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From: Arnaud K. <ax...@sa...> - 2003-03-05 16:40:33
|
Hi
I'm trying to run LoadTaxon plugin. Why some lines are commented out ?
#my $genCodes = $self->makeGeneticCode();
my $namesDmp = $self->getNames();
#my $nodesHash = $self->makeNodesHash($genCodes);
#my $rootAttArray = $self->getRootAttArray($genCodes);
#$self->makeTaxonEntry($rootAttArray, \$count);
#if ($self->getCla->{'restart'} && $self->getCla->{'restart'} > 1) {
#$self->getTaxonAtt($self->getCla->{'restart'},$nodesHash,\$count);
#}
#else {
#$self->getTaxonAtt($rootAttArray->[0],$nodesHash,\$count);
#}
Arnaud
|
|
From: Deborah F. P. <pi...@pc...> - 2003-03-05 17:07:42
|
This is my fault. I commited to cvs when I should not have. I have
uncommented those lines and recomitted to cvs.
Deboeah Pinney
On Wed, 5 Mar 2003, Arnaud
Kerhornou wrote:
> Hi
>
> I'm trying to run LoadTaxon plugin. Why some lines are commented out ?
>
> #my $genCodes = $self->makeGeneticCode();
>
> my $namesDmp = $self->getNames();
>
> #my $nodesHash = $self->makeNodesHash($genCodes);
>
> #my $rootAttArray = $self->getRootAttArray($genCodes);
>
> #$self->makeTaxonEntry($rootAttArray, \$count);
>
> #if ($self->getCla->{'restart'} && $self->getCla->{'restart'} > 1) {
> #$self->getTaxonAtt($self->getCla->{'restart'},$nodesHash,\$count);
> #}
> #else {
> #$self->getTaxonAtt($rootAttArray->[0],$nodesHash,\$count);
> #}
>
> Arnaud
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> for complex code. Debugging C/C++ programs can leave you feeling lost and
> disoriented. TotalView can help you find your way. Available on major UNIX
> and Linux platforms. Try it free. www.etnus.com
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: steve f. <sfi...@pc...> - 2003-03-05 17:55:18
|
just want to clarify why debbie "committed when i should not have".
the deal is that we are extremely rigorous about our tracking of bulk
changes to the db.
in particular, you cannot run a plugin with --commit unless that exact
revision of the plugin has been registered in the db. and, you cannot
do that registering unless you have checked in that version of the
plugin to cvs.
instead of checking in a crippled version of a plugin, hacks like this
can be accomplished by other ways, such as:
- introducing a temporary command line arg which the plugin tests for
to run its hacky code.
- copying the plugin to a new file, such as LoadTaxonDebbiesHack.pm,
and registering it as a new plugin
steve
Deborah F. Pinney wrote:
>This is my fault. I commited to cvs when I should not have. I have
>uncommented those lines and recomitted to cvs.
>
>
> Deboeah Pinney
>
>
>On Wed, 5 Mar 2003, Arnaud
>Kerhornou wrote:
>
>
>
>>Hi
>>
>>I'm trying to run LoadTaxon plugin. Why some lines are commented out ?
>>
>> #my $genCodes = $self->makeGeneticCode();
>>
>> my $namesDmp = $self->getNames();
>>
>> #my $nodesHash = $self->makeNodesHash($genCodes);
>>
>> #my $rootAttArray = $self->getRootAttArray($genCodes);
>>
>> #$self->makeTaxonEntry($rootAttArray, \$count);
>>
>> #if ($self->getCla->{'restart'} && $self->getCla->{'restart'} > 1) {
>> #$self->getTaxonAtt($self->getCla->{'restart'},$nodesHash,\$count);
>> #}
>> #else {
>> #$self->getTaxonAtt($rootAttArray->[0],$nodesHash,\$count);
>> #}
>>
>>Arnaud
>>
>>
>>
>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>>for complex code. Debugging C/C++ programs can leave you feeling lost and
>>disoriented. TotalView can help you find your way. Available on major UNIX
>>and Linux platforms. Try it free. www.etnus.com
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>
>
>
>-------------------------------------------------------
>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>for complex code. Debugging C/C++ programs can leave you feeling lost and
>disoriented. TotalView can help you find your way. Available on major UNIX
>and Linux platforms. Try it free. www.etnus.com
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
>
>
|
|
From: Arnaud K. <ax...@sa...> - 2003-03-07 10:57:23
|
Hi
I've tried to populate the taxonomy files from NCBI into GUS3. it's
working fine until it reaches the last node entry, ie the line 173295 in
the nodes.dmp file.
I now have these 2 errors when populating the nodes file:
> oerr ora 03113
03113, 00000, "end-of-file on communication channel"
// *Cause:
// *Action:
> oerr ora 01041
01041, 00000, "internal error. hostdef extension doesn't exist"
// *Cause: Pointer to hstdef extension in hstdef is null.
// *Action: Report as a bug
Have you come across the same problem ?
Any idea about the cause of this 'end-of-file on communication channel'
error ?
cheers
Arnaud
./bin/ga GUS::Common::Plugin::LoadTaxon
--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
--names=/nfs/pathsoft/databases/NCBI/names.dmp
--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
--------------------------->
[...]
RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
bindValues (89410)
sqlExec:
INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
genetic_code_id, row_project_id, taxon_id, group_r
ead, row_group_id, other_read, mitochondrial_genetic_code_id,
modification_date, user_read, row_alg_invocation_id, oth
er_write, ncbi_tax_id, rank )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
DbiHandle:sqlExec:insert succeeded 1 row(s)
processed ncbi_tax_id : 89410
^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
line 242, <NODES> line 173295.
DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
(perhaps you need to call execute first) at /nfs/t
eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
line 243, <NODES> line 173295.
RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
bindValues (110556)
sqlExec:
INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
genetic_code_id, row_project_id, taxon_id, group_r
ead, row_group_id, other_read, mitochondrial_genetic_code_id,
modification_date, user_read, row_alg_invocation_id, oth
er_write, ncbi_tax_id, rank )
VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
DbiHandle:sqlExec:insert succeeded 1 row(s)
processed ncbi_tax_id : 110556
DBD::Oracle::db prepare failed: Error while trying to retrieve text for
error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
cribe) at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
line 241, <NODES> line 1
73295.
sqlExec:
UPDATE Core.AlgorithmInvocation
SET
end_time = SYSDATE,
row_alg_invocation_id = ?,
modification_date = SYSDATE
WHERE algorithm_invocation_id = ?
bindValues (9, 9)
DbiHandle:sqlExec:insert succeeded 1 row(s)
Can't call method "execute" on an undefined value at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
lugin/LoadTaxon.pm line 242, <NODES> line 173295.
<------------------------------------
|
|
From: Deborah F. P. <pi...@pc...> - 2003-03-07 11:28:45
|
I didn't experience this problem. However, in looking over the
LoadTaxon.pm code I noticed that there was still a commented out line
that should have been corrected. This line is used only for restarting.
I have uncommented it and submitted to cvs. Please update your file.
Deborah Pinney
On
Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
> Hi
>
> I've tried to populate the taxonomy files from NCBI into GUS3. it's
> working fine until it reaches the last node entry, ie the line 173295 in
> the nodes.dmp file.
> I now have these 2 errors when populating the nodes file:
>
> > oerr ora 03113
> 03113, 00000, "end-of-file on communication channel"
> // *Cause:
> // *Action:
>
> > oerr ora 01041
> 01041, 00000, "internal error. hostdef extension doesn't exist"
> // *Cause: Pointer to hstdef extension in hstdef is null.
> // *Action: Report as a bug
>
> Have you come across the same problem ?
> Any idea about the cause of this 'end-of-file on communication channel'
> error ?
>
> cheers
> Arnaud
>
> ./bin/ga GUS::Common::Plugin::LoadTaxon
> --nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
> --names=/nfs/pathsoft/databases/NCBI/names.dmp
> --gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
>
> --------------------------->
> [...]
>
> RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> bindValues (89410)
>
> sqlExec:
> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> genetic_code_id, row_project_id, taxon_id, group_r
> ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> modification_date, user_read, row_alg_invocation_id, oth
> er_write, ncbi_tax_id, rank )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> processed ncbi_tax_id : 89410
>
> ^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
> communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
> team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 242, <NODES> line 173295.
> DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> (perhaps you need to call execute first) at /nfs/t
> eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 243, <NODES> line 173295.
>
> RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> bindValues (110556)
>
>
> sqlExec:
> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> genetic_code_id, row_project_id, taxon_id, group_r
> ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> modification_date, user_read, row_alg_invocation_id, oth
> er_write, ncbi_tax_id, rank )
> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> processed ncbi_tax_id : 110556
> DBD::Oracle::db prepare failed: Error while trying to retrieve text for
> error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
> cribe) at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 241, <NODES> line 1
> 73295.
>
>
> sqlExec:
> UPDATE Core.AlgorithmInvocation
> SET
> end_time = SYSDATE,
> row_alg_invocation_id = ?,
> modification_date = SYSDATE
> WHERE algorithm_invocation_id = ?
> bindValues (9, 9)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
> Can't call method "execute" on an undefined value at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
> lugin/LoadTaxon.pm line 242, <NODES> line 173295.
> <------------------------------------
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> for complex code. Debugging C/C++ programs can leave you feeling lost and
> disoriented. TotalView can help you find your way. Available on major UNIX
> and Linux platforms. Try it free. www.etnus.com
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Deborah F. P. <pi...@pc...> - 2003-03-07 11:33:08
|
The taxonomy file I loaded was from January 10, 2003. It may be that
there is a problem with the file itself. The problem could exist with the
NCBI file at NCBI or occured when you incompressed it.
Deborah Pinney
|
|
From: Arnaud K. <ax...@sa...> - 2003-03-07 14:50:29
|
It's working now. Just noticed something, when the option --commit is
not specified, the loading stops on the population of the TaxonName
table, because of the Foreign Key taxon_id integrity not respected.
with '--commit' option it seems to work fine.
------------->
RetrieveFromDB: select * from SRes.TaxonName where unique_name_variant
is NULL and name_class = ? and name = ? and
taxon_id is NULL
bindValues (synonym, all)
sqlExec:
INSERT INTO SRes.TaxonName ( row_user_id, other_read,
unique_name_variant, user_write, group_write, name_class, r
ow_project_id, name, taxon_id, modification_date, user_read,
row_alg_invocation_id, group_read, other_write, row_group
_id, taxon_name_id )
VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
bindValues (1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1)
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
("SRES"."TAXONNAME"."TAXON_ID") (DBD ERROR: OCIStmt
Execute) at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
line 137, <NODES> line 2.
sqlExec:
UPDATE Core.AlgorithmInvocation
SET
end_time = SYSDATE,
row_alg_invocation_id = ?,
modification_date = SYSDATE
WHERE algorithm_invocation_id = ?
bindValues (9, 9)
DbiHandle:sqlExec:insert succeeded 1 row(s)
SQL ERROR!! involving
INSERT INTO SRes.TaxonName ( row_user_id, other_read,
unique_name_variant, user_write, group_write, name_class, r
ow_project_id, name, taxon_id, modification_date, user_read,
row_alg_invocation_id, group_read, other_write, row_group
_id, taxon_name_id )
VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
Values: 1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1 at
/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Obj
RelP/DbiDbHandle.pm line 177, <NODES> line 2.
<--------------------
Arnaud
Deborah F. Pinney wrote:
>I didn't experience this problem. However, in looking over the
>LoadTaxon.pm code I noticed that there was still a commented out line
>that should have been corrected. This line is used only for restarting.
>I have uncommented it and submitted to cvs. Please update your file.
>
> Deborah Pinney
>
>
>
>On
>Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
>
>
>
>>Hi
>>
>>I've tried to populate the taxonomy files from NCBI into GUS3. it's
>>working fine until it reaches the last node entry, ie the line 173295 in
>>the nodes.dmp file.
>>I now have these 2 errors when populating the nodes file:
>>
>> > oerr ora 03113
>> 03113, 00000, "end-of-file on communication channel"
>> // *Cause:
>> // *Action:
>>
>> > oerr ora 01041
>> 01041, 00000, "internal error. hostdef extension doesn't exist"
>> // *Cause: Pointer to hstdef extension in hstdef is null.
>> // *Action: Report as a bug
>>
>>Have you come across the same problem ?
>>Any idea about the cause of this 'end-of-file on communication channel'
>>error ?
>>
>>cheers
>>Arnaud
>>
>>./bin/ga GUS::Common::Plugin::LoadTaxon
>>--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
>>--names=/nfs/pathsoft/databases/NCBI/names.dmp
>>--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
>>
>>--------------------------->
>>[...]
>>
>>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
>> bindValues (89410)
>>
>>sqlExec:
>> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
>>genetic_code_id, row_project_id, taxon_id, group_r
>>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
>>modification_date, user_read, row_alg_invocation_id, oth
>>er_write, ncbi_tax_id, rank )
>> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>> bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>processed ncbi_tax_id : 89410
>>
>>^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
>>communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
>>team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
>>line 242, <NODES> line 173295.
>>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
>>(perhaps you need to call execute first) at /nfs/t
>>eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
>>line 243, <NODES> line 173295.
>>
>>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
>> bindValues (110556)
>>
>>
>>sqlExec:
>> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
>>genetic_code_id, row_project_id, taxon_id, group_r
>>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
>>modification_date, user_read, row_alg_invocation_id, oth
>>er_write, ncbi_tax_id, rank )
>> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>> bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>processed ncbi_tax_id : 110556
>>DBD::Oracle::db prepare failed: Error while trying to retrieve text for
>>error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
>>cribe) at
>>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
>>line 241, <NODES> line 1
>>73295.
>>
>>
>>sqlExec:
>> UPDATE Core.AlgorithmInvocation
>> SET
>> end_time = SYSDATE,
>> row_alg_invocation_id = ?,
>> modification_date = SYSDATE
>> WHERE algorithm_invocation_id = ?
>> bindValues (9, 9)
>> DbiHandle:sqlExec:insert succeeded 1 row(s)
>>Can't call method "execute" on an undefined value at
>>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
>>lugin/LoadTaxon.pm line 242, <NODES> line 173295.
>><------------------------------------
>>
>>
>>
>>
>>
|
|
From: Chetna W. <ch...@ar...> - 2003-03-07 15:06:42
|
Hi,
That is because without --commit option the table TaxonName is empty and
thats why the loading stops. Oracle checks that is the specified row
present in the table TaxonName and only when this check is sucessful it
will allow loading of data into the table under consideration. This way
RDBMS's keep consistency in the database.
Thanks
Chetna
> It's working now. Just noticed something, when the option --commit is
> not specified, the loading stops on the population of the TaxonName
> table, because of the Foreign Key taxon_id integrity not respected.
>
> with '--commit' option it seems to work fine.
>
> ------------->
>
> RetrieveFromDB: select * from SRes.TaxonName where unique_name_variant
> is NULL and name_class = ? and name = ? and
> taxon_id is NULL
> bindValues (synonym, all)
>
>
> sqlExec:
> INSERT INTO SRes.TaxonName ( row_user_id, other_read,
> unique_name_variant, user_write, group_write, name_class, r
> ow_project_id, name, taxon_id, modification_date, user_read,
> row_alg_invocation_id, group_read, other_write, row_group
> _id, taxon_name_id )
> VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
> bindValues (1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1)
> DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into
> ("SRES"."TAXONNAME"."TAXON_ID") (DBD ERROR: OCIStmt
> Execute) at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 137, <NODES> line 2.
>
>
> sqlExec:
> UPDATE Core.AlgorithmInvocation
> SET
> end_time = SYSDATE,
> row_alg_invocation_id = ?,
> modification_date = SYSDATE
> WHERE algorithm_invocation_id = ?
> bindValues (9, 9)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
>
> SQL ERROR!! involving
>
> INSERT INTO SRes.TaxonName ( row_user_id, other_read,
> unique_name_variant, user_write, group_write, name_class, r
> ow_project_id, name, taxon_id, modification_date, user_read,
> row_alg_invocation_id, group_read, other_write, row_group
> _id, taxon_name_id )
> VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? )
> Values: 1, 1, 1, 1, synonym, 1, all, 1, 9, 1, 0, 1, 1 at
> /nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Obj
> RelP/DbiDbHandle.pm line 177, <NODES> line 2.
>
> <--------------------
>
> Arnaud
>
> Deborah F. Pinney wrote:
>
> >I didn't experience this problem. However, in looking over the
> >LoadTaxon.pm code I noticed that there was still a commented out line
> >that should have been corrected. This line is used only for restarting.
> >I have uncommented it and submitted to cvs. Please update your file.
> >
> > Deborah Pinney
> >
> >
> >
> >On
> >Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
> >
> >
> >
> >>Hi
> >>
> >>I've tried to populate the taxonomy files from NCBI into GUS3. it's
> >>working fine until it reaches the last node entry, ie the line 173295 in
> >>the nodes.dmp file.
> >>I now have these 2 errors when populating the nodes file:
> >>
> >> > oerr ora 03113
> >> 03113, 00000, "end-of-file on communication channel"
> >> // *Cause:
> >> // *Action:
> >>
> >> > oerr ora 01041
> >> 01041, 00000, "internal error. hostdef extension doesn't exist"
> >> // *Cause: Pointer to hstdef extension in hstdef is null.
> >> // *Action: Report as a bug
> >>
> >>Have you come across the same problem ?
> >>Any idea about the cause of this 'end-of-file on communication channel'
> >>error ?
> >>
> >>cheers
> >>Arnaud
> >>
> >>./bin/ga GUS::Common::Plugin::LoadTaxon
> >>--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp
> >>--names=/nfs/pathsoft/databases/NCBI/names.dmp
> >>--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
> >>
> >>--------------------------->
> >>[...]
> >>
> >>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> >> bindValues (89410)
> >>
> >>sqlExec:
> >> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> >>genetic_code_id, row_project_id, taxon_id, group_r
> >>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> >>modification_date, user_read, row_alg_invocation_id, oth
> >>er_write, ncbi_tax_id, rank )
> >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >> bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
> >> DbiHandle:sqlExec:insert succeeded 1 row(s)
> >>processed ncbi_tax_id : 89410
> >>
> >>^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on
> >>communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
> >>team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> >>line 242, <NODES> line 173295.
> >>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing
> >>(perhaps you need to call execute first) at /nfs/t
> >>eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> >>line 243, <NODES> line 173295.
> >>
> >>RetrieveFromDB: select * from SRes.Taxon where ncbi_tax_id = ?
> >> bindValues (110556)
> >>
> >>
> >>sqlExec:
> >> INSERT INTO SRes.Taxon ( row_user_id, user_write, group_write,
> >>genetic_code_id, row_project_id, taxon_id, group_r
> >>ead, row_group_id, other_read, mitochondrial_genetic_code_id,
> >>modification_date, user_read, row_alg_invocation_id, oth
> >>er_write, ncbi_tax_id, rank )
> >> VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
> >> bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556, species)
> >> DbiHandle:sqlExec:insert succeeded 1 row(s)
> >>processed ncbi_tax_id : 110556
> >>DBD::Oracle::db prepare failed: Error while trying to retrieve text for
> >>error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
> >>cribe) at
> >>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> >>line 241, <NODES> line 1
> >>73295.
> >>
> >>
> >>sqlExec:
> >> UPDATE Core.AlgorithmInvocation
> >> SET
> >> end_time = SYSDATE,
> >> row_alg_invocation_id = ?,
> >> modification_date = SYSDATE
> >> WHERE algorithm_invocation_id = ?
> >> bindValues (9, 9)
> >> DbiHandle:sqlExec:insert succeeded 1 row(s)
> >>Can't call method "execute" on an undefined value at
> >>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
> >>lugin/LoadTaxon.pm line 242, <NODES> line 173295.
> >><------------------------------------
> >>
> >>
> >>
> >>
> >>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> for complex code. Debugging C/C++ programs can leave you feeling lost and
> disoriented. TotalView can help you find your way. Available on major UNIX
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|
|
From: Jonathan C. <cra...@pc...> - 2003-03-07 16:14:05
|
Hi Chetna- > That is because without --commit option the table TaxonName is empty and > thats why the loading stops. Oracle checks that is the specified row That's not quite true (or at least it shouldn't be); without the --commit option the plugins will still do all of the same inserts that they would do with the --commit option. By default these inserts are all performed in a single transaction and until that transaction is either rolled back or committed, it is true that *other* transactions won't be able to see the new rows in TaxonName (or Taxon, actually, since the reference in question was TaxonName.taxon_id.) However, the plugin itself *should* be able to see the new rows in Taxon/TaxonName, so long as it doesn't roll the transaction back and start a new one. The crucial thing to realize is that a table can appear to be empty in one transaction/session, but not empty in another. So even though the Taxon table might not contain any rows that have been committed, it could still contain rows that are visible to the plugin itself (and that could be used to establish a foreign key constraint from TaxonName.) The crucial question (I think) is whether the plugin is doing a commit or rollback between the time it inserts the Taxon rows and the time it inserts the TaxonName rows. I don't think I've looked at this code but it should be easy to figure out why it's getting a null taxon_id and it should be possible to get it to work in no-commit mode. Jonathan -- Jonathan Crabtree Center for Bioinformatics, University of Pennsylvania 1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021 215-573-3115 |
|
From: Chetna W. <ch...@ar...> - 2003-03-07 16:44:55
|
Hi Jonathan, Thanks for the mail. I was thinking how the script would work without the --commit option and your explanation has clarified that and helped to clear my assumptions. Thanks Chetna > That's not quite true (or at least it shouldn't be); without the --commit > option the plugins will still do all of the same inserts that they would > do with the --commit option. By default these inserts are all performed > in a single transaction and until that transaction is either rolled back > or committed, it is true that *other* transactions won't be able to see the > new rows in TaxonName (or Taxon, actually, since the reference in question > was TaxonName.taxon_id.) However, the plugin itself *should* be able to see > the new rows in Taxon/TaxonName, so long as it doesn't roll the transaction > back and start a new one. The crucial thing to realize is that a table can > appear to be empty in one transaction/session, but not empty in another. > So even though the Taxon table might not contain any rows that have > been committed, it could still contain rows that are visible to the plugin > itself (and that could be used to establish a foreign key constraint from > TaxonName.) The crucial question (I think) is whether the plugin is doing > a commit or rollback between the time it inserts the Taxon rows and the time > it inserts the TaxonName rows. I don't think I've looked at this code but > it should be easy to figure out why it's getting a null taxon_id and it should > be possible to get it to work in no-commit mode. |
|
From: Arnaud K. <ax...@sa...> - 2003-03-07 15:18:12
|
Another thing. At some point the code is trying to analyse the
SRes.TaxonName table. I've got an insufficient privileges error.
I've got two database logins which are used for connecting the database
from the perl object layer:
* databaseLogin=GUSrw
* readOnlyDatabaseLogin=GUSro
I guess the effective login to populate GUS is GUSrw, is that correct?
Probably a question for you Martin. Does GUSrw have enough privileges to
execute analyse table statements on any schemas (in particular the SRes
shema) ?
Arnaud
---------------------->
DBD::Oracle::db do failed: ORA-01031: insufficient privileges (DBD
ERROR: OCIStmtExecute) at /nfs/team81/axk/projects/
gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm line 304,
<NODES> line 2.
<----------------------
line 304: $dbh->do("analyze table sres.TaxonName compute statistics");
Deborah F. Pinney wrote:
>I didn't experience this problem. However, in looking over the
>LoadTaxon.pm code I noticed that there was still a commented out line
>that should have been corrected. This line is used only for restarting.
>I have uncommented it and submitted to cvs. Please update your file.
>
> Deborah Pinney
>
>
>
>
>
|
|
From: Jonathan C. <cra...@pc...> - 2003-03-07 16:03:19
|
Hi Arnaud-
I agree with Martin about the "EOF on communication channel" error; all
this message means is that something happened to break your connection
to the database. What broke your connection was almost certainly the
server process crashing or shutting down in response to the *other* error
("hostdef extension doesn't exist"). I've never seen this error before
and have no idea what might have caused it. You could try looking at the
trace file dumped by Oracle when the process crashed to see what it was
doing at the time.
As for the problem running the plugin when the --commit flag is not
specified, I'm surprised that it crashes; the foreign key dependencies
should be created just fine in no-commit mode. However, all the inserts
do have to performed within a single transaction, which is then rolled
back before the plugin exits. Maybe the LoadTaxon plugin is doing
something to cause a premature rollback?
Arnaud Kerhornou wrote:
> Another thing. At some point the code is trying to analyse the
> SRes.TaxonName table. I've got an insufficient privileges error.
At the very least the plugin should have an option to let the user
specify whether they want to analyze the table, since not every site
will want to allow regular users the necessary privileges.
Jonathan
--
Jonathan Crabtree
Center for Bioinformatics, University of Pennsylvania
1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
215-573-3115
|
|
From: Deborah F. P. <pi...@pc...> - 2003-03-07 16:12:33
|
Several of the attributes in taxon (ncbi_tax_id, parent_id and taxon_id)
should be indexed or they will cause the plugin to run very slowly at
several points. That was the reason for the line: $dbh->do("analyze table
sres.Taxon compute statistics"); However, I suspect the line is not
accomplishing what I intended because of the permission issue and I
understand that it is platform specific. For those reasons, the line
should be removed (I will remove it now and update cvs).
Debbie
On Fri, 7 Mar 2003, Arnaud Kerhornou wrote:
> Another thing. At some point the code is trying to analyse the
> SRes.TaxonName table. I've got an insufficient privileges error.
>
> I've got two database logins which are used for connecting the database
> from the perl object layer:
> * databaseLogin=GUSrw
> * readOnlyDatabaseLogin=GUSro
>
> I guess the effective login to populate GUS is GUSrw, is that correct?
> Probably a question for you Martin. Does GUSrw have enough privileges to
> execute analyse table statements on any schemas (in particular the SRes
> shema) ?
>
> Arnaud
>
> ---------------------->
> DBD::Oracle::db do failed: ORA-01031: insufficient privileges (DBD
> ERROR: OCIStmtExecute) at /nfs/team81/axk/projects/
> gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTaxon.pm line 304,
> <NODES> line 2.
> <----------------------
>
> line 304: $dbh->do("analyze table sres.TaxonName compute statistics");
>
> Deborah F. Pinney wrote:
>
> >I didn't experience this problem. However, in looking over the
> >LoadTaxon.pm code I noticed that there was still a commented out line
> >that should have been corrected. This line is used only for restarting.
> >I have uncommented it and submitted to cvs. Please update your file.
> >
> > Deborah Pinney
> >
> >
> >
> >
> >
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> for complex code. Debugging C/C++ programs can leave you feeling lost and
> disoriented. TotalView can help you find your way. Available on major UNIX
> and Linux platforms. Try it free. www.etnus.com
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Jonathan C. <cra...@pc...> - 2003-03-07 16:17:30
|
Deborah F. Pinney wrote:
> Several of the attributes in taxon (ncbi_tax_id, parent_id and taxon_id)
> should be indexed or they will cause the plugin to run very slowly at
> several points. That was the reason for the line: $dbh->do("analyze table
> sres.Taxon compute statistics"); However, I suspect the line is not
Doing an analyze table won't help you if it's not properly indexed in the
first place. All it will do is provide the optimizer with up-to-date
statistics that might help it make a better decision about index usage.
Also, if the tables that you're querying from haven't been analyzed at all
then Oracle 8i/9i will revert to using the rule-based optimizer. Anyway,
this is typically something that's handled by the DBA, so removing it from
the plugin sounds like the best idea.
Jonathan
|
|
From: steve f. <sfi...@pc...> - 2003-03-14 15:18:06
|
sorry paul that we just haven't gotten to documenting this.
here is the sequence:
1. write the plugin initially
2. check it in to cvs first time
3. build
4. ga +create PLUGIN --commit
5. now you can debug and tweek your plugin by running ga PLUGIN (without
--commit)
6. when it is working enough to test with --commit:
- check it in to cvs
- build
- ga +update PLUGIN --commit
7. iterarate on steps 5 and 6
steve
pjm wrote:
>Steve,
>
>Ok, I dug out your old email on --commit registering plugins to find The Way of
>testing my LoadPfam plugin with a tiny subsection of the latest PFma release. It
>only creates records a few tables and they are all currently empty in my DB.
>Anything it creates I will quite happily (and easily) destroy (drop 3 tables).
>
>Thus, before I cvs commit I wanted to try out --commit. But I can't run it with
>out cvs commiting...
>
>I take it I can cvs commit, then `ga +update GUS::Common::Plugin::LoadPfam` as
>needed, right?
>
>UPDATE
>
>I cvs commited the code so far (it needs a tidy, some print statements removing)
>but its more or less there. Thinking it would get around the --commit problems I
>did a
>
> `ga +update GUS::Common::Plugin::LoadPfam`
>
>but because its already registered it won't update it. Doh! How do I get around
>this? What is The Way?
>
>Paul.
>
>steve fischer wrote:
>
>
>>just want to clarify why debbie "committed when i should not have".
>>
>>the deal is that we are extremely rigorous about our tracking of bulk
>>changes to the db.
>>
>>in particular, you cannot run a plugin with --commit unless that exact
>>revision of the plugin has been registered in the db. and, you cannot
>>do that registering unless you have checked in that version of the
>>plugin to cvs.
>>
>>instead of checking in a crippled version of a plugin, hacks like this
>>can be accomplished by other ways, such as:
>> - introducing a temporary command line arg which the plugin tests for
>>to run its hacky code.
>> - copying the plugin to a new file, such as LoadTaxonDebbiesHack.pm,
>>and registering it as a new plugin
>>
>>steve
>>
>>Deborah F. Pinney wrote:
>>
>>
>>
>>>This is my fault. I commited to cvs when I should not have. I have
>>>uncommented those lines and recomitted to cvs.
>>>
>>>
>>> Deboeah Pinney
>>>
>>>
>>>On Wed, 5 Mar 2003, Arnaud
>>>Kerhornou wrote:
>>>
>>>
>>>
>>>
>>>
>>>>Hi
>>>>
>>>>I'm trying to run LoadTaxon plugin. Why some lines are commented out ?
>>>>
>>>> #my $genCodes = $self->makeGeneticCode();
>>>>
>>>> my $namesDmp = $self->getNames();
>>>>
>>>> #my $nodesHash = $self->makeNodesHash($genCodes);
>>>>
>>>> #my $rootAttArray = $self->getRootAttArray($genCodes);
>>>>
>>>> #$self->makeTaxonEntry($rootAttArray, \$count);
>>>>
>>>> #if ($self->getCla->{'restart'} && $self->getCla->{'restart'} > 1) {
>>>> #$self->getTaxonAtt($self->getCla->{'restart'},$nodesHash,\$count);
>>>> #}
>>>> #else {
>>>> #$self->getTaxonAtt($rootAttArray->[0],$nodesHash,\$count);
>>>> #}
>>>>
>>>>Arnaud
>>>>
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>>>>for complex code. Debugging C/C++ programs can leave you feeling lost and
>>>>disoriented. TotalView can help you find your way. Available on major UNIX
>>>>and Linux platforms. Try it free. www.etnus.com
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>>>for complex code. Debugging C/C++ programs can leave you feeling lost and
>>>disoriented. TotalView can help you find your way. Available on major UNIX
>>>and Linux platforms. Try it free. www.etnus.com
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>>
>>>
>>>
>>-------------------------------------------------------
>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
>>for complex code. Debugging C/C++ programs can leave you feeling lost and
>>disoriented. TotalView can help you find your way. Available on major UNIX
>>and Linux platforms. Try it free. www.etnus.com
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
>
>
|
|
From: pjm <pj...@sa...> - 2003-03-14 15:40:24
|
Steve,
I've done a 'cvs update' and "build GUS install -append' so everything is
up-to-date and in sync.
I get a circular thing happening when told to
'ga +update GUS::PluginMgr::GusApplication --commit'
It keeps telling me to do it when it doesn't work! What should I do?
See;
pcs2b[pjm]136: ga +update GUS::Common::Plugin::LoadPfam --commit
Reading properties from /nfs/team81/pjm/GUS/config/GUS-PluginMgr.prop
Reading properties from /nfs/team81/pjm/.gus.properties
DBD::Oracle::db do failed: ORA-01534: rollback segment 'BIGRBS1' doesn't exist
(DBD ERROR: OCIStmtExecute) at
/nfs/team81/pjm/GUS/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 148.
USER ERROR: No Core.AlgorithmImplementation found for
GUS::PluginMgr::GusApplication cvs revision 1.35.
Please use 'ga +update GUS::PluginMgr::GusApplication --commit'
pcs2b[pjm]137:
pcs2b[pjm]137: ga +update GUS::PluginMgr::GusApplication --commit
Reading properties from /nfs/team81/pjm/GUS/config/GUS-PluginMgr.prop
Reading properties from /nfs/team81/pjm/.gus.properties
DBD::Oracle::db do failed: ORA-01534: rollback segment 'BIGRBS1' doesn't exist
(DBD ERROR: OCIStmtExecute) at
/nfs/team81/pjm/GUS/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 148.
USER ERROR: No Core.AlgorithmImplementation found for
GUS::PluginMgr::GusApplication cvs revision 1.35.
Please use 'ga +update GUS::PluginMgr::GusApplication --commit'
steve fischer wrote:
>
> sorry paul that we just haven't gotten to documenting this.
>
> here is the sequence:
>
> 1. write the plugin initially
> 2. check it in to cvs first time
> 3. build
> 4. ga +create PLUGIN --commit
> 5. now you can debug and tweek your plugin by running ga PLUGIN (without
> --commit)
> 6. when it is working enough to test with --commit:
> - check it in to cvs
> - build
> - ga +update PLUGIN --commit
> 7. iterarate on steps 5 and 6
>
> steve
>
> pjm wrote:
>
> >Steve,
> >
> >Ok, I dug out your old email on --commit registering plugins to find The Way of
> >testing my LoadPfam plugin with a tiny subsection of the latest PFma release. It
> >only creates records a few tables and they are all currently empty in my DB.
> >Anything it creates I will quite happily (and easily) destroy (drop 3 tables).
> >
> >Thus, before I cvs commit I wanted to try out --commit. But I can't run it with
> >out cvs commiting...
> >
> >I take it I can cvs commit, then `ga +update GUS::Common::Plugin::LoadPfam` as
> >needed, right?
> >
> >UPDATE
> >
> >I cvs commited the code so far (it needs a tidy, some print statements removing)
> >but its more or less there. Thinking it would get around the --commit problems I
> >did a
> >
> > `ga +update GUS::Common::Plugin::LoadPfam`
> >
> >but because its already registered it won't update it. Doh! How do I get around
> >this? What is The Way?
> >
> >Paul.
> >
> >steve fischer wrote:
> >
> >
> >>just want to clarify why debbie "committed when i should not have".
> >>
> >>the deal is that we are extremely rigorous about our tracking of bulk
> >>changes to the db.
> >>
> >>in particular, you cannot run a plugin with --commit unless that exact
> >>revision of the plugin has been registered in the db. and, you cannot
> >>do that registering unless you have checked in that version of the
> >>plugin to cvs.
> >>
> >>instead of checking in a crippled version of a plugin, hacks like this
> >>can be accomplished by other ways, such as:
> >> - introducing a temporary command line arg which the plugin tests for
> >>to run its hacky code.
> >> - copying the plugin to a new file, such as LoadTaxonDebbiesHack.pm,
> >>and registering it as a new plugin
> >>
> >>steve
> >>
> >>Deborah F. Pinney wrote:
> >>
> >>
> >>
> >>>This is my fault. I commited to cvs when I should not have. I have
> >>>uncommented those lines and recomitted to cvs.
> >>>
> >>>
> >>> Deboeah Pinney
> >>>
> >>>
> >>>On Wed, 5 Mar 2003, Arnaud
> >>>Kerhornou wrote:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>>Hi
> >>>>
> >>>>I'm trying to run LoadTaxon plugin. Why some lines are commented out ?
> >>>>
> >>>> #my $genCodes = $self->makeGeneticCode();
> >>>>
> >>>> my $namesDmp = $self->getNames();
> >>>>
> >>>> #my $nodesHash = $self->makeNodesHash($genCodes);
> >>>>
> >>>> #my $rootAttArray = $self->getRootAttArray($genCodes);
> >>>>
> >>>> #$self->makeTaxonEntry($rootAttArray, \$count);
> >>>>
> >>>> #if ($self->getCla->{'restart'} && $self->getCla->{'restart'} > 1) {
> >>>> #$self->getTaxonAtt($self->getCla->{'restart'},$nodesHash,\$count);
> >>>> #}
> >>>> #else {
> >>>> #$self->getTaxonAtt($rootAttArray->[0],$nodesHash,\$count);
> >>>> #}
> >>>>
> >>>>Arnaud
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>-------------------------------------------------------
> >>>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> >>>>for complex code. Debugging C/C++ programs can leave you feeling lost and
> >>>>disoriented. TotalView can help you find your way. Available on major UNIX
> >>>>and Linux platforms. Try it free. www.etnus.com
> >>>>_______________________________________________
> >>>>Gusdev-gusdev mailing list
> >>>>Gus...@li...
> >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>>-------------------------------------------------------
> >>>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> >>>for complex code. Debugging C/C++ programs can leave you feeling lost and
> >>>disoriented. TotalView can help you find your way. Available on major UNIX
> >>>and Linux platforms. Try it free. www.etnus.com
> >>>_______________________________________________
> >>>Gusdev-gusdev mailing list
> >>>Gus...@li...
> >>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>-------------------------------------------------------
> >>This SF.net email is sponsored by: Etnus, makers of TotalView, The debugger
> >>for complex code. Debugging C/C++ programs can leave you feeling lost and
> >>disoriented. TotalView can help you find your way. Available on major UNIX
> >>and Linux platforms. Try it free. www.etnus.com
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>
> >
> >
> >
> >
>
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