Re: Error when running 'make ontologies'

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Re: Error when running 'make ontologies'

Scott Cain
Hi Nicolas,

Are you familiar with the locate command?  Try try "locate go2fmt" to see if that turns anything up. If you don't know if the locate database has been updated since you installed, try "sudo updatedb" first. 

Also, are you sure go-perl was installed successfully?

Scott


Sent from my iPhone

On Jan 4, 2013, at 3:27 AM, Nicolas Joannin <[hidden email]> wrote:

Hello,

I am trying to install a Chado database on my local machine.
I've followed the instructions found in install.CHADO file. But when I reach the make ontologies part, I get the following error message:

Nicolas$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
fetching files for Relationship Ontology
    updated
    loading...sh: go2fmt.pl: command not found
sh: go-apply-xslt: command not found
System call 'go2fmt.pl -p obo_text -w xml /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.obo | go-apply-xslt oboxml_to_chadoxml - > /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.oboxml' failed: 32512
failed: 32512 at lib/Bio/Chado/Builder.pm line 346, <STDIN> line 1.
make: *** [ontologies] Error 2


I have installed GO::Parser, as specified in the install file.
I cannot locate any go2fmt.pl file, though... 

Any idea where the problem comes from?

Best regards,
Nicolas


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


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Re: Error when running 'make ontologies'

Nicolas Joannin
Hi Scott,

Thanks for the quick reply!
I didn't know about "locate", so thanks for pointing it out!
Here's the result:

Nicolas$ locate go2fmt
/usr/local/ActivePerl-5.14/site/bin/go2fmt.pl
/usr/local/ActivePerl-5.14/site/man/man1/go2fmt.pl.1

As for the installation of go-perl... I simply tried to install GO::Parser through cpan, which tells me that it is up-to-date. Also, running perldoc GO::Parser gives me its documentation.
Beyond that, is there a different way to check that it is installed?

Is /usr/local/ActivePerl-5.14/site/bin/ supposed to be in my Path? Because it currently isn't... Could that be the problem?

Best regards,
Nicolas 



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



On Fri, Jan 4, 2013 at 11:39 PM, Scott Cain <[hidden email]> wrote:
Hi Nicolas,

Are you familiar with the locate command?  Try try "locate go2fmt" to see if that turns anything up. If you don't know if the locate database has been updated since you installed, try "sudo updatedb" first. 

Also, are you sure go-perl was installed successfully?

Scott


Sent from my iPhone

On Jan 4, 2013, at 3:27 AM, Nicolas Joannin <[hidden email]> wrote:

Hello,

I am trying to install a Chado database on my local machine.
I've followed the instructions found in install.CHADO file. But when I reach the make ontologies part, I get the following error message:

Nicolas$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
fetching files for Relationship Ontology
    updated
    loading...sh: go2fmt.pl: command not found
sh: go-apply-xslt: command not found
System call 'go2fmt.pl -p obo_text -w xml /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.obo | go-apply-xslt oboxml_to_chadoxml - > /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.oboxml' failed: 32512
failed: 32512 at lib/Bio/Chado/Builder.pm line 346, <STDIN> line 1.
make: *** [ontologies] Error 2


I have installed GO::Parser, as specified in the install file.
I cannot locate any go2fmt.pl file, though... 

Any idea where the problem comes from?

Best regards,
Nicolas


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



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Re: Error when running 'make ontologies'

Scott Cain
That is almost certainly the problem. 

Sent from my iPhone

On Jan 4, 2013, at 7:14 PM, Nicolas Joannin <[hidden email]> wrote:

Hi Scott,

Thanks for the quick reply!
I didn't know about "locate", so thanks for pointing it out!
Here's the result:

Nicolas$ locate go2fmt
/usr/local/ActivePerl-5.14/site/bin/go2fmt.pl
/usr/local/ActivePerl-5.14/site/man/man1/go2fmt.pl.1

As for the installation of go-perl... I simply tried to install GO::Parser through cpan, which tells me that it is up-to-date. Also, running perldoc GO::Parser gives me its documentation.
Beyond that, is there a different way to check that it is installed?

Is /usr/local/ActivePerl-5.14/site/bin/ supposed to be in my Path? Because it currently isn't... Could that be the problem?

Best regards,
Nicolas 



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



On Fri, Jan 4, 2013 at 11:39 PM, Scott Cain <[hidden email]> wrote:
Hi Nicolas,

Are you familiar with the locate command?  Try try "locate go2fmt" to see if that turns anything up. If you don't know if the locate database has been updated since you installed, try "sudo updatedb" first. 

Also, are you sure go-perl was installed successfully?

Scott


Sent from my iPhone

On Jan 4, 2013, at 3:27 AM, Nicolas Joannin <[hidden email]> wrote:

Hello,

I am trying to install a Chado database on my local machine.
I've followed the instructions found in install.CHADO file. But when I reach the make ontologies part, I get the following error message:

Nicolas$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
fetching files for Relationship Ontology
    updated
    loading...sh: go2fmt.pl: command not found
sh: go-apply-xslt: command not found
System call 'go2fmt.pl -p obo_text -w xml /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.obo | go-apply-xslt oboxml_to_chadoxml - > /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.oboxml' failed: 32512
failed: 32512 at lib/Bio/Chado/Builder.pm line 346, <STDIN> line 1.
make: *** [ontologies] Error 2


I have installed GO::Parser, as specified in the install file.
I cannot locate any go2fmt.pl file, though... 

Any idea where the problem comes from?

Best regards,
Nicolas


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



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Re: Error when running 'make ontologies'

Nicolas Joannin
Hi Scott,

Easy fix then... Sorry I disturbed you for something so tribial.

Have a good week end!
Cheers,
Nicolas

On Saturday, January 5, 2013, Scott Cain wrote:
That is almost certainly the problem. 

Sent from my iPhone

On Jan 4, 2013, at 7:14 PM, Nicolas Joannin <<a href="javascript:_e({}, &#39;cvml&#39;, &#39;nicolas.joannin@gmail.com&#39;);" target="_blank">nicolas.joannin@...> wrote:

Hi Scott,

Thanks for the quick reply!
I didn't know about "locate", so thanks for pointing it out!
Here's the result:

Nicolas$ locate go2fmt
/usr/local/ActivePerl-5.14/site/bin/go2fmt.pl
/usr/local/ActivePerl-5.14/site/man/man1/go2fmt.pl.1

As for the installation of go-perl... I simply tried to install GO::Parser through cpan, which tells me that it is up-to-date. Also, running perldoc GO::Parser gives me its documentation.
Beyond that, is there a different way to check that it is installed?

Is /usr/local/ActivePerl-5.14/site/bin/ supposed to be in my Path? Because it currently isn't... Could that be the problem?

Best regards,
Nicolas 



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



On Fri, Jan 4, 2013 at 11:39 PM, Scott Cain <<a href="javascript:_e({}, &#39;cvml&#39;, &#39;scott@scottcain.net&#39;);" target="_blank">scott@...> wrote:
Hi Nicolas,

Are you familiar with the locate command?  Try try "locate go2fmt" to see if that turns anything up. If you don't know if the locate database has been updated since you installed, try "sudo updatedb" first. 

Also, are you sure go-perl was installed successfully?

Scott


Sent from my iPhone

On Jan 4, 2013, at 3:27 AM, Nicolas Joannin <<a href="javascript:_e({}, &#39;cvml&#39;, &#39;nicolas.joannin@gmail.com&#39;);" target="_blank">nicolas.joannin@...> wrote:

Hello,

I am trying to install a Chado database on my local machine.
I've followed the instructions found in install.CHADO file. But when I reach the make ontologies part, I get the following error message:

Nicolas$ make ontologies
./Build ontologies
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Plant Ontology

Which ontologies would you like to load (Comma delimited)? [0]  1,2,3,4
fetching files for Relationship Ontology
    updated
    loading...sh: go2fmt.pl: command not found
sh: go-apply-xslt: command not found
System call 'go2fmt.pl -p obo_text -w xml /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.obo | go-apply-xslt oboxml_to_chadoxml - > /Users/Nicolas/data/vardb_chado/tmp/obo/OBO_REL/ro.oboxml' failed: 32512
failed: 32512 at lib/Bio/Chado/Builder.pm line 346, <STDIN> line 1.
make: *** [ontologies] Error 2


I have installed GO::Parser, as specified in the install file.
I cannot locate any go2fmt.pl file, though... 

Any idea where the problem comes from?

Best regards,
Nicolas


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




--


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



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MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current
with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft
MVPs and experts. SALE $99.99 this month only -- learn more at:
http://p.sf.net/sfu/learnmore_122912
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