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From: Bryan C. <di...@pc...> - 2006-11-09 16:39:39
|
On Wed, Nov 08, 2006 at 07:44:48PM +0000, marc jackson wrote:
> Does anyone know why the dbadumpschema perl script returns an oracle error:
>
> ORA-00604
well, you didn't include it here, but from your previous
mail I found:
Exception in thread "main" java.lang.RuntimeException:
java.sql.SQLException: ORA-00604: error occurred at recursive SQL level 1
ORA-01000: maximum open cursors exceeded
it may just be that you need to increase the number of open
cursors allowed. I suggest this because I vaguely recall
having a similar issue on a fresh gus/oracle install several
years ago.
Cheers,
Bryan Cardillo
Penn Bioinformatics Core
University of Pennsylvania
|
|
From: <mro...@cs...> - 2006-11-09 15:45:33
|
I am resending this message because the original one was bounced back to =
me
---------------------------- Original Message ---------------------------=
-
Subject: ISF defaults
From: mro...@cs...
Date: Thu, November 9, 2006 10:39 am
To: gus...@li...
Cc: "Steve Fischer" <sfi...@pc...>
-------------------------------------------------------------------------=
-
Steve,
I understand that you are in charge of ISF.
I am trying to run the ISF plugin in a brand new install and I get the
following error:
No row in Core.ProjectInfo has name =3D Database Administration'. This
value was found in the project=3D property of your gus.config file. Ple=
ase
be sure it is correct and has been registered in the database
**** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' with
stderr:
Operation now in progress**** GUS::PluginMgr::PluginError Failed
running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --
commit' with stderr:
I already checked my gus.config file and it has the entry
project=3DDatabase Administration
I would like to know if this and maybe other default values must be
inserted into the database before trying to insert data.
I found in the gusdev site the following:
From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
for those of you who are using the beta version of the ISF plugin:
1. i will improve its documentation to indicate what it expects to
already be in the database:
- SequenceOntology (InsertSequenceOntology plugin)
- NCBI Taxon (LoadTaxon plugin)
- External database and release (InsertExternalDatabase and
InsertExternalDatabaseRls plugins)
- at least one row in SequenceType so you can say what type of
sequence you are loading (you can use LoadRow plugin for thi=
s)
2. i will improve the error messages so that it better detects the
absence of these, and makes it more clear what to do.
I am sorry if I ask the same question so many times but I am stuck and ca=
n
not continue until I find an answer.
Thank you
Michael Robinson
Bioinformatics Research Group (Biorg)
Florida International University
Miami, Florida, USA 33199
|
|
From: marc j. <de...@ho...> - 2006-11-08 19:45:06
|
Does anyone know why the dbadumpschema perl script returns an oracle error: ORA-00604 >From: Chris Stoeckert <sto...@pc...> >To: marc jackson <de...@ho...>, John Iodice <io...@pc...>, > F Innamarato <fr...@pc...> >CC: m...@sa... >Subject: Re: GUS dba scripts >Date: Wed, 8 Nov 2006 10:59:09 -0500 > >Hi Marc, >Will see if I can't get an answer for you. > >John? Frank? >Any ideas? > >Thanks, >Chris > >On Nov 8, 2006, at 9:52 AM, marc jackson wrote: > >>In GUS 3.5 you have a perl script called: dbaDumpSchema. >> >>This script is supposed to be able to read a database. >>How do I specify which database to read? >> >>I ask, because I used the command: ./gus_home/bin/dbaDumpSchema - >>sourceType db -targetType xml -target /var/tmp/report.xml >> >>and I get the error: Nov 8, 2006 6:42:11 AM >>org.gusdb.dbadmin.reader.SchemaReader doRead >>INFO: Reading Database >>Nov 8, 2006 6:42:11 AM org.gusdb.dbadmin.reader.OracleReader readDatabase >>INFO: Reading database: null >> >>Which seems to indicate that it doesn't know which database it's supposed >>to read. >> >>Regards, >> >>Marc >> >>ps. I sent a similar question to gus-dev, but no one has responded. >> >>_________________________________________________________________ >>Stay in touch with old friends and meet new ones with Windows Live Spaces >>http://clk.atdmt.com/MSN/go/msnnkwsp0070000001msn/direct/01/? >>href=http://spaces.live.com/spacesapi.aspx?wx_action=create&wx_url=/ >>friends.aspx&mkt=en-us > _________________________________________________________________ Get FREE company branded e-mail accounts and business Web site from Microsoft Office Live http://clk.atdmt.com/MRT/go/mcrssaub0050001411mrt/direct/01/ |
|
From: <mro...@cs...> - 2006-11-07 22:33:11
|
Fernan, Thanks for your answer, I did check my gus.config file in GUS/gus_home/co= nfig and found in it. I would like to know if this and maybe other default values must be inserted into the database before trying to insert data. Please, gusdev group let me know where I can find information about this. Thanks, Michael R > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > gus...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Gusdev-gusdev digest..." > > > Today's Topics: > > 1. problem inserting data using ISF (mro...@cs...) > 2. Re: problem inserting data using ISF (Fernan Aguero) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 3 Nov 2006 10:21:11 -0500 (EST) > From: mro...@cs... > Subject: [GUSDEV] problem inserting data using ISF > To: gus...@li... > Cc: sfi...@pc... > Message-ID: <328...@ww...> > Content-Type: text/plain;charset=3Diso-8859-1 > > Steve, > > > I have a new problem inserting data using ISF. > > I run: > > mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/gus_home > /lib/perl/GUS/Supported/Plugin 10% > ga GUS::Supported::Plugin::InsertSequenceFeatures > --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml > --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk > --fileFormat genbank --extDbName "Pseudomonas_aeruginosa" > --extDbRlsVer "1000" > --soCvsVersion "1.1.4" > --commit > > and got: > No row in Core.ProjectInfo has name =3D Database Administration'. > This value was found in the project=3D property of your gus.config fil= e. > > Please be sure it is correct and has been registered in the database > > **** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' wi= th > stderr: > > Operation now in progress**** GUS::PluginMgr::PluginError Failed > running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures > --commit' with stderr: > > > I went into the Core.ProjectInfo table and it is empty, so since this i= s a > brand new install and the data I am trying to load into ISF is the firs= t > data to be loaded, I am wondering if I need to put some other default > information in the GUS database tables before using ISF. > > Thanks for your help > > Michael > > > > > ------------------------------ > > Message: 2 > Date: Fri, 3 Nov 2006 14:37:02 -0300 > From: Fernan Aguero <fe...@ii...> > Subject: Re: [GUSDEV] problem inserting data using ISF > To: mro...@cs... > Cc: gus...@li..., sfi...@pc... > Message-ID: <200...@ii...> > Content-Type: text/plain; charset=3Dus-ascii > > +----[ mro...@cs... <mro...@cs...> (03.Nov.2006 12:56): > | > | and got: > | No row in Core.ProjectInfo has name =3D Database Administration'. > | This value was found in the project=3D property of your gus.config f= ile. > | > | Please be sure it is correct and has been registered in the database > > [snipped] > > | I went into the Core.ProjectInfo table and it is empty, so since this= is > a > | brand new install and the data I am trying to load into ISF is the fi= rst > | data to be loaded, I am wondering if I need to put some other default > | information in the GUS database tables before using ISF. > | > +----] > > Michael, > > check that you have > > project=3DDatabase Administration > > in the gus.config file in GUS_HOME. > > Fernan > |
|
From: Fernan A. <fe...@ii...> - 2006-11-03 17:37:16
|
+----[ mro...@cs... <mro...@cs...> (03.Nov.2006 12:56): | | and got: | No row in Core.ProjectInfo has name = Database Administration'. | This value was found in the project= property of your gus.config file. | | Please be sure it is correct and has been registered in the database [snipped] | I went into the Core.ProjectInfo table and it is empty, so since this is a | brand new install and the data I am trying to load into ISF is the first | data to be loaded, I am wondering if I need to put some other default | information in the GUS database tables before using ISF. | +----] Michael, check that you have project=Database Administration in the gus.config file in GUS_HOME. Fernan |
|
From: <mro...@cs...> - 2006-11-03 15:21:23
|
Steve, I have a new problem inserting data using ISF. I run: mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/gus_home /lib/perl/GUS/Supported/Plugin 10% ga GUS::Supported::Plugin::InsertSequenceFeatures --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk --fileFormat genbank --extDbName "Pseudomonas_aeruginosa" --extDbRlsVer "1000" --soCvsVersion "1.1.4" --commit and got: No row in Core.ProjectInfo has name =3D Database Administration'. This value was found in the project=3D property of your gus.config file. Please be sure it is correct and has been registered in the database **** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' with stderr: Operation now in progress**** GUS::PluginMgr::PluginError Failed running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --commit' with stderr: I went into the Core.ProjectInfo table and it is empty, so since this is = a brand new install and the data I am trying to load into ISF is the first data to be loaded, I am wondering if I need to put some other default information in the GUS database tables before using ISF. Thanks for your help Michael |
|
From: marc j. <de...@ho...> - 2006-11-02 18:47:27
|
I sent a message earlier this morning, but I didn't see it when I checked on sourceforge. mj 10:50 am. west coast time. _________________________________________________________________ Add a Yahoo! contact to Windows Live Messenger for a chance to win a free trip! http://www.imagine-windowslive.com/minisites/yahoo/default.aspx?locale=en-us&hmtagline |
|
From: marc j. <de...@ho...> - 2006-11-02 17:13:39
|
Hello,
It was unsuccessful, but I'm having a hard time understanding what the
error messages mean.
I ran: ./gus_home/bin/dbaDumpSchema -sourceType db -targetType xml -target
/var/tmp/report.xml.
I got:
Nov 2, 2006 9:03:23 AM org.gusdb.dbadmin.reader.SchemaReader doRead
INFO: Reading Database
Nov 2, 2006 9:03:23 AM org.gusdb.dbadmin.reader.OracleReader readDatabase
INFO: Reading database: null
Nov 2, 2006 9:03:33 AM org.gusdb.dbadmin.reader.OracleReader addColumns
SEVERE: Error querying for constraint columns: java.sql.SQLException:
ORA-00604: error occurred at recursive SQL level 1
ORA-01000: maximum open cursors exceeded
Exception in thread "main" java.lang.RuntimeException:
java.sql.SQLException: ORA-00604: error occurred at recursive SQL level 1
ORA-01000: maximum open cursors exceeded
at
org.gusdb.dbadmin.reader.OracleReader.addColumns(OracleReader.java:446)
at
org.gusdb.dbadmin.reader.OracleReader.addLocalConstraints(OracleReader.java:562)
at
org.gusdb.dbadmin.reader.OracleReader.addTables(OracleReader.java:200)
at
org.gusdb.dbadmin.reader.OracleReader.addSchemas(OracleReader.java:150)
at
org.gusdb.dbadmin.reader.OracleReader.readDatabase(OracleReader.java:107)
at
org.gusdb.dbadmin.reader.SchemaReader.doRead(SchemaReader.java:50)
at org.gusdb.dbadmin.reader.SchemaReader.read(SchemaReader.java:38)
at org.gusdb.dbadmin.util.SchemaDumper.main(SchemaDumper.java:98)
Caused by: java.sql.SQLException: ORA-00604: error occurred at recursive SQL
level 1
ORA-01000: maximum open cursors exceeded
at
oracle.jdbc.driver.DatabaseError.throwSqlException(DatabaseError.java:124)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:304)
at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:271)
at oracle.jdbc.driver.T4C8Oall.receive(T4C8Oall.java:622)
at oracle.jdbc.driver.T4CStatement.doOall8(T4CStatement.java:111)
at
oracle.jdbc.driver.T4CStatement.execute_for_describe(T4CStatement.java:350)
at
oracle.jdbc.driver.OracleStatement.execute_maybe_describe(OracleStatement.java:895)
at
oracle.jdbc.driver.T4CStatement.execute_maybe_describe(T4CStatement.java:382)
at
oracle.jdbc.driver.OracleStatement.doExecuteWithTimeout(OracleStatement.java:985)
at
oracle.jdbc.driver.OracleStatement.executeQuery(OracleStatement.java:1124)
at
org.gusdb.dbadmin.reader.OracleReader.addColumns(OracleReader.java:414)
... 7 more
What do these error messages mean and how do I fix them?
Regards,
Marc
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|
|
From: <mro...@cs...> - 2006-11-01 21:22:30
|
John, Mark
Yes it was an install problem
I found Error.pm at /depot/perl-5.6/lib/site_perl/5.6.1
and changed the PERL5LIB shell variable to that directory.
Thanks very much for your help.
Michael
> This still sounds like a package install problem....Which directory
> was the package installed into??
>
> Once you know that...from the command line try:
> perl -e 'map {print $_."\n"} @INC'
>
> ** If it was installed correctly, Error.pm should be in one of those
> directories in the @INC array (probably something like
> /usr/lib/perl5/site...)
> If it isn't... set your PERL5LIB shell variable to whatever directory
> Error.pm is in.
>
> A quick way you can tell if the package isn't being "seen" by perl is
> by trying to read the perldoc from the command line
> perldoc Error
>
> let me know what you find
> john
>
>
|
|
From: Mark S. H. <mh...@ug...> - 2006-11-01 19:59:08
|
On Oct 31, 2006, at 5:35 PM, mro...@cs... wrote: > Mark, > > I did: > > mrobi002@acrl-linux-1:~ 116% cd $HOME > mrobi002@acrl-linux-1:~ 117% perl -e 'use Error'; > mrobi002@acrl-linux-1:~ 118% > > > It gave not output, so does this means that perl found Error.pl, > correct? > That's my understanding of the world. hmmm. Now I'm at a loss to explain your 'ga' failure. Was your plugin command and the perl 'use Error' command executed in exactly the same environment? (that is, if running one immediately after the other, ga fails and 'use Error' succeeds ?) Anyone else have an idea? -Mark > Michael > >> >> On Oct 31, 2006, at 4:13 PM, mro...@cs... wrote: >>> We had the IT department install "Error.pm version 0.17006" >>> today, and >>> then I run >>> >>> ga GUS::Supported::Plugin::InsertSequenceFeatures --help >>> >>> Getting the same errors as before: >>> >>> Base class package "Error" is empty. >> >> Michael, >> >> Run this test: >> >> perl -e 'use Error'; >> >> It should give no output. If it complains that it "Can't locate >> Error.pm in @INC ......." show this test and error message to your IT >> department. They should be able to help your perl find the Error.pm >> they installed. It's not a GUS issue. >> >> Good luck, >> Mark >> > > |
|
From: Mark S. H. <mh...@ug...> - 2006-10-31 22:26:54
|
On Oct 31, 2006, at 4:13 PM, mro...@cs... wrote: > We had the IT department install "Error.pm version 0.17006" today, and > then I run > > ga GUS::Supported::Plugin::InsertSequenceFeatures --help > > Getting the same errors as before: > > Base class package "Error" is empty. Michael, Run this test: perl -e 'use Error'; It should give no output. If it complains that it "Can't locate Error.pm in @INC ......." show this test and error message to your IT department. They should be able to help your perl find the Error.pm they installed. It's not a GUS issue. Good luck, Mark |
|
From: <mro...@cs...> - 2006-10-31 21:13:47
|
John,
Help please....
This is a brand new GUS 3.5 from SVN install.
After installation i have only done:
+meta to ga and +create to all plugins.
At postgres:
insert into core.databaseversion (
database_version_id,
version,
modification_date,
user_read,
user_write,
group_read,
group_write,
other_read,
other_write,
row_user_id,
row_group_id,
row_project_id,
row_alg_invocation_id
) values (
nextval('core.databaseversion_sq'),
3.5,
now(),
1, 0, 1, 0, 1, 0,
1, 1, 1, 1
);
We had the IT department install "Error.pm version 0.17006" today, and
then I run
ga GUS::Supported::Plugin::InsertSequenceFeatures --help
Getting the same errors as before:
Base class package "Error" is empty.
(Perhaps you need to 'use' the module which defines that package first=
.)
at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr
/PluginError.pm line 3
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 3.
Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29.
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29.
Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27.
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27.
Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/bin/ga line 7.
BEGIN failed--compilation aborted at /home/acrl-storage-1/gusdb-dev/GUS/
gus_home/bin/ga line 7.
Could you please tell what I am doing wrong
Thank you
Michael
> Hi Michael - Sorry to just be responding...Mark is right that
> PluginError.pm is a subclass of Error.pm. Were you successful with
> the installation?
>
> I will add this to the documentation of required packages.
>
> thanks
> john
>
>
> At 07:46 PM 10/27/2006, you wrote:
>>Mark
>>
>>Yes I downloaded the tar file, I am going to read the installation
>>instructions and let you know how it went
>>
>>Thanks again
>>
>>Michael
>>
>>
>>
>> > See "HOW TO INSTALL IT" in the README that comes in the Error tar
>> > file (that's the actual letter case used; I'm not shouting at you).
>> >
>> > Did you download the tar file or just the Error.pm file? Get the tar
>> > file.
>> >
>> > By default it installs into your system-wide Perl library (so you'll
>> > likely need root privileges). Technically you could install it in
>> > your gus_home, but don't do tha
|
|
From: <mro...@cs...> - 2006-10-28 00:46:38
|
Mark Yes I downloaded the tar file, I am going to read the installation instructions and let you know how it went Thanks again Michael > See "HOW TO INSTALL IT" in the README that comes in the Error tar > file (that's the actual letter case used; I'm not shouting at you). > > Did you download the tar file or just the Error.pm file? Get the tar > file. > > By default it installs into your system-wide Perl library (so you'll > likely need root privileges). Technically you could install it in > your gus_home, but don't do that. > > GUS' PluginError.pm uses Error.pm. One is not a replacement for the > other. > > Good luck, > -Mark > > On Oct 27, 2006, at 7:22 PM, mro...@cs... wrote: > >> Mark, >> >> Thanks for you answer. >> >> I downloaded Error.pm version 0.17006, and I looked into every GUS >> folder >> to see if there is another file called Error.pm to replace it, but >> could >> not find any. >> >> The file called PluginError.pm which seems to be the one with >> errors is >> located at: >> /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr >> >> Do I need to replace PluginError.pm with Error.pm version 0.17006, >> rename >> it Error.pm to PluginError.pm, or added in the same directory? >> >> Thanks again >> >> Michael >> >> >>> I'm coming in late to this thread but it looks like you need to >>> install the Error module from CPAN. >>> >>> http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm >>> >>> I had to install version 0.17006, the latest 0.17008 version didn't >>> compile for me out of the box. >>> >>> -M >>> On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: >>> >>>> Steve, >>>> >>>> I am sorry to be a pain, but I was wondering if you have received >>>> any news >>>> from John concerning the PluginError.pm >>>> >>>> Thank you >>>> >>>> >>>> Michael >>>> >>>> >>>> >>>>> john- >>>>> >>>>> this GUS user, michael, has downloaded and installed the latest >>>>> GUS. >>>>> >>>>> your new PluginError.pm is giving him problems. see below. >>>>> >>>>> steve >>>>> >>>>> mrobi002@cs.f |
|
From: Mark S. H. <mh...@ug...> - 2006-10-27 23:52:58
|
See "HOW TO INSTALL IT" in the README that comes in the Error tar file (that's the actual letter case used; I'm not shouting at you). Did you download the tar file or just the Error.pm file? Get the tar file. By default it installs into your system-wide Perl library (so you'll likely need root privileges). Technically you could install it in your gus_home, but don't do that. GUS' PluginError.pm uses Error.pm. One is not a replacement for the other. Good luck, -Mark On Oct 27, 2006, at 7:22 PM, mro...@cs... wrote: > Mark, > > Thanks for you answer. > > I downloaded Error.pm version 0.17006, and I looked into every GUS > folder > to see if there is another file called Error.pm to replace it, but > could > not find any. > > The file called PluginError.pm which seems to be the one with > errors is > located at: > /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr > > Do I need to replace PluginError.pm with Error.pm version 0.17006, > rename > it Error.pm to PluginError.pm, or added in the same directory? > > Thanks again > > Michael > > >> I'm coming in late to this thread but it looks like you need to >> install the Error module from CPAN. >> >> http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm >> >> I had to install version 0.17006, the latest 0.17008 version didn't >> compile for me out of the box. >> >> -M >> On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: >> >>> Steve, >>> >>> I am sorry to be a pain, but I was wondering if you have received >>> any news >>> from John concerning the PluginError.pm >>> >>> Thank you >>> >>> >>> Michael >>> >>> >>> >>>> john- >>>> >>>> this GUS user, michael, has downloaded and installed the latest >>>> GUS. >>>> >>>> your new PluginError.pm is giving him problems. see below. >>>> >>>> steve >>>> >>>> mro...@cs... wrote: >>>> >>>>> Steve, >>>>> >>>>> Thanks for the phone orientation offer, tomorrow will be great, I >>>>> am on >>>>> my >>>>> way to a 3 hour class. >>>>> >>>>> In the meantime I run: >>>>> >>>>> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >>>>> gus_home/lib/perl/GUS/Supported/Plugin 9% >>>>> ga GUS::Supported::Plugin::InsertSequenceFeatures >>>>> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >>>>> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/ >>>>> NC_002516.gbk >>>>> --fileFormat genbank >>>>> --extDbName "Pseudomonas_aeruginosa" >>>>> --extDbRlsVer "1000" >>>>> --soCvsVersion "1.1.4" >>>>> --commit >>>>> >>>>> >>>>> and got: >>>>> >>>>> Base class package "Error" is empty. >>>>> (Perhaps you need to 'use' the module which defines that >>>>> package > % > |
|
From: <mro...@cs...> - 2006-10-27 23:22:45
|
Mark, Thanks for you answer. I downloaded Error.pm version 0.17006, and I looked into every GUS folder to see if there is another file called Error.pm to replace it, but could not find any. The file called PluginError.pm which seems to be the one with errors is located at: /home/acrl-storage-1/gusdb-dev/GUS/gus_home/lib/perl/GUS/PluginMgr Do I need to replace PluginError.pm with Error.pm version 0.17006, rename it Error.pm to PluginError.pm, or added in the same directory? Thanks again Michael > I'm coming in late to this thread but it looks like you need to > install the Error module from CPAN. > > http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm > > I had to install version 0.17006, the latest 0.17008 version didn't > compile for me out of the box. > > -M > On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: > >> Steve, >> >> I am sorry to be a pain, but I was wondering if you have received >> any news >> from John concerning the PluginError.pm >> >> Thank you >> >> >> Michael >> >> >> >>> john- >>> >>> this GUS user, michael, has downloaded and installed the latest GUS. >>> >>> your new PluginError.pm is giving him problems. see below. >>> >>> steve >>> >>> mro...@cs... wrote: >>> >>>> Steve, >>>> >>>> Thanks for the phone orientation offer, tomorrow will be great, I >>>> am on >>>> my >>>> way to a 3 hour class. >>>> >>>> In the meantime I run: >>>> >>>> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >>>> gus_home/lib/perl/GUS/Supported/Plugin 9% >>>> ga GUS::Supported::Plugin::InsertSequenceFeatures >>>> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >>>> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >>>> --fileFormat genbank >>>> --extDbName "Pseudomonas_aeruginosa" >>>> --extDbRlsVer "1000" >>>> --soCvsVersion "1.1.4" >>>> --commit >>>> >>>> >>>> and got: >>>> >>>> Base class package "Error" is empty. >>>> (Perhaps you need to 'use' the module which defines that package % |
|
From: Mark S. H. <mh...@ug...> - 2006-10-27 13:20:46
|
I'm coming in late to this thread but it looks like you need to install the Error module from CPAN. http://search.cpan.org/~shlomif/Error-0.17008/lib/Error.pm I had to install version 0.17006, the latest 0.17008 version didn't compile for me out of the box. -M On Oct 27, 2006, at 8:21 AM, mro...@cs... wrote: > Steve, > > I am sorry to be a pain, but I was wondering if you have received > any news > from John concerning the PluginError.pm > > Thank you > > > Michael > > > >> john- >> >> this GUS user, michael, has downloaded and installed the latest GUS. >> >> your new PluginError.pm is giving him problems. see below. >> >> steve >> >> mro...@cs... wrote: >> >>> Steve, >>> >>> Thanks for the phone orientation offer, tomorrow will be great, I >>> am on >>> my >>> way to a 3 hour class. >>> >>> In the meantime I run: >>> >>> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/Supported/Plugin 9% >>> ga GUS::Supported::Plugin::InsertSequenceFeatures >>> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >>> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >>> --fileFormat genbank >>> --extDbName "Pseudomonas_aeruginosa" >>> --extDbRlsVer "1000" >>> --soCvsVersion "1.1.4" >>> --commit >>> >>> >>> and got: >>> >>> Base class package "Error" is empty. >>> (Perhaps you need to 'use' the module which defines that package >>> first.) >>> at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/ >>> lib/perl/GUS/PluginMgr/PluginError.pm line 2 >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2. >>> >>> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ >>> GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >>> >>> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ >>> GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >>> >>> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/ >>> GUS/ >>> gus_home/bin/ga line 7. >>> >>> BEGIN failed--compilation aborted at >>> /home/acrl-storage-1/gusdb-dev/GUS/ >>> gus_home/bin/ga line 7. >>> >>> >>> I examined the errors by looking in the programs and all errors have >>> something in common: >>> >>> use GUS::PluginMgr::GusApplication; #at ga.pm line 7 >>> use GUS::PluginMgr::Plugin; #at GusApplication.pm line 27 >>> use GUS::PluginMgr::PluginError; #at Plugin.pm line 29 >>> use base qw(Error); #at PluginError.pm line 2 >>> >>> >>> It probably is a stupid mistake on my part, but I can not see >>> >>> All help will be very much appreciated. >>> >>> >>> Thanks again >>> >>> Michael >>> >>> >>> >>> >>> >>>> the only documentation is what you get by running the plugin w/ >>>> --help >>>> >>>> i can (try to) answer questions as they come up. >>>> >>>> it may turn out that the best way to proceed is an orientation >>>> by phone. >>>> >>>> steve >>>> >>>> mro...@cs... wrote: >>>> >>>> >>>> >>>>> Steve, >>>>> >>>>> I am almost ready to insert some bacteria sequences from >>>>> genebank, and >>>>> i >>>>> have some questions. >>>>> >>>>> a - i found in the gusdev site the following: >>>>> >>>>> From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 >>>>> for those of you who are using the beta version of the ISF plugin: >>>>> 1. i will improve its documentation to indicate what it >>>>> expects to >>>>> already be in the database: >>>>> - SequenceOntology (InsertSequenceOntology plugin) >>>>> - NCBI Taxon (LoadTaxon plugin) >>>>> - External database and release (InsertExternalDatabase >>>>> and >>>>> InsertExternalDatabaseRls >>>>> plugins) >>>>> - at least one row in SequenceType so you can say what >>>>> type of >>>>> sequence you are loading (you can use LoadRow plugin for >>>>> this) >>>>> >>>>> 2. i will improve the error messages so that it better >>>>> detects the >>>>> absence of these, and makes it more clear what to do. >>>>> >>>>> About loading SO: >>>>> 1. can you send the SO term with definition that is too big? >>>>> >>>>> 2. i understand about the rollback. we have been discussing >>>>> how to >>>>> undo a plugin. for now, you need to do it with sql. >>>>> >>>>> Thanks for helping us make this plugin better. >>>>> >>>>> steve >>>>> >>>>> We did a new GUS install two weeks ago and i wonder if this >>>>> applies to >>>>> me, >>>>> if it does could you tell me where do i find the documentation >>>>> that you >>>>> mention above. >>>>> >>>>> b - When I do a search in gusdev for "InsertSequenceFeatures" >>>>> or parts >>>>> of >>>>> it, i get very little replies and somotimes none. Is there >>>>> another way >>>>> to >>>>> find all documents in gusdev relating to this. >>>>> >>>>> Thank you >>>>> >>>>> Michael R >>>>> >>>>> >>>>> -------------------------------------------- >>>>> >>>>> >> > > > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
|
From: <mro...@cs...> - 2006-10-27 12:21:58
|
Steve, I am sorry to be a pain, but I was wondering if you have received any new= s from John concerning the PluginError.pm Thank you Michael > john- > > this GUS user, michael, has downloaded and installed the latest GUS. > > your new PluginError.pm is giving him problems. see below. > > steve > > mro...@cs... wrote: > >>Steve, >> >>Thanks for the phone orientation offer, tomorrow will be great, I am on >> my >>way to a 3 hour class. >> >>In the meantime I run: >> >> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/Supported/Plugin 9% >> ga GUS::Supported::Plugin::InsertSequenceFeatures >> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >> --fileFormat genbank >> --extDbName "Pseudomonas_aeruginosa" >> --extDbRlsVer "1000" >> --soCvsVersion "1.1.4" >> --commit >> >> >>and got: >> >> Base class package "Error" is empty. >> (Perhaps you need to 'use' the module which defines that package >> first.) >> at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/ >> lib/perl/GUS/PluginMgr/PluginError.pm line 2 >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> >>I examined the errors by looking in the programs and all errors have >>something in common: >> >> use GUS::PluginMgr::GusApplication; #at ga.pm line 7 >> use GUS::PluginMgr::Plugin; #at GusApplication.pm line 27 >> use GUS::PluginMgr::PluginError; #at Plugin.pm line 29 >> use base qw(Error); #at PluginError.pm line 2 >> >> >>It probably is a stupid mistake on my part, but I can not see >> >>All help will be very much appreciated. >> >> >>Thanks again >> >>Michael >> >> >> >> >> >>>the only documentation is what you get by running the plugin w/ --help >>> >>>i can (try to) answer questions as they come up. >>> >>>it may turn out that the best way to proceed is an orientation by phon= e. >>> >>>steve >>> >>>mro...@cs... wrote: >>> >>> >>> >>>>Steve, >>>> >>>>I am almost ready to insert some bacteria sequences from genebank, an= d >>>> i >>>>have some questions. >>>> >>>>a - i found in the gusdev site the following: >>>> >>>>From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 >>>>for those of you who are using the beta version of the ISF plugin: >>>> 1. i will improve its documentation to indicate what it expects to >>>> already be in the database: >>>> - SequenceOntology (InsertSequenceOntology plugin) >>>> - NCBI Taxon (LoadTaxon plugin) >>>> - External database and release (InsertExternalDatabase and >>>> InsertExternalDatabaseRls plugins) >>>> - at least one row in SequenceType so you can say what type = of >>>> sequence you are loading (you can use LoadRow plugin for >>>>this) >>>> >>>> 2. i will improve the error messages so that it better detects the >>>> absence of these, and makes it more clear what to do. >>>> >>>> About loading SO: >>>> 1. can you send the SO term with definition that is too big? >>>> >>>> 2. i understand about the rollback. we have been discussing how t= o >>>> undo a plugin. for now, you need to do it with sql. >>>> >>>> Thanks for helping us make this plugin better. >>>> >>>> steve >>>> >>>>We did a new GUS install two weeks ago and i wonder if this applies t= o >>>>me, >>>>if it does could you tell me where do i find the documentation that y= ou >>>>mention above. >>>> >>>>b - When I do a search in gusdev for "InsertSequenceFeatures" or part= s >>>> of >>>>it, i get very little replies and somotimes none. Is there another wa= y >>>> to >>>>find all documents in gusdev relating to this. >>>> >>>>Thank you >>>> >>>>Michael R >>>> >>>> >>>>-------------------------------------------- >>>> >>>> > |
|
From: <mro...@cs...> - 2006-10-25 18:02:43
|
Steve, When changes are made to the plugins in GUS (improvements, bugs etc) do you have "patches" (like in windows programs) that can be applied to GUS, or how it is handle? Thanks Michael R > john- > > this GUS user, michael, has downloaded and installed the latest GUS. > > your new PluginError.pm is giving him problems. see below. > > steve > > mro...@cs... wrote: > >>Steve, >> >>Thanks for the phone orientation offer, tomorrow will be great, I am on >> my >>way to a 3 hour class. >> >>In the meantime I run: >> >> mrobi002@acrl-linux-1:/home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/Supported/Plugin 9% >> ga GUS::Supported::Plugin::InsertSequenceFeatures >> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml >> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk >> --fileFormat genbank >> --extDbName "Pseudomonas_aeruginosa" >> --extDbRlsVer "1000" >> --soCvsVersion "1.1.4" >> --commit >> >> >>and got: >> >> Base class package "Error" is empty. >> (Perhaps you need to 'use' the module which defines that package >> first.) >> at /home/acrl-storage-1/gusdb-dev/GUS/gus_home/ >> lib/perl/GUS/PluginMgr/PluginError.pm line 2 >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/PluginError.pm line 2. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 29. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 27. >> >> Compilation failed in require at /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> BEGIN failed--compilation aborted at >> /home/acrl-storage-1/gusdb-dev/GUS/ >> gus_home/bin/ga line 7. >> >> >>I examined the errors by looking in the programs and all errors have >>something in common: >> >> use GUS::PluginMgr::GusApplication; #at ga.pm line 7 >> use GUS::PluginMgr::Plugin; #at GusApplication.pm line 27 >> use GUS::PluginMgr::PluginError; #at Plugin.pm line 29 >> use base qw(Error); #at PluginError.pm line 2 >> >> >>It probably is a stupid mistake on my part, but I can not see >> >>All help will be very much appreciated. >> >> >>Thanks again >> >>Michael >> >> >> >> >> >>>the only documentation is what you get by running the plugin w/ --help >>> >>>i can (try to) answer questions as they come up. >>> >>>it may turn out that the best way to proceed is an orientation by phon= e. >>> >>>steve >>> >>>mro...@cs... wrote: >>> >>> >>> >>>>Steve, >>>> >>>>I am almost ready to insert some bacteria sequences from genebank, an= d >>>> i >>>>have some questions. >>>> >>>>a - i found in the gusdev site the following: >>>> >>>>From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 >>>>for those of you who are using the beta version of the ISF plugin: >>>> 1. i will improve its documentation to indicate what it expects to >>>> already be in the database: >>>> - SequenceOntology (InsertSequenceOntology plugin) >>>> - NCBI Taxon (LoadTaxon plugin) >>>> - External database and release (InsertExternalDatabase and >>>> InsertExternalDatabaseRls plugins) >>>> - at least one row in SequenceType so you can say what type = of >>>> sequence you are loading (you can use LoadRow plugin for >>>>this) >>>> >>>> 2. i will improve the error messages so that it better detects the >>>> absence of these, and makes it more clear what to do. >>>> >>>> About loading SO: >>>> 1. can you send the SO term with definition that is too big? >>>> >>>> 2. i understand about the rollback. we have been discussing how t= o >>>> undo a plugin. for now, you need to do it with sql. >>>> >>>> Thanks for helping us make this plugin better. >>>> >>>> steve >>>> >>>>We did a new GUS install two weeks ago and i wonder if this applies t= o >>>>me, >>>>if it does could you tell me where do i find the documentation that y= ou >>>>mention above. >>>> >>>>b - When I do a search in gusdev for "InsertSequenceFeatures" or part= s >>>> of >>>>it, i get very little replies and somotimes none. Is there another wa= y >>>> to >>>>find all documents in gusdev relating to this. >>>> >>>>Thank you >>>> >>>>Michael R >>>> >>>> >>>>-------------------------------------------- >>>> >>>> > |
|
From: Steve F. <sfi...@pc...> - 2006-10-24 20:59:44
|
the only documentation is what you get by running the plugin w/ --help i can (try to) answer questions as they come up. it may turn out that the best way to proceed is an orientation by phone. steve mro...@cs... wrote: >Steve, > >I am almost ready to insert some bacteria sequences from genebank, and i >have some questions. > >a - i found in the gusdev site the following: > > From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32 > for those of you who are using the beta version of the ISF plugin: > 1. i will improve its documentation to indicate what it expects to > already be in the database: > - SequenceOntology (InsertSequenceOntology plugin) > - NCBI Taxon (LoadTaxon plugin) > - External database and release (InsertExternalDatabase and > InsertExternalDatabaseRls plugins) > - at least one row in SequenceType so you can say what type of > sequence you are loading (you can use LoadRow plugin for this) > > 2. i will improve the error messages so that it better detects the > absence of these, and makes it more clear what to do. > > About loading SO: > 1. can you send the SO term with definition that is too big? > > 2. i understand about the rollback. we have been discussing how to > undo a plugin. for now, you need to do it with sql. > > Thanks for helping us make this plugin better. > > steve > >We did a new GUS install two weeks ago and i wonder if this applies to me, >if it does could you tell me where do i find the documentation that you >mention above. > >b - When I do a search in gusdev for "InsertSequenceFeatures" or parts of >it, i get very little replies and somotimes none. Is there another way to >find all documents in gusdev relating to this. > >Thank you > >Michael R > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: <mro...@cs...> - 2006-10-24 20:45:15
|
Steve,
I am almost ready to insert some bacteria sequences from genebank, and i
have some questions.
a - i found in the gusdev site the following:
From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
for those of you who are using the beta version of the ISF plugin:
1. i will improve its documentation to indicate what it expects to
already be in the database:
- SequenceOntology (InsertSequenceOntology plugin)
- NCBI Taxon (LoadTaxon plugin)
- External database and release (InsertExternalDatabase and
InsertExternalDatabaseRls plugins)
- at least one row in SequenceType so you can say what type of
sequence you are loading (you can use LoadRow plugin for this=
)
2. i will improve the error messages so that it better detects the
absence of these, and makes it more clear what to do.
About loading SO:
1. can you send the SO term with definition that is too big?
2. i understand about the rollback. we have been discussing how to
undo a plugin. for now, you need to do it with sql.
Thanks for helping us make this plugin better.
steve
We did a new GUS install two weeks ago and i wonder if this applies to me=
,
if it does could you tell me where do i find the documentation that you
mention above.
b - When I do a search in gusdev for "InsertSequenceFeatures" or parts of
it, i get very little replies and somotimes none. Is there another way to
find all documents in gusdev relating to this.
Thank you
Michael R
|
|
From: <mro...@cs...> - 2006-10-24 20:44:10
|
Steve,
I am almost ready to insert some bacteria sequences from genebank, and i
have some questions.
a - i found in the gusdev site the following:
From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
for those of you who are using the beta version of the ISF plugin:
1. i will improve its documentation to indicate what it expects to
already be in the database:
- SequenceOntology (InsertSequenceOntology plugin)
- NCBI Taxon (LoadTaxon plugin)
- External database and release (InsertExternalDatabase and
InsertExternalDatabaseRls plugins)
- at least one row in SequenceType so you can say what type of
sequence you are loading (you can use LoadRow plugin for this=
)
2. i will improve the error messages so that it better detects the
absence of these, and makes it more clear what to do.
About loading SO:
1. can you send the SO term with definition that is too big?
2. i understand about the rollback. we have been discussing how to
undo a plugin. for now, you need to do it with sql.
Thanks for helping us make this plugin better.
steve
We did a new GUS install two weeks ago and i wonder if this applies to me=
,
if it does could you tell me where do i find the documentation that you
mention above.
b - When I do a search in gusdev for "InsertSequenceFeatures" or parts of
it, i get very little replies and somotimes none. Is there another way to
find all documents in gusdev relating to this.
Thank you
Michael R
|
|
From: Steve F. <sfi...@pc...> - 2006-10-23 18:55:44
|
there is a property called 'perl=' in $GUS_HOME/config/gus.config change that accordingly (and delete all the files in $GUS_HOME/bin so that they get rebuilt) steve marc jackson wrote: >Yes, my "ant" was screwed up. I re-installed it. > >That allowed the build to work, but it has not fixed my problem. > >specifically: $gus_home/bin/*.pl aren't being rebuilt. This means >that they're not taking advantage of the structure of the perl on >this machine. Which means that they don't work. How do I >rebuild this scripts? > >Regards, > >marc > > > >>From: Steve Fischer <sfi...@pc...> >>To: marc jackson <de...@ho...> >>CC: gus...@li... >>Subject: Re: [GUSDEV] Building 3.5 >>Date: Mon, 23 Oct 2006 13:18:18 -0400 >> >>hmm. looks like there is something fishy with your ant install. >> >>type 'ant -v' and send the results >> >>steve >> >>marc jackson wrote: >> >> >> >>>build GUS install -append >>> >>>It generates: >>> >>>java.lang.NullPointerException >>> at >>>org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:262) >>> at >>>org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:212) >>> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:128) >>> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:55) >>> >>> >>> >>> >>> >>> >>>>From: Steve Fischer <sfi...@pc...> >>>>To: marc jackson <de...@ho...> >>>>CC: gus...@li... >>>>Subject: Re: [GUSDEV] Building 3.5 >>>>Date: Mon, 23 Oct 2006 12:57:27 -0400 >>>> >>>>marc- >>>> >>>>can you provide the entire error message, including what you typed in. >>>> >>>>thanks >>>>steve >>>> >>>>marc jackson wrote: >>>> >>>> >>>> >>>> >>>> >>>>>Hello, >>>>> >>>>>I'm trying to install the GUS 3.5 framwork. >>>>>I've modified the config file appopriately. >>>>> >>>>>Why am I getting the following error at the beginning >>>>>of the build? >>>>> >>>>>error: java.lang.NullPointerException >>>>> >>>>>Regards, >>>>> >>>>>Marc >>>>> >>>>>_________________________________________________________________ >>>>>All-in-one security and maintenance for your PC. Get a free 90-day >>>>>trial! >>>>>http://clk.atdmt.com/MSN/go/msnnkwlo0050000002msn/direct/01/?href=http://www.windowsonecare.com/?sc_cid=msn_hotmail >>>>> >>>>> >>>>>------------------------------------------------------------------------- >>>>>Using Tomcat but need to do more? Need to support web services, >>>>>security? >>>>>Get stuff done quickly with pre-integrated technology to make your job >>>>>easier >>>>>Download IBM WebSphere Application Server v.1.0.1 based on Apache >>>>>Geronimo >>>>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>>>>_______________________________________________ >>>>>Gusdev-gusdev mailing list >>>>>Gus...@li... >>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>_________________________________________________________________ >>>Try the next generation of search with Windows Live Search today! >>>http://imagine-windowslive.com/minisites/searchlaunch/?locale=en-us&source=hmtagline >>> >>> >>>------------------------------------------------------------------------- >>>Using Tomcat but need to do more? Need to support web services, security? >>>Get stuff done quickly with pre-integrated technology to make your job >>>easier >>>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> > >_________________________________________________________________ >All-in-one security and maintenance for your PC. Get a free 90-day trial! >http://clk.atdmt.com/MSN/go/msnnkwlo0050000002msn/direct/01/?href=http://www.windowsonecare.com/?sc_cid=msn_hotmail > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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From: marc j. <de...@ho...> - 2006-10-23 17:52:37
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Yes, my "ant" was screwed up. I re-installed it. That allowed the build to work, but it has not fixed my problem. specifically: $gus_home/bin/*.pl aren't being rebuilt. This means that they're not taking advantage of the structure of the perl on this machine. Which means that they don't work. How do I rebuild this scripts? Regards, marc >From: Steve Fischer <sfi...@pc...> >To: marc jackson <de...@ho...> >CC: gus...@li... >Subject: Re: [GUSDEV] Building 3.5 >Date: Mon, 23 Oct 2006 13:18:18 -0400 > >hmm. looks like there is something fishy with your ant install. > >type 'ant -v' and send the results > >steve > >marc jackson wrote: > >>build GUS install -append >> >>It generates: >> >>java.lang.NullPointerException >> at >>org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:262) >> at >>org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:212) >> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:128) >> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:55) >> >> >> >> >>>From: Steve Fischer <sfi...@pc...> >>>To: marc jackson <de...@ho...> >>>CC: gus...@li... >>>Subject: Re: [GUSDEV] Building 3.5 >>>Date: Mon, 23 Oct 2006 12:57:27 -0400 >>> >>>marc- >>> >>>can you provide the entire error message, including what you typed in. >>> >>>thanks >>>steve >>> >>>marc jackson wrote: >>> >>> >>> >>>>Hello, >>>> >>>>I'm trying to install the GUS 3.5 framwork. >>>>I've modified the config file appopriately. >>>> >>>>Why am I getting the following error at the beginning >>>>of the build? >>>> >>>>error: java.lang.NullPointerException >>>> >>>>Regards, >>>> >>>>Marc >>>> >>>>_________________________________________________________________ >>>>All-in-one security and maintenance for your PC. Get a free 90-day >>>>trial! >>>>http://clk.atdmt.com/MSN/go/msnnkwlo0050000002msn/direct/01/?href=http://www.windowsonecare.com/?sc_cid=msn_hotmail >>>> >>>> >>>>------------------------------------------------------------------------- >>>>Using Tomcat but need to do more? Need to support web services, >>>>security? >>>>Get stuff done quickly with pre-integrated technology to make your job >>>>easier >>>>Download IBM WebSphere Application Server v.1.0.1 based on Apache >>>>Geronimo >>>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>>>_______________________________________________ >>>>Gusdev-gusdev mailing list >>>>Gus...@li... >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >>>> >> >>_________________________________________________________________ >>Try the next generation of search with Windows Live Search today! >>http://imagine-windowslive.com/minisites/searchlaunch/?locale=en-us&source=hmtagline >> >> >>------------------------------------------------------------------------- >>Using Tomcat but need to do more? Need to support web services, security? >>Get stuff done quickly with pre-integrated technology to make your job >>easier >>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> _________________________________________________________________ All-in-one security and maintenance for your PC. Get a free 90-day trial! http://clk.atdmt.com/MSN/go/msnnkwlo0050000002msn/direct/01/?href=http://www.windowsonecare.com/?sc_cid=msn_hotmail |
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From: Steve F. <sfi...@pc...> - 2006-10-23 17:18:22
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hmm. looks like there is something fishy with your ant install. type 'ant -v' and send the results steve marc jackson wrote: >build GUS install -append > >It generates: > >java.lang.NullPointerException > at >org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:262) > at >org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:212) > at org.apache.tools.ant.launch.Launcher.run(Launcher.java:128) > at org.apache.tools.ant.launch.Launcher.main(Launcher.java:55) > > > > >>From: Steve Fischer <sfi...@pc...> >>To: marc jackson <de...@ho...> >>CC: gus...@li... >>Subject: Re: [GUSDEV] Building 3.5 >>Date: Mon, 23 Oct 2006 12:57:27 -0400 >> >>marc- >> >>can you provide the entire error message, including what you typed in. >> >>thanks >>steve >> >>marc jackson wrote: >> >> >> >>>Hello, >>> >>>I'm trying to install the GUS 3.5 framwork. >>>I've modified the config file appopriately. >>> >>>Why am I getting the following error at the beginning >>>of the build? >>> >>>error: java.lang.NullPointerException >>> >>>Regards, >>> >>>Marc >>> >>>_________________________________________________________________ >>>All-in-one security and maintenance for your PC. Get a free 90-day trial! >>>http://clk.atdmt.com/MSN/go/msnnkwlo0050000002msn/direct/01/?href=http://www.windowsonecare.com/?sc_cid=msn_hotmail >>> >>> >>>------------------------------------------------------------------------- >>>Using Tomcat but need to do more? Need to support web services, security? >>>Get stuff done quickly with pre-integrated technology to make your job >>>easier >>>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >>>_______________________________________________ >>>Gusdev-gusdev mailing list >>>Gus...@li... >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >>> >>> >>> > >_________________________________________________________________ >Try the next generation of search with Windows Live Search today! >http://imagine-windowslive.com/minisites/searchlaunch/?locale=en-us&source=hmtagline > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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From: marc j. <de...@ho...> - 2006-10-23 17:01:06
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build GUS install -append
It generates:
java.lang.NullPointerException
at
org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:262)
at
org.apache.tools.ant.launch.Locator.getLocationURLs(Locator.java:212)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:128)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:55)
>From: Steve Fischer <sfi...@pc...>
>To: marc jackson <de...@ho...>
>CC: gus...@li...
>Subject: Re: [GUSDEV] Building 3.5
>Date: Mon, 23 Oct 2006 12:57:27 -0400
>
>marc-
>
>can you provide the entire error message, including what you typed in.
>
>thanks
>steve
>
>marc jackson wrote:
>
>>Hello,
>>
>>I'm trying to install the GUS 3.5 framwork.
>>I've modified the config file appopriately.
>>
>>Why am I getting the following error at the beginning
>>of the build?
>>
>>error: java.lang.NullPointerException
>>
>>Regards,
>>
>>Marc
>>
>>_________________________________________________________________
>>All-in-one security and maintenance for your PC. Get a free 90-day trial!
>>http://clk.atdmt.com/MSN/go/msnnkwlo0050000002msn/direct/01/?href=http://www.windowsonecare.com/?sc_cid=msn_hotmail
>>
>>
>>-------------------------------------------------------------------------
>>Using Tomcat but need to do more? Need to support web services, security?
>>Get stuff done quickly with pre-integrated technology to make your job
>>easier
>>Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
_________________________________________________________________
Try the next generation of search with Windows Live Search today!
http://imagine-windowslive.com/minisites/searchlaunch/?locale=en-us&source=hmtagline
|
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