Install problem at make prepdb...

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Install problem at make prepdb...

Nicolas Joannin
Hello everybody,

I am having a small problem with installing CHADO on my local machine.
When I run the "make prepdb" command, I get some error messages related to the initialization process:

"Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7."

(See full output below.)
I'm a bit confused why the @INC would contain such a list of locations...

I did modify the load/etc/initialize.sql file to add my default organism. But I don't really see how that could be the source of the error...

Any ideas what I might have done wrong?

Best regards,
Nicolas


Output of make prepdb:

Nicolass-MacBook-Air:chado-1.2 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
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INSERT 0 1
INSERT 0 1
INSERT 0 1
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INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
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INSERT 0 1
INSERT 0 1
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INSERT 0 1
psql:/Users/NicojoAir11/gmod/chado-1.2/load/etc/initialize.sql:235: NOTICE:  CREATE TABLE will create implicit sequence "materialized_view_materialized_view_id_seq" for serial column "materialized_view.materialized_view_id"
psql:/Users/NicojoAir11/gmod/chado-1.2/load/etc/initialize.sql:235: NOTICE:  CREATE TABLE / UNIQUE will create implicit index "materialized_view_name_key" for table "materialized_view"
CREATE TABLE
Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7.
Adding Plasmodium falciparum to the database...
Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7.

------------------------------------------------------------------------------
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Re: Install problem at make prepdb...

Scott Cain
Hi Nicolas,

Are you using the 1.2 release of chado?  That's a few years old. You should really be using the 1.23 release which is the most recent. Do you have BIo::Chado::Schema installed? It's a prerequisite, but one of the bugs fixed since the 1.2 release is making the makefile warn you when it isn't present. 

Another thing I'm pretty sure I fixed was taking out the references to my development paths in @INC. 

Scott

Sent from my iPhone

On Apr 8, 2013, at 3:43 PM, Nicolas Joannin <[hidden email]> wrote:

Hello everybody,

I am having a small problem with installing CHADO on my local machine.
When I run the "make prepdb" command, I get some error messages related to the initialization process:

"Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7."

(See full output below.)
I'm a bit confused why the @INC would contain such a list of locations...

I did modify the load/etc/initialize.sql file to add my default organism. But I don't really see how that could be the source of the error...

Any ideas what I might have done wrong?

Best regards,
Nicolas


Output of make prepdb:

Nicolass-MacBook-Air:chado-1.2 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
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INSERT 0 1
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INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
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INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
psql:/Users/NicojoAir11/gmod/chado-1.2/load/etc/initialize.sql:235: NOTICE:  CREATE TABLE will create implicit sequence "materialized_view_materialized_view_id_seq" for serial column "materialized_view.materialized_view_id"
psql:/Users/NicojoAir11/gmod/chado-1.2/load/etc/initialize.sql:235: NOTICE:  CREATE TABLE / UNIQUE will create implicit index "materialized_view_name_key" for table "materialized_view"
CREATE TABLE
Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7.
Adding Plasmodium falciparum to the database...
Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7.
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema

------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
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Re: Install problem at make prepdb...

Nicolas Joannin
Hi Scott,

Thanks for the quick reply!
Yes, I downloaded version 1.2 from the GMOD website... I guess the best is to checkout the latest from svn.
Will do so tomorrow morning!

Thanks again!
Nicolas

On Monday, April 8, 2013, Scott Cain wrote:
Hi Nicolas,

Are you using the 1.2 release of chado?  That's a few years old. You should really be using the 1.23 release which is the most recent. Do you have BIo::Chado::Schema installed? It's a prerequisite, but one of the bugs fixed since the 1.2 release is making the makefile warn you when it isn't present. 

Another thing I'm pretty sure I fixed was taking out the references to my development paths in @INC. 

Scott

Sent from my iPhone

On Apr 8, 2013, at 3:43 PM, Nicolas Joannin <[hidden email]> wrote:

Hello everybody,

I am having a small problem with installing CHADO on my local machine.
When I run the "make prepdb" command, I get some error messages related to the initialization process:

"Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7."

(See full output below.)
I'm a bit confused why the @INC would contain such a list of locations...

I did modify the load/etc/initialize.sql file to add my default organism. But I don't really see how that could be the source of the error...

Any ideas what I might have done wrong?

Best regards,
Nicolas


Output of make prepdb:

Nicolass-MacBook-Air:chado-1.2 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
I
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
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--


Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



------------------------------------------------------------------------------
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Re: Install problem at make prepdb...

Scott Cain
No, don't checkout from svn (though I think that should work too; I don't think I've broken anything recently).  The 1.23 release should be downloadable from SF as well. 


On Apr 8, 2013, at 4:03 PM, Nicolas Joannin <[hidden email]> wrote:

Hi Scott,

Thanks for the quick reply!
Yes, I downloaded version 1.2 from the GMOD website... I guess the best is to checkout the latest from svn.
Will do so tomorrow morning!

Thanks again!
Nicolas

On Monday, April 8, 2013, Scott Cain wrote:
Hi Nicolas,

Are you using the 1.2 release of chado?  That's a few years old. You should really be using the 1.23 release which is the most recent. Do you have BIo::Chado::Schema installed? It's a prerequisite, but one of the bugs fixed since the 1.2 release is making the makefile warn you when it isn't present. 

Another thing I'm pretty sure I fixed was taking out the references to my development paths in @INC. 

Scott

Sent from my iPhone

On Apr 8, 2013, at 3:43 PM, Nicolas Joannin <[hidden email]> wrote:

Hello everybody,

I am having a small problem with installing CHADO on my local machine.
When I run the "make prepdb" command, I get some error messages related to the initialization process:

"Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7."

(See full output below.)
I'm a bit confused why the @INC would contain such a list of locations...

I did modify the load/etc/initialize.sql file to add my default organism. But I don't really see how that could be the source of the error...

Any ideas what I might have done wrong?

Best regards,
Nicolas


Output of make prepdb:

Nicolass-MacBook-Air:chado-1.2 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
I
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
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<a href="javascript:_e({}, 'cvml', 'Gmod-schema@lists.sourceforge.net');" target="_blank">Gmod-schema@...
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--


Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



------------------------------------------------------------------------------
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Reduce network management and security costs.Learn how to hire
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Re: Install problem at make prepdb...

Nicolas Joannin
Hi Scott,

Thanks for the link.
I came to the 1.2 version through the GMOD link to download CHADO.
Maybe it would be good to change that to the 1.23 version?

Best regards,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Tue, Apr 9, 2013 at 12:14 AM, Scott Cain <[hidden email]> wrote:
No, don't checkout from svn (though I think that should work too; I don't think I've broken anything recently).  The 1.23 release should be downloadable from SF as well. 


On Apr 8, 2013, at 4:03 PM, Nicolas Joannin <[hidden email]> wrote:

Hi Scott,

Thanks for the quick reply!
Yes, I downloaded version 1.2 from the GMOD website... I guess the best is to checkout the latest from svn.
Will do so tomorrow morning!

Thanks again!
Nicolas

On Monday, April 8, 2013, Scott Cain wrote:
Hi Nicolas,

Are you using the 1.2 release of chado?  That's a few years old. You should really be using the 1.23 release which is the most recent. Do you have BIo::Chado::Schema installed? It's a prerequisite, but one of the bugs fixed since the 1.2 release is making the makefile warn you when it isn't present. 

Another thing I'm pretty sure I fixed was taking out the references to my development paths in @INC. 

Scott

Sent from my iPhone

On Apr 8, 2013, at 3:43 PM, Nicolas Joannin <[hidden email]> wrote:

Hello everybody,

I am having a small problem with installing CHADO on my local machine.
When I run the "make prepdb" command, I get some error messages related to the initialization process:

"Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7."

(See full output below.)
I'm a bit confused why the @INC would contain such a list of locations...

I did modify the load/etc/initialize.sql file to add my default organism. But I don't really see how that could be the source of the error...

Any ideas what I might have done wrong?

Best regards,
Nicolas


Output of make prepdb:

Nicolass-MacBook-Air:chado-1.2 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
I
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


--


Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan




------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
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Re: Install problem at make prepdb...

Nicolas Joannin
Hi again,

I am in the process of installing version 1.23 and this time I got a different problem with 'make prepdb' (see full output below):

"Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104."

I checked and that file is present with the others in the bin folder.
However, when I checked the line 104 in Builder.pm, I realized that 'bin/' was missing in front of the file name in the command:

system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

instead of:

system("bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

When executing the command after the modification, it worked fine.
I guess that is a bug? Or was there something else that needs changing instead?

Thanks in advance for your help!
Best regards,

Nicolas




Nicolass-MacBook-Air:chado-1.23 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE will create implicit sequence "materialized_view_materialized_view_id_seq" for serial column "materialized_view.materialized_view_id"
psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE / UNIQUE will create implicit index "materialized_view_name_key" for table "materialized_view"
CREATE TABLE
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Adding Plasmodium falciparum to the database...
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK

Both genus and species are required; please provide them below

Organism's genus?  Plasmodium
Organism's species?  falciparum
Organism's abbreviation? [P.falciparum] 
Comment (can be empty)?  
There was already an organism with that genus and species in the database;
exiting...
Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104.


------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-schema mailing list
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Re: Install problem at make prepdb...

Nicolas Joannin
Hello again, again...

I think I got this one wrong: the real problem is that my ActivePerl site/bin folder is not in my path (for whatever reason I can't figure out)...

Anyhow, no need to change the Build.pm file, it was a problem on my side!
Sorry for the disturbance!

Best regards,
Nicolas




Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Tue, Apr 9, 2013 at 12:52 PM, Nicolas Joannin <[hidden email]> wrote:
Hi again,

I am in the process of installing version 1.23 and this time I got a different problem with 'make prepdb' (see full output below):

"Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104."

I checked and that file is present with the others in the bin folder.
However, when I checked the line 104 in Builder.pm, I realized that 'bin/' was missing in front of the file name in the command:

system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

instead of:

system("bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

When executing the command after the modification, it worked fine.
I guess that is a bug? Or was there something else that needs changing instead?

Thanks in advance for your help!
Best regards,

Nicolas




Nicolass-MacBook-Air:chado-1.23 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE will create implicit sequence "materialized_view_materialized_view_id_seq" for serial column "materialized_view.materialized_view_id"
psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE / UNIQUE will create implicit index "materialized_view_name_key" for table "materialized_view"
CREATE TABLE
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Adding Plasmodium falciparum to the database...
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK

Both genus and species are required; please provide them below

Organism's genus?  Plasmodium
Organism's species?  falciparum
Organism's abbreviation? [P.falciparum] 
Comment (can be empty)?  
There was already an organism with that genus and species in the database;
exiting...
Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104.



------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-schema mailing list
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Re: Install problem at make prepdb...

Scott Cain
In reply to this post by Nicolas Joannin
Hi Nicolas,

Thanks so much for pointing that out--it should have been pointing at a link one directory up, so that you'd get the entire list of Chado releases and you could pick the last one.  I fixed the link now.

Scott



On Tue, Apr 9, 2013 at 3:41 AM, Nicolas Joannin <[hidden email]> wrote:
Hi Scott,

Thanks for the link.
I came to the 1.2 version through the GMOD link to download CHADO.
Maybe it would be good to change that to the 1.23 version?

Best regards,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Tue, Apr 9, 2013 at 12:14 AM, Scott Cain <[hidden email]> wrote:
No, don't checkout from svn (though I think that should work too; I don't think I've broken anything recently).  The 1.23 release should be downloadable from SF as well. 


On Apr 8, 2013, at 4:03 PM, Nicolas Joannin <[hidden email]> wrote:

Hi Scott,

Thanks for the quick reply!
Yes, I downloaded version 1.2 from the GMOD website... I guess the best is to checkout the latest from svn.
Will do so tomorrow morning!

Thanks again!
Nicolas

On Monday, April 8, 2013, Scott Cain wrote:
Hi Nicolas,

Are you using the 1.2 release of chado?  That's a few years old. You should really be using the 1.23 release which is the most recent. Do you have BIo::Chado::Schema installed? It's a prerequisite, but one of the bugs fixed since the 1.2 release is making the makefile warn you when it isn't present. 

Another thing I'm pretty sure I fixed was taking out the references to my development paths in @INC. 

Scott

Sent from my iPhone

On Apr 8, 2013, at 3:43 PM, Nicolas Joannin <[hidden email]> wrote:

Hello everybody,

I am having a small problem with installing CHADO on my local machine.
When I run the "make prepdb" command, I get some error messages related to the initialization process:

"Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: /home/scott/cvs_stuff/schema/chado/lib /home/cain/cvs_stuff/schema/chado/lib /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.4 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at bin/gmod_add_organism.pl line 7.
BEGIN failed--compilation aborted at bin/gmod_add_organism.pl line 7."

(See full output below.)
I'm a bit confused why the @INC would contain such a list of locations...

I did modify the load/etc/initialize.sql file to add my default organism. But I don't really see how that could be the source of the error...

Any ideas what I might have done wrong?

Best regards,
Nicolas


Output of make prepdb:

Nicolass-MacBook-Air:chado-1.2 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
I
------------------------------------------------------------------------------
Minimize network downtime and maximize team effectiveness.
Reduce network management and security costs.Learn how to hire
the most talented Cisco Certified professionals. Visit the
Employer Resources Portal
http://www.cisco.com/web/learning/employer_resources/index.html
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


--


Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan






--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
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Re: Install problem at make prepdb...

Scott Cain
In reply to this post by Nicolas Joannin
Hi Nicolas,

Interesting--are you installing on a Windows machine?  If so, please let me know how it goes.  While I can't think of anything off hand that will keep it from working, I also don't know of anybody whose tried on Windows.

Scott



On Tue, Apr 9, 2013 at 5:10 AM, Nicolas Joannin <[hidden email]> wrote:
Hello again, again...

I think I got this one wrong: the real problem is that my ActivePerl site/bin folder is not in my path (for whatever reason I can't figure out)...

Anyhow, no need to change the Build.pm file, it was a problem on my side!
Sorry for the disturbance!

Best regards,
Nicolas




Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Tue, Apr 9, 2013 at 12:52 PM, Nicolas Joannin <[hidden email]> wrote:
Hi again,

I am in the process of installing version 1.23 and this time I got a different problem with 'make prepdb' (see full output below):

"Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104."

I checked and that file is present with the others in the bin folder.
However, when I checked the line 104 in Builder.pm, I realized that 'bin/' was missing in front of the file name in the command:

system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

instead of:

system("bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

When executing the command after the modification, it worked fine.
I guess that is a bug? Or was there something else that needs changing instead?

Thanks in advance for your help!
Best regards,

Nicolas




Nicolass-MacBook-Air:chado-1.23 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
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psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE will create implicit sequence "materialized_view_materialized_view_id_seq" for serial column "materialized_view.materialized_view_id"
psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE / UNIQUE will create implicit index "materialized_view_name_key" for table "materialized_view"
CREATE TABLE
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Adding Plasmodium falciparum to the database...
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK

Both genus and species are required; please provide them below

Organism's genus?  Plasmodium
Organism's species?  falciparum
Organism's abbreviation? [P.falciparum] 
Comment (can be empty)?  
There was already an organism with that genus and species in the database;
exiting...
Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
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Re: Install problem at make prepdb...

Nicolas Joannin
Hi Scott,

No, not on Windows... I abandoned that a few years back.
Working on Mac OSX (10.6 and 10.8).
In any case, I greatly appreciate all your help!

Best regards,
Nicolas



Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Tue, Apr 9, 2013 at 6:00 PM, Scott Cain <[hidden email]> wrote:
Hi Nicolas,

Interesting--are you installing on a Windows machine?  If so, please let me know how it goes.  While I can't think of anything off hand that will keep it from working, I also don't know of anybody whose tried on Windows.

Scott



On Tue, Apr 9, 2013 at 5:10 AM, Nicolas Joannin <[hidden email]> wrote:
Hello again, again...

I think I got this one wrong: the real problem is that my ActivePerl site/bin folder is not in my path (for whatever reason I can't figure out)...

Anyhow, no need to change the Build.pm file, it was a problem on my side!
Sorry for the disturbance!

Best regards,
Nicolas




Nicolas Joannin, Ph.D.
Bioinformatics Center
Kyoto University, Uji campus, Japan



On Tue, Apr 9, 2013 at 12:52 PM, Nicolas Joannin <[hidden email]> wrote:
Hi again,

I am in the process of installing version 1.23 and this time I got a different problem with 'make prepdb' (see full output below):

"Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104."

I checked and that file is present with the others in the bin folder.
However, when I checked the line 104 in Builder.pm, I realized that 'bin/' was missing in front of the file name in the command:

system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

instead of:

system("bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version");

When executing the command after the modification, it worked fine.
I guess that is a bug? Or was there something else that needs changing instead?

Thanks in advance for your help!
Best regards,

Nicolas




Nicolass-MacBook-Air:chado-1.23 NicojoAir11$ make prepdb
./Build prepdb
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
could not find ParserDetails.ini in /usr/local/ActivePerl-5.16/site/lib/XML/SAX
INSERT 0 1
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INSERT 0 1
psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE will create implicit sequence "materialized_view_materialized_view_id_seq" for serial column "materialized_view.materialized_view_id"
psql:/Users/NicojoAir11/gmod/chado-1.23/load/etc/initialize.sql:237: NOTICE:  CREATE TABLE / UNIQUE will create implicit index "materialized_view_name_key" for table "materialized_view"
CREATE TABLE
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK
Adding Plasmodium falciparum to the database...
Setting up build environment with MacOSX10.8 SDK instead of MacOSX10.6 SDK

Both genus and species are required; please provide them below

Organism's genus?  Plasmodium
Organism's species?  falciparum
Organism's abbreviation? [P.falciparum] 
Comment (can be empty)?  
There was already an organism with that genus and species in the database;
exiting...
Can't exec "gmod_chado_properties.pl": No such file or directory at lib/Bio/Chado/Builder.pm line 104.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Precog is a next-generation analytics platform capable of advanced
analytics on semi-structured data. The platform includes APIs for building
apps and a phenomenal toolset for data science. Developers can use
our toolset for easy data analysis & visualization. Get a free account!
http://www2.precog.com/precogplatform/slashdotnewsletter
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema