightning" talks. Accepted 
 abstracts will be published on the BOSC web site.
 
 If you are interested in speaking at BOSC 2004, 
 please send us:
 
 * an abstract (no more than a few paragraphs)
 * a URL for the project page, if applicable
 * information about the open source license used for your software or 
   your release plans.

*** Abstracts for formal presentations must be recieved by 5-May-2004. ***

 LIGHTNING-TALK SPEAKERS WANTED!
 
 The program committee is currently seeking speakers for the lightning 
 talks at BOSC 2004. Lightning talks are quick - only five minutes 
 long - and a great opportunity for you to give people a quick 
 summary of your open source project, code, idea, or vision of the future.

 If you are interested in giving a lightning talk at BOSC 2004, 
 please send us:

 * a brief title and summary (one or two lines)
 * a URL for the project page, if applicable
 * information about the open source license used for your software or 
   your release plans.

 We will accept entries on-line until BOSC starts, but
 space for demos and lightning talks is limited.<br/>
    
 SOFTWARE DEMONSTRATIONS WANTED!
 If you are involved in the development of Open Source Bioinformatics 
 Software, you are invited to provide a short demonstration to attendees 
 of BOSC 2004.

 If you are interested in giving a software demonstration at BOSC 2004,
 please send us:

 * a brief title and summary (one or two lines)
 * a URL for the project page, if applicable
 * Internet connectivity requirements (e.g. website Application served on 
the  world wide web, or web based client application).

 We will accept entries on-line until the BOSC starts, but
 space for demos and lightning talks is limited. 

** Because the mission of the OBF is to promote Open Source software, we 
will favor submissions for projects that apply a recognized Open Source 
License, or adhere to the general Open Source Philosophy.
   See the following websites for further details:
   href="http://www.opensource.org/licenses/
   href="http://www.opensource.org/docs/definition.php


cheers,

-- 
Darin London dlondon@ebi.ac.uk    European Bioinformatics Institute, 
+44 (0)1223 49 2566               Wellcome Trust Genome Campus, Hinxton 
+44 (0)1223 49 4468 (fax)         Cambridgeshire CB10 1SD, UK

From michel at biodevnet.org  Tue Apr 27 22:38:44 2004
From: michel at biodevnet.org (Michel Dumontier)
Date: Mon May 10 20:39:19 2004
Subject: [DAS] perl module failed test
Message-ID: <000001c42cc9$f9c28520$f500a8c0@fission>

Just reporting a failed test on installing the bio-das perl module (Bio-Das-0.97) from CPAN... 


Running make test
/usr/bin/perl.exe "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'b
lib/arch')" t/*.t
t/01das....ok 22/36Argument "COUNT" isn't numeric in foreach loop entry at t/01d
as.t line 29.
t/01das....FAILED tests 15, 23-36
        Failed 15/36 tests, 58.33% okay
Failed Test Stat Wstat Total Fail  Failed  List of Failed
-------------------------------------------------------------------------------
t/01das.t                 36   15  41.67%  15 23-36
Failed 1/1 test scripts, 0.00% okay. 15/36 subtests failed, 58.33% okay.
make: *** [test_dynamic] Error 255
  /usr/bin/make test -- NOT OK