gusdev-gusdev

[GUSDEV] ISF release

[<hen...@gm...>]

Hi everyone...


I just downloaded every file needed for ISF, rebuilded GUS, and when I
tried to upload some files in my database, it printed the following
message:

ga GUS::Supported::Plugin::InsertSequenceFeatures - -mapfile
/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile /home/juca/GUS-File
s/ISF/Z_mobilis.fasta --fileFormat genbank --extDbName 'TESTE'
--extDbRlsVer '2 005-09-06' --soCvsVersion 1.42
The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
include a revision number, then the plugin has never been checked into
CVS.  Please do so to give it an intial revision at
/usr/local/GUS/gus_home/lib/perl/GUS/Plugin Mgr/Plugin.pm line 347.
Issuing rollback() for database handle being DESTROY'd without
explicit disconn ect().

I had to enter ISF .pm archive and fill that line myself, but CVS
should do it, shouldn't it?


Thanks and nice weekend,


--
Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] ISF release

[Steve F. <sfi...@pc...>]

henrique-

thanks for reporting this.   we have seen this before.   it is a mystery=20
why subversion fails sometimes to fill that in.

we'll look into it.

steve

Henrique Juc=E1 wrote:

>Hi everyone...
>
>
>I just downloaded every file needed for ISF, rebuilded GUS, and when I
>tried to upload some files in my database, it printed the following
>message:
>
>ga GUS::Supported::Plugin::InsertSequenceFeatures - -mapfile
>/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile /home/juca/GUS-File
>s/ISF/Z_mobilis.fasta --fileFormat genbank --extDbName 'TESTE'
>--extDbRlsVer '2 005-09-06' --soCvsVersion 1.42
>The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
>include a revision number, then the plugin has never been checked into
>CVS.  Please do so to give it an intial revision at
>/usr/local/GUS/gus_home/lib/perl/GUS/Plugin Mgr/Plugin.pm line 347.
>Issuing rollback() for database handle being DESTROY'd without
>explicit disconn ect().
>
>I had to enter ISF .pm archive and fill that line myself, but CVS
>should do it, shouldn't it?
>
>
>Thanks and nice weekend,
>
>
>--
>Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>
>"As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>you create an opening in your heart for maliciousness to enter. Testing,
>competing with, and criticizing others weaken and defeat you."
>
>Morihei Ueshiba, O-Sensei (1883-1969)
>
>
>-------------------------------------------------------
>SF.Net email is sponsored by:
>Tame your development challenges with Apache's Geronimo App Server.=20
>Download it for free - -and be entered to win a 42" plasma tv or your ve=
ry
>own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.ph=
p
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> =20
>

Re: [GUSDEV] ISF release

[Michael S. <msa...@pc...>]

Before anything else, make sure you do an svn update so that you're working
from the latest version.

--Mike


On 9/23/05 4:15 PM, "Steve Fischer" <sfi...@pc...> wrote:

> henrique-
>=20
> thanks for reporting this.   we have seen this before.   it is a mystery
> why subversion fails sometimes to fill that in.
>=20
> we'll look into it.
>=20
> steve
>=20
> Henrique Juc=E1 wrote:
>=20
>> Hi everyone...
>>=20
>>=20
>> I just downloaded every file needed for ISF, rebuilded GUS, and when I
>> tried to upload some files in my database, it printed the following
>> message:
>>=20
>> ga GUS::Supported::Plugin::InsertSequenceFeatures - -mapfile
>> /home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile /home/juca/GUS-File
>> s/ISF/Z_mobilis.fasta --fileFormat genbank --extDbName 'TESTE'
>> --extDbRlsVer '2 005-09-06' --soCvsVersion 1.42
>> The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
>> include a revision number, then the plugin has never been checked into
>> CVS.  Please do so to give it an intial revision at
>> /usr/local/GUS/gus_home/lib/perl/GUS/Plugin Mgr/Plugin.pm line 347.
>> Issuing rollback() for database handle being DESTROY'd without
>> explicit disconn ect().
>>=20
>> I had to enter ISF .pm archive and fill that line myself, but CVS
>> should do it, shouldn't it?
>>=20
>>=20
>> Thanks and nice weekend,
>>=20
>>=20
>> --
>> Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>>=20
>> "As soon as you concern yourself with the "good" and "bad" of your fello=
ws,
>> you create an opening in your heart for maliciousness to enter. Testing,
>> competing with, and criticizing others weaken and defeat you."
>>=20
>> Morihei Ueshiba, O-Sensei (1883-1969)
>>=20
>>=20
>> -------------------------------------------------------
>> SF.Net email is sponsored by:
>> Tame your development challenges with Apache's Geronimo App Server.
>> Download it for free - -and be entered to win a 42" plasma tv or your ve=
ry
>> own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.ph=
p
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>> =20
>>=20
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.
> Download it for free - -and be entered to win a 42" plasma tv or your ver=
y
> own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] ISF release

[<hen...@gm...>]

Thanks for the quick answers.

Well, I did update all files needed by ISF plugin, as Steve instructed
me a while ago. However, I'm not updating all GUS as a whole, since
the version installed here is somewhat "mutant" - it comes from a
mixture of the old tar.gz from the homepage and from manual updating
of several files...
Is the installation from
"svn checkout https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk
GUS" working?

I do remember people here having some trouble trying to install from it.




Kindest regards,



Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)

Re: [GUSDEV] ISF release

[Michael S. <msa...@pc...>]

Why are you using the "mutant" install?  If your schema is 3.5, you should
be using either the trunk, or the download from the GUS website.  If your
not using 3.5 (which I recommend, of course), then you probably shouldn't
use ISF since (Steve correct me if this is wrong) it's been designed for
3.5+ only.

There haven't been any major difficulties installing 3.5.  If do you use th=
e
trunk, you'll also need to get GusSchema.

This is correct:

svn checkout https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk GUS

--Mike

On 9/23/05 4:30 PM, "Henrique Juc=E1" <hen...@gm...> wrote:

> Thanks for the quick answers.
>=20
> Well, I did update all files needed by ISF plugin, as Steve instructed
> me a while ago. However, I'm not updating all GUS as a whole, since
> the version installed here is somewhat "mutant" - it comes from a
> mixture of the old tar.gz from the homepage and from manual updating
> of several files...
> Is the installation from
> "svn checkout https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk
> GUS" working?
>=20
> I do remember people here having some trouble trying to install from it.
>=20
>=20
>=20
>=20
> Kindest regards,
>=20
>=20
>=20
> Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br
>=20
> "As soon as you concern yourself with the "good" and "bad" of your fellow=
s,
> you create an opening in your heart for maliciousness to enter. Testing,
> competing with, and criticizing others weaken and defeat you."
>=20
> Morihei Ueshiba, O-Sensei (1883-1969)
>=20
>=20
> -------------------------------------------------------
> SF.Net email is sponsored by:
> Tame your development challenges with Apache's Geronimo App Server.
> Download it for free - -and be entered to win a 42" plasma tv or your ver=
y
> own Sony(tm)PSP.  Click here to play: http://sourceforge.net/geronimo.php
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev