trying to connect to chado database

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trying to connect to chado database

Jeang, David - ARS

I’ve installed Gbrowse 2.49 on the local server, and am trying to connect to a chado database on the same server.

 

This is how I set the conf file for Gbrowse

 

[GENERAL]

db_adaptor           = Bio::DB::Das::Chado

db_args                     = -adaptor Bio::DB::Das::Chado

                     -dsn dbi:Pg:dbname=tripal;host=localhost

                     -user tripaldemo

                     -pass tripal2demo

psql=# ALTER USER tripaldemo SET search_path TO chado;

config_base            = /etc/gbrowse2   # overridden by environment variable GBROWSE_CONF

htdocs_base            = /var/www/html/gbrowse2

url_base               = /gbrowse2

tmp_base               = /var/tmp/gbrowse2

persistent_base        = /var/lib/gbrowse2

userdata_base          = /var/lib/gbrowse2/userdata

db_base                = /var/www/cgi-bin/gb2/gbrowse

 

 

However, when I try to access the link:

http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse

 

I get:

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Please contact the server administrator, root@localhost and inform them of the time the error occurred, and anything you might have done that may have caused the error.

More information about this error may be available in the server error log.


Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80

 

 

I’m at a dead end, the configurations are right, and I even accounted for PostgreSQL creating a separate path to chado. What am I missing?

 

David Jeang

 





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
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Re: trying to connect to chado database

Scott Cain
Hi David,

You configuration stuff looks OK.  What is the error in the error log?
 It's probably in /var/httpd/log (though possibly /var/apache2/log).

Scott


On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS
<[hidden email]> wrote:

> I’ve installed Gbrowse 2.49 on the local server, and am trying to connect to
> a chado database on the same server.
>
>
>
> This is how I set the conf file for Gbrowse
>
>
>
> [GENERAL]
>
> db_adaptor           = Bio::DB::Das::Chado
>
> db_args                     = -adaptor Bio::DB::Das::Chado
>
>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>
>                      -user tripaldemo
>
>                      -pass tripal2demo
>
> psql=# ALTER USER tripaldemo SET search_path TO chado;
>
> config_base            = /etc/gbrowse2   # overridden by environment
> variable GBROWSE_CONF
>
> htdocs_base            = /var/www/html/gbrowse2
>
> url_base               = /gbrowse2
>
> tmp_base               = /var/tmp/gbrowse2
>
> persistent_base        = /var/lib/gbrowse2
>
> userdata_base          = /var/lib/gbrowse2/userdata
>
> db_base                = /var/www/cgi-bin/gb2/gbrowse
>
>
>
>
>
> However, when I try to access the link:
>
> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>
>
>
> I get:
>
> Internal Server Error
>
> The server encountered an internal error or misconfiguration and was unable
> to complete your request.
>
> Please contact the server administrator, root@localhost and inform them of
> the time the error occurred, and anything you might have done that may have
> caused the error.
>
> More information about this error may be available in the server error log.
>
> ________________________________
>
> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>
>
>
>
>
> I’m at a dead end, the configurations are right, and I even accounted for
> PostgreSQL creating a separate path to chado. What am I missing?
>
>
>
> David Jeang
>
>
>
>
>
>
>
> This electronic message contains information generated by the USDA solely
> for the intended recipients. Any unauthorized interception of this message
> or the use or disclosure of the information it contains may violate the law
> and subject the violator to civil or criminal penalties. If you believe you
> have received this message in error, please notify the sender and delete the
> email immediately.
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>



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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Scott Cain
Hi David,

Please keep the GBrowse mailing list cc'ed.

Debugging this without access to the error log will be essentially
impossible.  Please bug whoever you have to to get access.

Scott


On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS
<[hidden email]> wrote:

> On closer inspection, there is var/log/httpd,
>
> But I'm denied access....
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 12:02 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> You configuration stuff looks OK.  What is the error in the error log?
>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>> I've installed Gbrowse 2.49 on the local server, and am trying to
>> connect to a chado database on the same server.
>>
>>
>>
>> This is how I set the conf file for Gbrowse
>>
>>
>>
>> [GENERAL]
>>
>> db_adaptor           = Bio::DB::Das::Chado
>>
>> db_args                     = -adaptor Bio::DB::Das::Chado
>>
>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>
>>                      -user tripaldemo
>>
>>                      -pass tripal2demo
>>
>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>
>> config_base            = /etc/gbrowse2   # overridden by environment
>> variable GBROWSE_CONF
>>
>> htdocs_base            = /var/www/html/gbrowse2
>>
>> url_base               = /gbrowse2
>>
>> tmp_base               = /var/tmp/gbrowse2
>>
>> persistent_base        = /var/lib/gbrowse2
>>
>> userdata_base          = /var/lib/gbrowse2/userdata
>>
>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>
>>
>>
>>
>>
>> However, when I try to access the link:
>>
>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>
>>
>>
>> I get:
>>
>> Internal Server Error
>>
>> The server encountered an internal error or misconfiguration and was
>> unable to complete your request.
>>
>> Please contact the server administrator, root@localhost and inform
>> them of the time the error occurred, and anything you might have done
>> that may have caused the error.
>>
>> More information about this error may be available in the server error log.
>>
>> ________________________________
>>
>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>
>>
>>
>>
>>
>> I'm at a dead end, the configurations are right, and I even accounted
>> for PostgreSQL creating a separate path to chado. What am I missing?
>>
>>
>>
>> David Jeang
>>
>>
>>
>>
>>
>>
>>
>> This electronic message contains information generated by the USDA
>> solely for the intended recipients. Any unauthorized interception of
>> this message or the use or disclosure of the information it contains
>> may violate the law and subject the violator to civil or criminal
>> penalties. If you believe you have received this message in error,
>> please notify the sender and delete the email immediately.
>>
>> ----------------------------------------------------------------------
>> --------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond.
>> Discussions will include endpoint security, mobile security and the
>> latest in malware threats.
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (http://gmod.org/)                     216-392-3087 Ontario Institute for Cancer Research
>
>



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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
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Re: trying to connect to chado database

Jeang, David - ARS
I've managed to use a root login through a shell account in putty, risky, but doable.

There are a ton of logs here though, I'm not sure which one to look at.
I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
Just guessing, but this is the log for error:

[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/v
endor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr
/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
o/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilatio
n aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
hics/Browser2/SendMail.pm line 8.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in re
quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico
[Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:18:26 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=%3A5432%3Aallow
[Tue Jun 26 10:18:26 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=%3A5432%3Aallow
[Tue Jun 26 10:18:26 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
[Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
[Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&server=%3A5432%3Aallow&database=tripal&
[Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&server=%3A5432%3Aallow&database=tripal&
[Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
[Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict Standards:  O

I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
David Jeang

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 12:35 PM
To: Jeang, David - ARS
Cc: Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

Please keep the GBrowse mailing list cc'ed.
Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.

Scott


On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:

> On closer inspection, there is var/log/httpd,
>
> But I'm denied access....
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 12:02 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> You configuration stuff looks OK.  What is the error in the error log?
>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>> I've installed Gbrowse 2.49 on the local server, and am trying to
>> connect to a chado database on the same server.
>>
>>
>>
>> This is how I set the conf file for Gbrowse
>>
>>
>>
>> [GENERAL]
>>
>> db_adaptor           = Bio::DB::Das::Chado
>>
>> db_args                     = -adaptor Bio::DB::Das::Chado
>>
>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>
>>                      -user tripaldemo
>>
>>                      -pass tripal2demo
>>
>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>
>> config_base            = /etc/gbrowse2   # overridden by environment
>> variable GBROWSE_CONF
>>
>> htdocs_base            = /var/www/html/gbrowse2
>>
>> url_base               = /gbrowse2
>>
>> tmp_base               = /var/tmp/gbrowse2
>>
>> persistent_base        = /var/lib/gbrowse2
>>
>> userdata_base          = /var/lib/gbrowse2/userdata
>>
>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>
>>
>>
>>
>>
>> However, when I try to access the link:
>>
>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>
>>
>>
>> I get:
>>
>> Internal Server Error
>>
>> The server encountered an internal error or misconfiguration and was
>> unable to complete your request.
>>
>> Please contact the server administrator, root@localhost and inform
>> them of the time the error occurred, and anything you might have done
>> that may have caused the error.
>>
>> More information about this error may be available in the server error log.
>>
>> ________________________________
>>
>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>
>>
>>
>>
>>
>> I'm at a dead end, the configurations are right, and I even accounted
>> for PostgreSQL creating a separate path to chado. What am I missing?
>>
>>
>>
>> David Jeang
>>
>>
>>
>>
>>
>>
>>
>> This electronic message contains information generated by the USDA
>> solely for the intended recipients. Any unauthorized interception of
>> this message or the use or disclosure of the information it contains
>> may violate the law and subject the violator to civil or criminal
>> penalties. If you believe you have received this message in error,
>> please notify the sender and delete the email immediately.
>>
>> ---------------------------------------------------------------------
>> -
>> --------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond.
>> Discussions will include endpoint security, mobile security and the
>> latest in malware threats.
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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Re: trying to connect to chado database

Scott Cain
This is pretty important:

[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate
Digest/SHA.pm in @INC (@INC contains:
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
.) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm
line 8.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
failed--compilation aborted at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm
line 8.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
failed in require at
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm
line 11.

It means that Digest::SHA, a perl module that is a prereq for GBrowse,
isn't installed (at least not in a place that GBrowse can find it).
If that's not installed, chances are other things aren't as well.

Scott


On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS
<[hidden email]> wrote:

> I've managed to use a root login through a shell account in putty, risky, but doable.
>
> There are a ton of logs here though, I'm not sure which one to look at.
> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
> Just guessing, but this is the log for error:
>
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
> pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/v
> endor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr
> /lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
> /perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
> o/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilatio
> n aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
> hics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in re
> quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
> [Tue Jun 26 10:18:26 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=%3A5432%3Aallow
> [Tue Jun 26 10:18:26 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=%3A5432%3Aallow
> [Tue Jun 26 10:18:26 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&server=%3A5432%3Aallow&database=tripal&
> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&server=%3A5432%3Aallow&database=tripal&
> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict Standards:  O
>
> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
> David Jeang
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 12:35 PM
> To: Jeang, David - ARS
> Cc: Gbrowse (E-mail)
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> Please keep the GBrowse mailing list cc'ed.
> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>> On closer inspection, there is var/log/httpd,
>>
>> But I'm denied access....
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 12:02 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> You configuration stuff looks OK.  What is the error in the error log?
>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>> connect to a chado database on the same server.
>>>
>>>
>>>
>>> This is how I set the conf file for Gbrowse
>>>
>>>
>>>
>>> [GENERAL]
>>>
>>> db_adaptor           = Bio::DB::Das::Chado
>>>
>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>
>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>
>>>                      -user tripaldemo
>>>
>>>                      -pass tripal2demo
>>>
>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>
>>> config_base            = /etc/gbrowse2   # overridden by environment
>>> variable GBROWSE_CONF
>>>
>>> htdocs_base            = /var/www/html/gbrowse2
>>>
>>> url_base               = /gbrowse2
>>>
>>> tmp_base               = /var/tmp/gbrowse2
>>>
>>> persistent_base        = /var/lib/gbrowse2
>>>
>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>
>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>
>>>
>>>
>>>
>>>
>>> However, when I try to access the link:
>>>
>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>
>>>
>>>
>>> I get:
>>>
>>> Internal Server Error
>>>
>>> The server encountered an internal error or misconfiguration and was
>>> unable to complete your request.
>>>
>>> Please contact the server administrator, root@localhost and inform
>>> them of the time the error occurred, and anything you might have done
>>> that may have caused the error.
>>>
>>> More information about this error may be available in the server error log.
>>>
>>> ________________________________
>>>
>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>
>>>
>>>
>>>
>>>
>>> I'm at a dead end, the configurations are right, and I even accounted
>>> for PostgreSQL creating a separate path to chado. What am I missing?
>>>
>>>
>>>
>>> David Jeang
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> This electronic message contains information generated by the USDA
>>> solely for the intended recipients. Any unauthorized interception of
>>> this message or the use or disclosure of the information it contains
>>> may violate the law and subject the violator to civil or criminal
>>> penalties. If you believe you have received this message in error,
>>> please notify the sender and delete the email immediately.
>>>
>>> ---------------------------------------------------------------------
>>> -
>>> --------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond.
>>> Discussions will include endpoint security, mobile security and the
>>> latest in malware threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------------
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (http://gmod.org/)                     216-392-3087 Ontario Institute for Cancer Research
>
>



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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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Re: trying to connect to chado database

Jeang, David - ARS
In reply to this post by Scott Cain
[Tue Jun 26 10:27:13 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=schema&server=%3A5432%3Aallow&database=postgres&schema=public&
[Tue Jun 26 10:27:29 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?server=%3A5432%3Aallow&subject=server
[Tue Jun 26 10:27:29 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?server=%3A5432%3Aallow&subject=server
[Tue Jun 26 10:27:31 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&server=%3A5432%3Aallow&database=tripal&
[Tue Jun 26 10:27:31 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&server=%3A5432%3Aallow&database=tripal&
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:28:41 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib /perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:29:09 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:29:10 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:29:12 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:29:20 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=schema&server=%3A5432%3Aallow&database=tripal&schema=chado&
[Tue Jun 26 10:29:55 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
[Tue Jun 26 10:29:56 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
[Tue Jun 26 10:30:46 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=schema&server=%3A5432%3Aallow&database=tripal&schema=chado&
[Tue Jun 26 10:31:01 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=schema&server=%3A5432%3Aallow&database=tripal&schema=chado&
[Tue Jun 26 10:31:01 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=schema&server=%3A5432%3Aallow&database=tripal&schema=chado&
[Tue Jun 26 10:31:07 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php?server=%3A5432%3Aallow&subject=database&database=tripal
[Tue Jun 26 10:31:09 2012] [error] [client 10.12.20.67] PHP Strict Standards:  Only variables should be assigned by reference in /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23, referer: http://i5k.nal.usda.gov/phppgadmin/database.php?subject=database&action=sql&new=1&server=%3A5432%3Aallow&database=tripal
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:32:24 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:32:25 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse
[Tue Jun 26 10:43:26 2012] [error] [client 10.12.20.67] PHP Parse error:  syntax error, unexpected 'if' (T_IF) in /var/www/drupal-6.26/includes/common.inc(1730) : eval()'d code on line 1, referer: http://i5k.nal.usda.gov/Dmelanogaster
[Tue Jun 26 10:43:26 2012] [error] [client 10.12.20.67] PHP Parse error:  syntax error, unexpected 'if' (T_IF) in /var/www/drupal-6.26/includes/common.inc(1730) : eval()'d code on line 1, referer: http://i5k.nal.usda.gov/Dmelanogaster
[Tue Jun 26 10:43:27 2012] [error] [client 10.12.20.67] PHP Parse error:  syntax error, unexpected 'if' (T_IF) in /var/www/drupal-6.26/includes/common.inc(1730) : eval()'d code on line 1, referer: http://i5k.nal.usda.gov/Dmelanogaster
[Tue Jun 26 10:43:27 2012] [error] [client 10.12.20.67] PHP Parse error:  syntax error, unexpected 'if' (T_IF) in /var/www/drupal-6.26/includes/common.inc(1730) : eval()'d code on line 1, referer: http://i5k.nal.usda.gov/Dmelanogaster
[Tue Jun 26 10:43:27 2012] [error] [client 10.12.20.67] PHP Parse error:  syntax error, unexpected 'if' (T_IF) in /var/www/drupal-6.26/includes/common.inc(1730) : eval()'d code on line 1, referer: http://i5k.nal.usda.gov/Dmelanogaster
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
[Tue Jun 26 10:44:36 2012] [error] [client 10.12.20.67] Premature end of script headers: gbrowse

Forgot the rest of the error log.

David Jeang
-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 12:35 PM
To: Jeang, David - ARS
Cc: Gbrowse (E-mail)
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

Please keep the GBrowse mailing list cc'ed.

Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.

Scott


On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:

> On closer inspection, there is var/log/httpd,
>
> But I'm denied access....
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 12:02 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> You configuration stuff looks OK.  What is the error in the error log?
>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>> I've installed Gbrowse 2.49 on the local server, and am trying to
>> connect to a chado database on the same server.
>>
>>
>>
>> This is how I set the conf file for Gbrowse
>>
>>
>>
>> [GENERAL]
>>
>> db_adaptor           = Bio::DB::Das::Chado
>>
>> db_args                     = -adaptor Bio::DB::Das::Chado
>>
>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>
>>                      -user tripaldemo
>>
>>                      -pass tripal2demo
>>
>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>
>> config_base            = /etc/gbrowse2   # overridden by environment
>> variable GBROWSE_CONF
>>
>> htdocs_base            = /var/www/html/gbrowse2
>>
>> url_base               = /gbrowse2
>>
>> tmp_base               = /var/tmp/gbrowse2
>>
>> persistent_base        = /var/lib/gbrowse2
>>
>> userdata_base          = /var/lib/gbrowse2/userdata
>>
>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>
>>
>>
>>
>>
>> However, when I try to access the link:
>>
>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>
>>
>>
>> I get:
>>
>> Internal Server Error
>>
>> The server encountered an internal error or misconfiguration and was
>> unable to complete your request.
>>
>> Please contact the server administrator, root@localhost and inform
>> them of the time the error occurred, and anything you might have done
>> that may have caused the error.
>>
>> More information about this error may be available in the server error log.
>>
>> ________________________________
>>
>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>
>>
>>
>>
>>
>> I'm at a dead end, the configurations are right, and I even accounted
>> for PostgreSQL creating a separate path to chado. What am I missing?
>>
>>
>>
>> David Jeang
>>
>>
>>
>>
>>
>>
>>
>> This electronic message contains information generated by the USDA
>> solely for the intended recipients. Any unauthorized interception of
>> this message or the use or disclosure of the information it contains
>> may violate the law and subject the violator to civil or criminal
>> penalties. If you believe you have received this message in error,
>> please notify the sender and delete the email immediately.
>>
>> ---------------------------------------------------------------------
>> -
>> --------
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond.
>> Discussions will include endpoint security, mobile security and the
>> latest in malware threats.
>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Jeang, David - ARS
In reply to this post by Scott Cain
Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.

David Jeang

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 1:41 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

This is pretty important:

[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
.) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm
line 8.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm
line 8.
[Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm
line 11.

It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
If that's not installed, chances are other things aren't as well.

Scott


On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:

> I've managed to use a root login through a shell account in putty, risky, but doable.
>
> There are a ton of logs here though, I'm not sure which one to look at.
> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
> Just guessing, but this is the log for error:
>
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
> pm in @INC (@INC contains:
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
> /perl5/5.8.8 .) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
> o/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
> failed--compilatio n aborted at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
> hics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end
> of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error] [client
> 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun
> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end
> of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end
> of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end
> of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error] [client
> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
> by reference in
> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
> referer:
> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=
> %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
> 10.12.20.67] PHP Strict Standards:  Only variables should be passed by
> reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
> referer:
> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=
> %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
> by reference in
> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end
> of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error] [client
> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
> by reference in
> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
> Standards:  Only variables should be passed by reference in
> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
> http://i5k.nal.usda.gov/phppgadmin/redirect.php
> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
> Standards:  Only variables should be assigned by reference in
> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
> referer:
> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serve
> r=%3A5432%3Aallow&database=tripal&
> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
> Standards:  Only variables should be passed by reference in
> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serve
> r=%3A5432%3Aallow&database=tripal&
> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
> Standards:  Only variables should be assigned by reference in
> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
> Standards:  O
>
> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
> David Jeang
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 12:35 PM
> To: Jeang, David - ARS
> Cc: Gbrowse (E-mail)
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> Please keep the GBrowse mailing list cc'ed.
> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>> On closer inspection, there is var/log/httpd,
>>
>> But I'm denied access....
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 12:02 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> You configuration stuff looks OK.  What is the error in the error log?
>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>> connect to a chado database on the same server.
>>>
>>>
>>>
>>> This is how I set the conf file for Gbrowse
>>>
>>>
>>>
>>> [GENERAL]
>>>
>>> db_adaptor           = Bio::DB::Das::Chado
>>>
>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>
>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>
>>>                      -user tripaldemo
>>>
>>>                      -pass tripal2demo
>>>
>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>
>>> config_base            = /etc/gbrowse2   # overridden by environment
>>> variable GBROWSE_CONF
>>>
>>> htdocs_base            = /var/www/html/gbrowse2
>>>
>>> url_base               = /gbrowse2
>>>
>>> tmp_base               = /var/tmp/gbrowse2
>>>
>>> persistent_base        = /var/lib/gbrowse2
>>>
>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>
>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>
>>>
>>>
>>>
>>>
>>> However, when I try to access the link:
>>>
>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>
>>>
>>>
>>> I get:
>>>
>>> Internal Server Error
>>>
>>> The server encountered an internal error or misconfiguration and was
>>> unable to complete your request.
>>>
>>> Please contact the server administrator, root@localhost and inform
>>> them of the time the error occurred, and anything you might have
>>> done that may have caused the error.
>>>
>>> More information about this error may be available in the server error log.
>>>
>>> ________________________________
>>>
>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>
>>>
>>>
>>>
>>>
>>> I'm at a dead end, the configurations are right, and I even
>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>
>>>
>>>
>>> David Jeang
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> This electronic message contains information generated by the USDA
>>> solely for the intended recipients. Any unauthorized interception of
>>> this message or the use or disclosure of the information it contains
>>> may violate the law and subject the violator to civil or criminal
>>> penalties. If you believe you have received this message in error,
>>> please notify the sender and delete the email immediately.
>>>
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> --------
>>> Live Security Virtual Conference
>>> Exclusive live event will cover all the ways today's security and
>>> threat landscape has changed and how IT managers can respond.
>>> Discussions will include endpoint security, mobile security and the
>>> latest in malware threats.
>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Scott Cain
Hi David,

How did you install GBrowse?  It should have warned you that there
were missing prereqs.  I'll put the list at the end of this email, but
really the easiest way to see if there are prereqs missing is to run
perl Build.PL again.

Scott

    requires     => {
        'perl'                => '5.008',
        'Bio::Root::Version'  => '1.0069',
        'Bio::Graphics'       => '2.28',
        'CGI::Session'        => '4.02',
        'Digest::MD5'         => 0,
        'ExtUtils::CBuilder'  => 0,
        'File::Temp'          => 0,
        'GD'                  => '2.07',
        'Text::ParseWords'    => '3.27',
        'IO::String'          => 0,
        'JSON'                => 0,
        'LWP'                 => 0,
        'Statistics::Descriptive'  => 0,
        'Storable'            => 0,
        'Time::HiRes'         => 0,
        'Digest::SHA'         => 0,
        'Date::Parse'         => 0,
        'Term::ReadKey'       => 0,
    },
    build_requires => {'Capture::Tiny'       => 0,},
    recommends  => {
        'Bio::Das'                 => 0,
        'Bio::DB::Sam'             => 1.20,
        'Bio::DB::BigFile'         => 1.00,
        'Crypt::SSLeay'            => 0,
        'DB_File::Lock'            => 0,
        'DBI'                      => 0,
        'DBD::mysql'               => 0,
        'DBD::Pg'                  => 0,
        'DBD::SQLite'              => 0,
        'Digest::SHA'              => 0,
        'FCGI'                     => 0,
        'File::NFSLock'            => 0,
        'GD::SVG'                  => 0,
        'Math::BigInt'             => 0,
        'Net::OpenID::Consumer'    => 0,
        'Net::SMTP::SSL'           => 0,
        $] <= 5.008 ? ('Safe::World'  => 0)
                    : ()               ,
        'Template'                 => 2.20,
        'Term::ReadKey'            => 0,
    },



On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS
<[hidden email]> wrote:

> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>
> David Jeang
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 1:41 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> This is pretty important:
>
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm
> line 11.
>
> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
> If that's not installed, chances are other things aren't as well.
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>
>> There are a ton of logs here though, I'm not sure which one to look at.
>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>> Just guessing, but this is the log for error:
>>
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>> pm in @INC (@INC contains:
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>> /perl5/5.8.8 .) at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>> o/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>> failed--compilatio n aborted at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>> hics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error] [client
>> 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun
>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=
>> %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed by
>> reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server=
>> %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serve
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serve
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  O
>>
>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>> David Jeang
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 12:35 PM
>> To: Jeang, David - ARS
>> Cc: Gbrowse (E-mail)
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> Please keep the GBrowse mailing list cc'ed.
>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> On closer inspection, there is var/log/httpd,
>>>
>>> But I'm denied access....
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> You configuration stuff looks OK.  What is the error in the error log?
>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>> connect to a chado database on the same server.
>>>>
>>>>
>>>>
>>>> This is how I set the conf file for Gbrowse
>>>>
>>>>
>>>>
>>>> [GENERAL]
>>>>
>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>
>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>
>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>
>>>>                      -user tripaldemo
>>>>
>>>>                      -pass tripal2demo
>>>>
>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>
>>>> config_base            = /etc/gbrowse2   # overridden by environment
>>>> variable GBROWSE_CONF
>>>>
>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>
>>>> url_base               = /gbrowse2
>>>>
>>>> tmp_base               = /var/tmp/gbrowse2
>>>>
>>>> persistent_base        = /var/lib/gbrowse2
>>>>
>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>
>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> However, when I try to access the link:
>>>>
>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>> I get:
>>>>
>>>> Internal Server Error
>>>>
>>>> The server encountered an internal error or misconfiguration and was
>>>> unable to complete your request.
>>>>
>>>> Please contact the server administrator, root@localhost and inform
>>>> them of the time the error occurred, and anything you might have
>>>> done that may have caused the error.
>>>>
>>>> More information about this error may be available in the server error log.
>>>>
>>>> ________________________________
>>>>
>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> I'm at a dead end, the configurations are right, and I even
>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>
>>>>
>>>>
>>>> David Jeang
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> This electronic message contains information generated by the USDA
>>>> solely for the intended recipients. Any unauthorized interception of
>>>> this message or the use or disclosure of the information it contains
>>>> may violate the law and subject the violator to civil or criminal
>>>> penalties. If you believe you have received this message in error,
>>>> please notify the sender and delete the email immediately.
>>>>
>>>> --------------------------------------------------------------------
>>>> -
>>>> -
>>>> --------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond.
>>>> Discussions will include endpoint security, mobile security and the
>>>> latest in malware threats.
>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> ---------------------------------------------------------------------
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------------
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (http://gmod.org/)                     216-392-3087 Ontario Institute for Cancer Research
>
>



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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Jeang, David - ARS
I tried this:

[djeang@metagenomics GBrowse-2.49]$ perl Makefile.PL
This module requires Module::Build to install itself.
  Install Module::Build now from CPAN? [y] y
Can't locate CPAN/FTP/netrc.pm in @INC (@INC contains: /var/www/GBrowse-2.49/install_util /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 /var/www/GBrowse-2.49) at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 9, <STDIN> line 1.
BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.8/CPAN/FTP.pm line 9, <STDIN> line 1.
Compilation failed in require at /usr/lib/perl5/5.8.8/CPAN.pm line 27, <STDIN> line 1.
BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.8/CPAN.pm line 27, <STDIN> line 1.
Compilation failed in require at Makefile.PL line 17, <STDIN> line 1.

What seems to be the problem?
-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 2:17 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.

Scott

    requires     => {
        'perl'                => '5.008',
        'Bio::Root::Version'  => '1.0069',
        'Bio::Graphics'       => '2.28',
        'CGI::Session'        => '4.02',
        'Digest::MD5'         => 0,
        'ExtUtils::CBuilder'  => 0,
        'File::Temp'          => 0,
        'GD'                  => '2.07',
        'Text::ParseWords'    => '3.27',
        'IO::String'          => 0,
        'JSON'                => 0,
        'LWP'                 => 0,
        'Statistics::Descriptive'  => 0,
        'Storable'            => 0,
        'Time::HiRes'         => 0,
        'Digest::SHA'         => 0,
        'Date::Parse'         => 0,
        'Term::ReadKey'       => 0,
    },
    build_requires => {'Capture::Tiny'       => 0,},
    recommends  => {
        'Bio::Das'                 => 0,
        'Bio::DB::Sam'             => 1.20,
        'Bio::DB::BigFile'         => 1.00,
        'Crypt::SSLeay'            => 0,
        'DB_File::Lock'            => 0,
        'DBI'                      => 0,
        'DBD::mysql'               => 0,
        'DBD::Pg'                  => 0,
        'DBD::SQLite'              => 0,
        'Digest::SHA'              => 0,
        'FCGI'                     => 0,
        'File::NFSLock'            => 0,
        'GD::SVG'                  => 0,
        'Math::BigInt'             => 0,
        'Net::OpenID::Consumer'    => 0,
        'Net::SMTP::SSL'           => 0,
        $] <= 5.008 ? ('Safe::World'  => 0)
                    : ()               ,
        'Template'                 => 2.20,
        'Term::ReadKey'            => 0,
    },



On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:

> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>
> David Jeang
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 1:41 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> This is pretty important:
>
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> .) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
> failed--compilation aborted at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
> failed in require at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/Action.pm
> line 11.
>
> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
> If that's not installed, chances are other things aren't as well.
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>
>> There are a ton of logs here though, I'm not sure which one to look at.
>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>> Just guessing, but this is the log for error:
>>
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>> pm in @INC (@INC contains:
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>> /perl5/5.8.8 .) at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>> o/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>> failed--compilatio n aborted at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>> hics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error] [client
>> 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue
>> Jun
>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>> e
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>> e
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  O
>>
>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>> David Jeang
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 12:35 PM
>> To: Jeang, David - ARS
>> Cc: Gbrowse (E-mail)
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> Please keep the GBrowse mailing list cc'ed.
>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> On closer inspection, there is var/log/httpd,
>>>
>>> But I'm denied access....
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> You configuration stuff looks OK.  What is the error in the error log?
>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>> connect to a chado database on the same server.
>>>>
>>>>
>>>>
>>>> This is how I set the conf file for Gbrowse
>>>>
>>>>
>>>>
>>>> [GENERAL]
>>>>
>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>
>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>
>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>
>>>>                      -user tripaldemo
>>>>
>>>>                      -pass tripal2demo
>>>>
>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>
>>>> config_base            = /etc/gbrowse2   # overridden by
>>>> environment variable GBROWSE_CONF
>>>>
>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>
>>>> url_base               = /gbrowse2
>>>>
>>>> tmp_base               = /var/tmp/gbrowse2
>>>>
>>>> persistent_base        = /var/lib/gbrowse2
>>>>
>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>
>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> However, when I try to access the link:
>>>>
>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>> I get:
>>>>
>>>> Internal Server Error
>>>>
>>>> The server encountered an internal error or misconfiguration and
>>>> was unable to complete your request.
>>>>
>>>> Please contact the server administrator, root@localhost and inform
>>>> them of the time the error occurred, and anything you might have
>>>> done that may have caused the error.
>>>>
>>>> More information about this error may be available in the server error log.
>>>>
>>>> ________________________________
>>>>
>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> I'm at a dead end, the configurations are right, and I even
>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>
>>>>
>>>>
>>>> David Jeang
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> This electronic message contains information generated by the USDA
>>>> solely for the intended recipients. Any unauthorized interception
>>>> of this message or the use or disclosure of the information it
>>>> contains may violate the law and subject the violator to civil or
>>>> criminal penalties. If you believe you have received this message
>>>> in error, please notify the sender and delete the email immediately.
>>>>
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> --------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond.
>>>> Discussions will include endpoint security, mobile security and the
>>>> latest in malware threats.
>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Jeang, David - ARS
In reply to this post by Scott Cain
Scratch my last response, I just forgot to use sudo.

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 2:17 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.

Scott

    requires     => {
        'perl'                => '5.008',
        'Bio::Root::Version'  => '1.0069',
        'Bio::Graphics'       => '2.28',
        'CGI::Session'        => '4.02',
        'Digest::MD5'         => 0,
        'ExtUtils::CBuilder'  => 0,
        'File::Temp'          => 0,
        'GD'                  => '2.07',
        'Text::ParseWords'    => '3.27',
        'IO::String'          => 0,
        'JSON'                => 0,
        'LWP'                 => 0,
        'Statistics::Descriptive'  => 0,
        'Storable'            => 0,
        'Time::HiRes'         => 0,
        'Digest::SHA'         => 0,
        'Date::Parse'         => 0,
        'Term::ReadKey'       => 0,
    },
    build_requires => {'Capture::Tiny'       => 0,},
    recommends  => {
        'Bio::Das'                 => 0,
        'Bio::DB::Sam'             => 1.20,
        'Bio::DB::BigFile'         => 1.00,
        'Crypt::SSLeay'            => 0,
        'DB_File::Lock'            => 0,
        'DBI'                      => 0,
        'DBD::mysql'               => 0,
        'DBD::Pg'                  => 0,
        'DBD::SQLite'              => 0,
        'Digest::SHA'              => 0,
        'FCGI'                     => 0,
        'File::NFSLock'            => 0,
        'GD::SVG'                  => 0,
        'Math::BigInt'             => 0,
        'Net::OpenID::Consumer'    => 0,
        'Net::SMTP::SSL'           => 0,
        $] <= 5.008 ? ('Safe::World'  => 0)
                    : ()               ,
        'Template'                 => 2.20,
        'Term::ReadKey'            => 0,
    },



On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:

> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>
> David Jeang
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 1:41 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> This is pretty important:
>
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> .) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
> failed--compilation aborted at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
> failed in require at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/Action.pm
> line 11.
>
> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
> If that's not installed, chances are other things aren't as well.
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>
>> There are a ton of logs here though, I'm not sure which one to look at.
>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>> Just guessing, but this is the log for error:
>>
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>> pm in @INC (@INC contains:
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>> /perl5/5.8.8 .) at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>> o/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>> failed--compilatio n aborted at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>> hics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error] [client
>> 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue
>> Jun
>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>> e
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>> e
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  O
>>
>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>> David Jeang
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 12:35 PM
>> To: Jeang, David - ARS
>> Cc: Gbrowse (E-mail)
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> Please keep the GBrowse mailing list cc'ed.
>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> On closer inspection, there is var/log/httpd,
>>>
>>> But I'm denied access....
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> You configuration stuff looks OK.  What is the error in the error log?
>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>> connect to a chado database on the same server.
>>>>
>>>>
>>>>
>>>> This is how I set the conf file for Gbrowse
>>>>
>>>>
>>>>
>>>> [GENERAL]
>>>>
>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>
>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>
>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>
>>>>                      -user tripaldemo
>>>>
>>>>                      -pass tripal2demo
>>>>
>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>
>>>> config_base            = /etc/gbrowse2   # overridden by
>>>> environment variable GBROWSE_CONF
>>>>
>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>
>>>> url_base               = /gbrowse2
>>>>
>>>> tmp_base               = /var/tmp/gbrowse2
>>>>
>>>> persistent_base        = /var/lib/gbrowse2
>>>>
>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>
>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> However, when I try to access the link:
>>>>
>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>> I get:
>>>>
>>>> Internal Server Error
>>>>
>>>> The server encountered an internal error or misconfiguration and
>>>> was unable to complete your request.
>>>>
>>>> Please contact the server administrator, root@localhost and inform
>>>> them of the time the error occurred, and anything you might have
>>>> done that may have caused the error.
>>>>
>>>> More information about this error may be available in the server error log.
>>>>
>>>> ________________________________
>>>>
>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> I'm at a dead end, the configurations are right, and I even
>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>
>>>>
>>>>
>>>> David Jeang
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> This electronic message contains information generated by the USDA
>>>> solely for the intended recipients. Any unauthorized interception
>>>> of this message or the use or disclosure of the information it
>>>> contains may violate the law and subject the violator to civil or
>>>> criminal penalties. If you believe you have received this message
>>>> in error, please notify the sender and delete the email immediately.
>>>>
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> --------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond.
>>>> Discussions will include endpoint security, mobile security and the
>>>> latest in malware threats.
>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Jeang, David - ARS
In reply to this post by Scott Cain
I have this when I run the Build. What do I do to install them?

[djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL
Checking prerequisites...
  recommends:
    *  Bio::DB::BigFile is not installed
    *  Bio::DB::Sam is not installed
    *  Net::OpenID::Consumer is not installed

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 2:17 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.

Scott

    requires     => {
        'perl'                => '5.008',
        'Bio::Root::Version'  => '1.0069',
        'Bio::Graphics'       => '2.28',
        'CGI::Session'        => '4.02',
        'Digest::MD5'         => 0,
        'ExtUtils::CBuilder'  => 0,
        'File::Temp'          => 0,
        'GD'                  => '2.07',
        'Text::ParseWords'    => '3.27',
        'IO::String'          => 0,
        'JSON'                => 0,
        'LWP'                 => 0,
        'Statistics::Descriptive'  => 0,
        'Storable'            => 0,
        'Time::HiRes'         => 0,
        'Digest::SHA'         => 0,
        'Date::Parse'         => 0,
        'Term::ReadKey'       => 0,
    },
    build_requires => {'Capture::Tiny'       => 0,},
    recommends  => {
        'Bio::Das'                 => 0,
        'Bio::DB::Sam'             => 1.20,
        'Bio::DB::BigFile'         => 1.00,
        'Crypt::SSLeay'            => 0,
        'DB_File::Lock'            => 0,
        'DBI'                      => 0,
        'DBD::mysql'               => 0,
        'DBD::Pg'                  => 0,
        'DBD::SQLite'              => 0,
        'Digest::SHA'              => 0,
        'FCGI'                     => 0,
        'File::NFSLock'            => 0,
        'GD::SVG'                  => 0,
        'Math::BigInt'             => 0,
        'Net::OpenID::Consumer'    => 0,
        'Net::SMTP::SSL'           => 0,
        $] <= 5.008 ? ('Safe::World'  => 0)
                    : ()               ,
        'Template'                 => 2.20,
        'Term::ReadKey'            => 0,
    },



On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:

> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>
> David Jeang
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 1:41 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> This is pretty important:
>
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
> .) at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
> failed--compilation aborted at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/SendMail.pm
> line 8.
> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
> failed in require at
> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
> s/Browser2/Action.pm
> line 11.
>
> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
> If that's not installed, chances are other things aren't as well.
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>
>> There are a ton of logs here though, I'm not sure which one to look at.
>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>> Just guessing, but this is the log for error:
>>
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>> pm in @INC (@INC contains:
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>> /perl5/5.8.8 .) at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>> o/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>> failed--compilatio n aborted at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>> hics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error] [client
>> 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue
>> Jun
>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end
>> of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error] [client
>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>> by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>> e
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be passed by reference in
>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>> e
>> r=%3A5432%3Aallow&database=tripal&
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  Only variables should be assigned by reference in
>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>> Standards:  O
>>
>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>> David Jeang
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 12:35 PM
>> To: Jeang, David - ARS
>> Cc: Gbrowse (E-mail)
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> Please keep the GBrowse mailing list cc'ed.
>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> On closer inspection, there is var/log/httpd,
>>>
>>> But I'm denied access....
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> You configuration stuff looks OK.  What is the error in the error log?
>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>> connect to a chado database on the same server.
>>>>
>>>>
>>>>
>>>> This is how I set the conf file for Gbrowse
>>>>
>>>>
>>>>
>>>> [GENERAL]
>>>>
>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>
>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>
>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>
>>>>                      -user tripaldemo
>>>>
>>>>                      -pass tripal2demo
>>>>
>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>
>>>> config_base            = /etc/gbrowse2   # overridden by
>>>> environment variable GBROWSE_CONF
>>>>
>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>
>>>> url_base               = /gbrowse2
>>>>
>>>> tmp_base               = /var/tmp/gbrowse2
>>>>
>>>> persistent_base        = /var/lib/gbrowse2
>>>>
>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>
>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> However, when I try to access the link:
>>>>
>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>
>>>>
>>>>
>>>> I get:
>>>>
>>>> Internal Server Error
>>>>
>>>> The server encountered an internal error or misconfiguration and
>>>> was unable to complete your request.
>>>>
>>>> Please contact the server administrator, root@localhost and inform
>>>> them of the time the error occurred, and anything you might have
>>>> done that may have caused the error.
>>>>
>>>> More information about this error may be available in the server error log.
>>>>
>>>> ________________________________
>>>>
>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> I'm at a dead end, the configurations are right, and I even
>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>
>>>>
>>>>
>>>> David Jeang
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> This electronic message contains information generated by the USDA
>>>> solely for the intended recipients. Any unauthorized interception
>>>> of this message or the use or disclosure of the information it
>>>> contains may violate the law and subject the violator to civil or
>>>> criminal penalties. If you believe you have received this message
>>>> in error, please notify the sender and delete the email immediately.
>>>>
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> --------
>>>> Live Security Virtual Conference
>>>> Exclusive live event will cover all the ways today's security and
>>>> threat landscape has changed and how IT managers can respond.
>>>> Discussions will include endpoint security, mobile security and the
>>>> latest in malware threats.
>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>> _______________________________________________
>>>> Gmod-gbrowse mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Scott Cain
Hi David,

You don't need those right now (that's while they're labeled
"recommends").  Can you access the built in yeast database now?

Scott


On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS
<[hidden email]> wrote:

> I have this when I run the Build. What do I do to install them?
>
> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL
> Checking prerequisites...
>  recommends:
>    *  Bio::DB::BigFile is not installed
>    *  Bio::DB::Sam is not installed
>    *  Net::OpenID::Consumer is not installed
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 2:17 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>
> Scott
>
>    requires     => {
>        'perl'                => '5.008',
>        'Bio::Root::Version'  => '1.0069',
>        'Bio::Graphics'       => '2.28',
>        'CGI::Session'        => '4.02',
>        'Digest::MD5'         => 0,
>        'ExtUtils::CBuilder'  => 0,
>        'File::Temp'          => 0,
>        'GD'                  => '2.07',
>        'Text::ParseWords'    => '3.27',
>        'IO::String'          => 0,
>        'JSON'                => 0,
>        'LWP'                 => 0,
>        'Statistics::Descriptive'  => 0,
>        'Storable'            => 0,
>        'Time::HiRes'         => 0,
>        'Digest::SHA'         => 0,
>        'Date::Parse'         => 0,
>        'Term::ReadKey'       => 0,
>    },
>    build_requires => {'Capture::Tiny'       => 0,},
>    recommends  => {
>        'Bio::Das'                 => 0,
>        'Bio::DB::Sam'             => 1.20,
>        'Bio::DB::BigFile'         => 1.00,
>        'Crypt::SSLeay'            => 0,
>        'DB_File::Lock'            => 0,
>        'DBI'                      => 0,
>        'DBD::mysql'               => 0,
>        'DBD::Pg'                  => 0,
>        'DBD::SQLite'              => 0,
>        'Digest::SHA'              => 0,
>        'FCGI'                     => 0,
>        'File::NFSLock'            => 0,
>        'GD::SVG'                  => 0,
>        'Math::BigInt'             => 0,
>        'Net::OpenID::Consumer'    => 0,
>        'Net::SMTP::SSL'           => 0,
>        $] <= 5.008 ? ('Safe::World'  => 0)
>                    : ()               ,
>        'Template'                 => 2.20,
>        'Term::ReadKey'            => 0,
>    },
>
>
>
> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>
>> David Jeang
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 1:41 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> This is pretty important:
>>
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
>> .) at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
>> s/Browser2/SendMail.pm
>> line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>> failed--compilation aborted at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
>> s/Browser2/SendMail.pm
>> line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
>> failed in require at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphic
>> s/Browser2/Action.pm
>> line 11.
>>
>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>> If that's not installed, chances are other things aren't as well.
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>
>>> There are a ton of logs here though, I'm not sure which one to look at.
>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>> Just guessing, but this is the log for error:
>>>
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>> pm in @INC (@INC contains:
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>> /perl5/5.8.8 .) at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>> o/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>> failed--compilatio n aborted at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>> hics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature end
>>> of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error] [client
>>> 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue
>>> Jun
>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature end
>>> of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature end
>>> of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature end
>>> of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error] [client
>>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>>> by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>>> referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>>> referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&server
>>> = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>>> by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature end
>>> of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error] [client
>>> 10.12.20.67] PHP Strict Standards:  Only variables should be assigned
>>> by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be passed by reference in
>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be assigned by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>>> referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>>> e
>>> r=%3A5432%3Aallow&database=tripal&
>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be passed by reference in
>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&serv
>>> e
>>> r=%3A5432%3Aallow&database=tripal&
>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be assigned by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line 23,
>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  O
>>>
>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>> David Jeang
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>> To: Jeang, David - ARS
>>> Cc: Gbrowse (E-mail)
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> Please keep the GBrowse mailing list cc'ed.
>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> On closer inspection, there is var/log/httpd,
>>>>
>>>> But I'm denied access....
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>> To: Jeang, David - ARS
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> Hi David,
>>>>
>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>>> connect to a chado database on the same server.
>>>>>
>>>>>
>>>>>
>>>>> This is how I set the conf file for Gbrowse
>>>>>
>>>>>
>>>>>
>>>>> [GENERAL]
>>>>>
>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>
>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>
>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>
>>>>>                      -user tripaldemo
>>>>>
>>>>>                      -pass tripal2demo
>>>>>
>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>
>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>> environment variable GBROWSE_CONF
>>>>>
>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>
>>>>> url_base               = /gbrowse2
>>>>>
>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>
>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>
>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>
>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> However, when I try to access the link:
>>>>>
>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>
>>>>>
>>>>>
>>>>> I get:
>>>>>
>>>>> Internal Server Error
>>>>>
>>>>> The server encountered an internal error or misconfiguration and
>>>>> was unable to complete your request.
>>>>>
>>>>> Please contact the server administrator, root@localhost and inform
>>>>> them of the time the error occurred, and anything you might have
>>>>> done that may have caused the error.
>>>>>
>>>>> More information about this error may be available in the server error log.
>>>>>
>>>>> ________________________________
>>>>>
>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I'm at a dead end, the configurations are right, and I even
>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>
>>>>>
>>>>>
>>>>> David Jeang
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> This electronic message contains information generated by the USDA
>>>>> solely for the intended recipients. Any unauthorized interception
>>>>> of this message or the use or disclosure of the information it
>>>>> contains may violate the law and subject the violator to civil or
>>>>> criminal penalties. If you believe you have received this message
>>>>> in error, please notify the sender and delete the email immediately.
>>>>>
>>>>> -------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> --------
>>>>> Live Security Virtual Conference
>>>>> Exclusive live event will cover all the ways today's security and
>>>>> threat landscape has changed and how IT managers can respond.
>>>>> Discussions will include endpoint security, mobile security and the
>>>>> latest in malware threats.
>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> --------------------------------------------------------------------
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ---------------------------------------------------------------------
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------------
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (http://gmod.org/)                     216-392-3087 Ontario Institute for Cancer Research
>
>



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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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Re: trying to connect to chado database

Jeang, David - ARS
No, I'm getting the same error unless I'm doing it wrong.

It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 2:42 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?

Scott


On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:

> I have this when I run the Build. What do I do to install them?
>
> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
> prerequisites...
>  recommends:
>    *  Bio::DB::BigFile is not installed
>    *  Bio::DB::Sam is not installed
>    *  Net::OpenID::Consumer is not installed
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 2:17 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>
> Scott
>
>    requires     => {
>        'perl'                => '5.008',
>        'Bio::Root::Version'  => '1.0069',
>        'Bio::Graphics'       => '2.28',
>        'CGI::Session'        => '4.02',
>        'Digest::MD5'         => 0,
>        'ExtUtils::CBuilder'  => 0,
>        'File::Temp'          => 0,
>        'GD'                  => '2.07',
>        'Text::ParseWords'    => '3.27',
>        'IO::String'          => 0,
>        'JSON'                => 0,
>        'LWP'                 => 0,
>        'Statistics::Descriptive'  => 0,
>        'Storable'            => 0,
>        'Time::HiRes'         => 0,
>        'Digest::SHA'         => 0,
>        'Date::Parse'         => 0,
>        'Term::ReadKey'       => 0,
>    },
>    build_requires => {'Capture::Tiny'       => 0,},
>    recommends  => {
>        'Bio::Das'                 => 0,
>        'Bio::DB::Sam'             => 1.20,
>        'Bio::DB::BigFile'         => 1.00,
>        'Crypt::SSLeay'            => 0,
>        'DB_File::Lock'            => 0,
>        'DBI'                      => 0,
>        'DBD::mysql'               => 0,
>        'DBD::Pg'                  => 0,
>        'DBD::SQLite'              => 0,
>        'Digest::SHA'              => 0,
>        'FCGI'                     => 0,
>        'File::NFSLock'            => 0,
>        'GD::SVG'                  => 0,
>        'Math::BigInt'             => 0,
>        'Net::OpenID::Consumer'    => 0,
>        'Net::SMTP::SSL'           => 0,
>        $] <= 5.008 ? ('Safe::World'  => 0)
>                    : ()               ,
>        'Template'                 => 2.20,
>        'Term::ReadKey'            => 0,
>    },
>
>
>
> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>
>> David Jeang
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 1:41 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> This is pretty important:
>>
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
>> .) at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphi
>> c
>> s/Browser2/SendMail.pm
>> line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>> failed--compilation aborted at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphi
>> c
>> s/Browser2/SendMail.pm
>> line 8.
>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
>> failed in require at
>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphi
>> c
>> s/Browser2/Action.pm
>> line 11.
>>
>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>> If that's not installed, chances are other things aren't as well.
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>
>>> There are a ton of logs here though, I'm not sure which one to look at.
>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>> Just guessing, but this is the log for error:
>>>
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>> pm in @INC (@INC contains:
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>> /perl5/5.8.8 .) at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>> o/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>> failed--compilatio n aborted at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>> hics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>> [client 10.12.20.67] File does not exist:
>>> /var/www/drupal/favicon.ico [Tue Jun
>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should be
>>> assigned by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>> 23,
>>> referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serve
>>> r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>>> referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serve
>>> r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>> assigned by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>> 23,
>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should be
>>> assigned by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>> 23,
>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be passed by reference in
>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be assigned by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>> 23,
>>> referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&ser
>>> v
>>> e
>>> r=%3A5432%3Aallow&database=tripal&
>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be passed by reference in
>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&ser
>>> v
>>> e
>>> r=%3A5432%3Aallow&database=tripal&
>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  Only variables should be assigned by reference in
>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>> 23,
>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>> Standards:  O
>>>
>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>> David Jeang
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>> To: Jeang, David - ARS
>>> Cc: Gbrowse (E-mail)
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> Please keep the GBrowse mailing list cc'ed.
>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> On closer inspection, there is var/log/httpd,
>>>>
>>>> But I'm denied access....
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>> To: Jeang, David - ARS
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> Hi David,
>>>>
>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>>> connect to a chado database on the same server.
>>>>>
>>>>>
>>>>>
>>>>> This is how I set the conf file for Gbrowse
>>>>>
>>>>>
>>>>>
>>>>> [GENERAL]
>>>>>
>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>
>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>
>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>
>>>>>                      -user tripaldemo
>>>>>
>>>>>                      -pass tripal2demo
>>>>>
>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>
>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>> environment variable GBROWSE_CONF
>>>>>
>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>
>>>>> url_base               = /gbrowse2
>>>>>
>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>
>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>
>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>
>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> However, when I try to access the link:
>>>>>
>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>
>>>>>
>>>>>
>>>>> I get:
>>>>>
>>>>> Internal Server Error
>>>>>
>>>>> The server encountered an internal error or misconfiguration and
>>>>> was unable to complete your request.
>>>>>
>>>>> Please contact the server administrator, root@localhost and inform
>>>>> them of the time the error occurred, and anything you might have
>>>>> done that may have caused the error.
>>>>>
>>>>> More information about this error may be available in the server error log.
>>>>>
>>>>> ________________________________
>>>>>
>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I'm at a dead end, the configurations are right, and I even
>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>
>>>>>
>>>>>
>>>>> David Jeang
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> This electronic message contains information generated by the USDA
>>>>> solely for the intended recipients. Any unauthorized interception
>>>>> of this message or the use or disclosure of the information it
>>>>> contains may violate the law and subject the violator to civil or
>>>>> criminal penalties. If you believe you have received this message
>>>>> in error, please notify the sender and delete the email immediately.
>>>>>
>>>>> ------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> -
>>>>> --------
>>>>> Live Security Virtual Conference
>>>>> Exclusive live event will cover all the ways today's security and
>>>>> threat landscape has changed and how IT managers can respond.
>>>>> Discussions will include endpoint security, mobile security and
>>>>> the latest in malware threats.
>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>> _______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Scott Cain
HI David,

The same error about Digest/SHA.pm?  That means it didn't get
installed correctly or in a place that apache can find it.  Where is
it?

Scott


On Tue, Jun 26, 2012 at 2:46 PM, Jeang, David - ARS
<[hidden email]> wrote:

> No, I'm getting the same error unless I'm doing it wrong.
>
> It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 2:42 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:
>> I have this when I run the Build. What do I do to install them?
>>
>> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
>> prerequisites...
>>  recommends:
>>    *  Bio::DB::BigFile is not installed
>>    *  Bio::DB::Sam is not installed
>>    *  Net::OpenID::Consumer is not installed
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 2:17 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>>
>> Scott
>>
>>    requires     => {
>>        'perl'                => '5.008',
>>        'Bio::Root::Version'  => '1.0069',
>>        'Bio::Graphics'       => '2.28',
>>        'CGI::Session'        => '4.02',
>>        'Digest::MD5'         => 0,
>>        'ExtUtils::CBuilder'  => 0,
>>        'File::Temp'          => 0,
>>        'GD'                  => '2.07',
>>        'Text::ParseWords'    => '3.27',
>>        'IO::String'          => 0,
>>        'JSON'                => 0,
>>        'LWP'                 => 0,
>>        'Statistics::Descriptive'  => 0,
>>        'Storable'            => 0,
>>        'Time::HiRes'         => 0,
>>        'Digest::SHA'         => 0,
>>        'Date::Parse'         => 0,
>>        'Term::ReadKey'       => 0,
>>    },
>>    build_requires => {'Capture::Tiny'       => 0,},
>>    recommends  => {
>>        'Bio::Das'                 => 0,
>>        'Bio::DB::Sam'             => 1.20,
>>        'Bio::DB::BigFile'         => 1.00,
>>        'Crypt::SSLeay'            => 0,
>>        'DB_File::Lock'            => 0,
>>        'DBI'                      => 0,
>>        'DBD::mysql'               => 0,
>>        'DBD::Pg'                  => 0,
>>        'DBD::SQLite'              => 0,
>>        'Digest::SHA'              => 0,
>>        'FCGI'                     => 0,
>>        'File::NFSLock'            => 0,
>>        'GD::SVG'                  => 0,
>>        'Math::BigInt'             => 0,
>>        'Net::OpenID::Consumer'    => 0,
>>        'Net::SMTP::SSL'           => 0,
>>        $] <= 5.008 ? ('Safe::World'  => 0)
>>                    : ()               ,
>>        'Template'                 => 2.20,
>>        'Term::ReadKey'            => 0,
>>    },
>>
>>
>>
>> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>>
>>> David Jeang
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 1:41 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> This is pretty important:
>>>
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8
>>> .) at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphi
>>> c
>>> s/Browser2/SendMail.pm
>>> line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>>> failed--compilation aborted at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphi
>>> c
>>> s/Browser2/SendMail.pm
>>> line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
>>> failed in require at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphi
>>> c
>>> s/Browser2/Action.pm
>>> line 11.
>>>
>>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>>> If that's not installed, chances are other things aren't as well.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>>
>>>> There are a ton of logs here though, I'm not sure which one to look at.
>>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>>> Just guessing, but this is the log for error:
>>>>
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>>> pm in @INC (@INC contains:
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>>> /perl5/5.8.8 .) at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>>> o/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>>> failed--compilatio n aborted at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>> hics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>>>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>>> [client 10.12.20.67] File does not exist:
>>>> /var/www/drupal/favicon.ico [Tue Jun
>>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>> assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serve
>>>> r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>>>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>>>> referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serve
>>>> r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>> assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>> assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be passed by reference in
>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&ser
>>>> v
>>>> e
>>>> r=%3A5432%3Aallow&database=tripal&
>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be passed by reference in
>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&ser
>>>> v
>>>> e
>>>> r=%3A5432%3Aallow&database=tripal&
>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  O
>>>>
>>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>>> David Jeang
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>>> To: Jeang, David - ARS
>>>> Cc: Gbrowse (E-mail)
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> Hi David,
>>>>
>>>> Please keep the GBrowse mailing list cc'ed.
>>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> On closer inspection, there is var/log/httpd,
>>>>>
>>>>> But I'm denied access....
>>>>>
>>>>> -----Original Message-----
>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>>> To: Jeang, David - ARS
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>
>>>>> Hi David,
>>>>>
>>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>>>> connect to a chado database on the same server.
>>>>>>
>>>>>>
>>>>>>
>>>>>> This is how I set the conf file for Gbrowse
>>>>>>
>>>>>>
>>>>>>
>>>>>> [GENERAL]
>>>>>>
>>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>>
>>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>>
>>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>>
>>>>>>                      -user tripaldemo
>>>>>>
>>>>>>                      -pass tripal2demo
>>>>>>
>>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>>
>>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>>> environment variable GBROWSE_CONF
>>>>>>
>>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>>
>>>>>> url_base               = /gbrowse2
>>>>>>
>>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>>
>>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>>
>>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>>
>>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> However, when I try to access the link:
>>>>>>
>>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>>
>>>>>>
>>>>>>
>>>>>> I get:
>>>>>>
>>>>>> Internal Server Error
>>>>>>
>>>>>> The server encountered an internal error or misconfiguration and
>>>>>> was unable to complete your request.
>>>>>>
>>>>>> Please contact the server administrator, root@localhost and inform
>>>>>> them of the time the error occurred, and anything you might have
>>>>>> done that may have caused the error.
>>>>>>
>>>>>> More information about this error may be available in the server error log.
>>>>>>
>>>>>> ________________________________
>>>>>>
>>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> I'm at a dead end, the configurations are right, and I even
>>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>>
>>>>>>
>>>>>>
>>>>>> David Jeang
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> This electronic message contains information generated by the USDA
>>>>>> solely for the intended recipients. Any unauthorized interception
>>>>>> of this message or the use or disclosure of the information it
>>>>>> contains may violate the law and subject the violator to civil or
>>>>>> criminal penalties. If you believe you have received this message
>>>>>> in error, please notify the sender and delete the email immediately.
>>>>>>
>>>>>> ------------------------------------------------------------------
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> --------
>>>>>> Live Security Virtual Conference
>>>>>> Exclusive live event will cover all the ways today's security and
>>>>>> threat landscape has changed and how IT managers can respond.
>>>>>> Discussions will include endpoint security, mobile security and
>>>>>> the latest in malware threats.
>>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> -------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> --------------------------------------------------------------------
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ---------------------------------------------------------------------
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------------
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (http://gmod.org/)                     216-392-3087 Ontario Institute for Cancer Research
>
>



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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Jeang, David - ARS
Just double checking, the file I'm looking for is DigestSHA.pm?

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 3:00 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

HI David,

The same error about Digest/SHA.pm?  That means it didn't get installed correctly or in a place that apache can find it.  Where is it?

Scott


On Tue, Jun 26, 2012 at 2:46 PM, Jeang, David - ARS <[hidden email]> wrote:

> No, I'm getting the same error unless I'm doing it wrong.
>
> It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 2:42 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Hi David,
>
> You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:
>> I have this when I run the Build. What do I do to install them?
>>
>> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
>> prerequisites...
>>  recommends:
>>    *  Bio::DB::BigFile is not installed
>>    *  Bio::DB::Sam is not installed
>>    *  Net::OpenID::Consumer is not installed
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 2:17 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>>
>> Scott
>>
>>    requires     => {
>>        'perl'                => '5.008',
>>        'Bio::Root::Version'  => '1.0069',
>>        'Bio::Graphics'       => '2.28',
>>        'CGI::Session'        => '4.02',
>>        'Digest::MD5'         => 0,
>>        'ExtUtils::CBuilder'  => 0,
>>        'File::Temp'          => 0,
>>        'GD'                  => '2.07',
>>        'Text::ParseWords'    => '3.27',
>>        'IO::String'          => 0,
>>        'JSON'                => 0,
>>        'LWP'                 => 0,
>>        'Statistics::Descriptive'  => 0,
>>        'Storable'            => 0,
>>        'Time::HiRes'         => 0,
>>        'Digest::SHA'         => 0,
>>        'Date::Parse'         => 0,
>>        'Term::ReadKey'       => 0,
>>    },
>>    build_requires => {'Capture::Tiny'       => 0,},
>>    recommends  => {
>>        'Bio::Das'                 => 0,
>>        'Bio::DB::Sam'             => 1.20,
>>        'Bio::DB::BigFile'         => 1.00,
>>        'Crypt::SSLeay'            => 0,
>>        'DB_File::Lock'            => 0,
>>        'DBI'                      => 0,
>>        'DBD::mysql'               => 0,
>>        'DBD::Pg'                  => 0,
>>        'DBD::SQLite'              => 0,
>>        'Digest::SHA'              => 0,
>>        'FCGI'                     => 0,
>>        'File::NFSLock'            => 0,
>>        'GD::SVG'                  => 0,
>>        'Math::BigInt'             => 0,
>>        'Net::OpenID::Consumer'    => 0,
>>        'Net::SMTP::SSL'           => 0,
>>        $] <= 5.008 ? ('Safe::World'  => 0)
>>                    : ()               ,
>>        'Template'                 => 2.20,
>>        'Term::ReadKey'            => 0,
>>    },
>>
>>
>>
>> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>>
>>> David Jeang
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 1:41 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> This is pretty important:
>>>
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>>> /usr/lib/perl5/5.8.8
>>> .) at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graph
>>> i
>>> c
>>> s/Browser2/SendMail.pm
>>> line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>>> failed--compilation aborted at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graph
>>> i
>>> c
>>> s/Browser2/SendMail.pm
>>> line 8.
>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
>>> failed in require at
>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graph
>>> i
>>> c
>>> s/Browser2/Action.pm
>>> line 11.
>>>
>>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>>> If that's not installed, chances are other things aren't as well.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>>
>>>> There are a ton of logs here though, I'm not sure which one to look at.
>>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>>> Just guessing, but this is the log for error:
>>>>
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>>> pm in @INC (@INC contains:
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>>> /perl5/5.8.8 .) at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>>> o/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>>> failed--compilatio n aborted at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>> hics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>>>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>>> [client 10.12.20.67] File does not exist:
>>>> /var/www/drupal/favicon.ico [Tue Jun
>>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>> be assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serv
>>>> e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>>>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>>>> referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serv
>>>> e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>> assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>> be assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be passed by reference in
>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&se
>>>> r
>>>> v
>>>> e
>>>> r=%3A5432%3Aallow&database=tripal&
>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be passed by reference in
>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&se
>>>> r
>>>> v
>>>> e
>>>> r=%3A5432%3Aallow&database=tripal&
>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  Only variables should be assigned by reference in
>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>> 23,
>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>> Standards:  O
>>>>
>>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>>> David Jeang
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>>> To: Jeang, David - ARS
>>>> Cc: Gbrowse (E-mail)
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> Hi David,
>>>>
>>>> Please keep the GBrowse mailing list cc'ed.
>>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> On closer inspection, there is var/log/httpd,
>>>>>
>>>>> But I'm denied access....
>>>>>
>>>>> -----Original Message-----
>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>>> To: Jeang, David - ARS
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>
>>>>> Hi David,
>>>>>
>>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>>>> connect to a chado database on the same server.
>>>>>>
>>>>>>
>>>>>>
>>>>>> This is how I set the conf file for Gbrowse
>>>>>>
>>>>>>
>>>>>>
>>>>>> [GENERAL]
>>>>>>
>>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>>
>>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>>
>>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>>
>>>>>>                      -user tripaldemo
>>>>>>
>>>>>>                      -pass tripal2demo
>>>>>>
>>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>>
>>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>>> environment variable GBROWSE_CONF
>>>>>>
>>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>>
>>>>>> url_base               = /gbrowse2
>>>>>>
>>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>>
>>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>>
>>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>>
>>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> However, when I try to access the link:
>>>>>>
>>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>>
>>>>>>
>>>>>>
>>>>>> I get:
>>>>>>
>>>>>> Internal Server Error
>>>>>>
>>>>>> The server encountered an internal error or misconfiguration and
>>>>>> was unable to complete your request.
>>>>>>
>>>>>> Please contact the server administrator, root@localhost and
>>>>>> inform them of the time the error occurred, and anything you
>>>>>> might have done that may have caused the error.
>>>>>>
>>>>>> More information about this error may be available in the server error log.
>>>>>>
>>>>>> ________________________________
>>>>>>
>>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> I'm at a dead end, the configurations are right, and I even
>>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>>
>>>>>>
>>>>>>
>>>>>> David Jeang
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> This electronic message contains information generated by the
>>>>>> USDA solely for the intended recipients. Any unauthorized
>>>>>> interception of this message or the use or disclosure of the
>>>>>> information it contains may violate the law and subject the
>>>>>> violator to civil or criminal penalties. If you believe you have
>>>>>> received this message in error, please notify the sender and delete the email immediately.
>>>>>>
>>>>>> -----------------------------------------------------------------
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> --------
>>>>>> Live Security Virtual Conference
>>>>>> Exclusive live event will cover all the ways today's security and
>>>>>> threat landscape has changed and how IT managers can respond.
>>>>>> Discussions will include endpoint security, mobile security and
>>>>>> the latest in malware threats.
>>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> -
>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Scott Cain
Nope: you're looking for SHA.pm in a directory called Digest.

On Tue, Jun 26, 2012 at 3:01 PM, Jeang, David - ARS
<[hidden email]> wrote:

> Just double checking, the file I'm looking for is DigestSHA.pm?
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 3:00 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> HI David,
>
> The same error about Digest/SHA.pm?  That means it didn't get installed correctly or in a place that apache can find it.  Where is it?
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 2:46 PM, Jeang, David - ARS <[hidden email]> wrote:
>> No, I'm getting the same error unless I'm doing it wrong.
>>
>> It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 2:42 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> I have this when I run the Build. What do I do to install them?
>>>
>>> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
>>> prerequisites...
>>>  recommends:
>>>    *  Bio::DB::BigFile is not installed
>>>    *  Bio::DB::Sam is not installed
>>>    *  Net::OpenID::Consumer is not installed
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 2:17 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>>>
>>> Scott
>>>
>>>    requires     => {
>>>        'perl'                => '5.008',
>>>        'Bio::Root::Version'  => '1.0069',
>>>        'Bio::Graphics'       => '2.28',
>>>        'CGI::Session'        => '4.02',
>>>        'Digest::MD5'         => 0,
>>>        'ExtUtils::CBuilder'  => 0,
>>>        'File::Temp'          => 0,
>>>        'GD'                  => '2.07',
>>>        'Text::ParseWords'    => '3.27',
>>>        'IO::String'          => 0,
>>>        'JSON'                => 0,
>>>        'LWP'                 => 0,
>>>        'Statistics::Descriptive'  => 0,
>>>        'Storable'            => 0,
>>>        'Time::HiRes'         => 0,
>>>        'Digest::SHA'         => 0,
>>>        'Date::Parse'         => 0,
>>>        'Term::ReadKey'       => 0,
>>>    },
>>>    build_requires => {'Capture::Tiny'       => 0,},
>>>    recommends  => {
>>>        'Bio::Das'                 => 0,
>>>        'Bio::DB::Sam'             => 1.20,
>>>        'Bio::DB::BigFile'         => 1.00,
>>>        'Crypt::SSLeay'            => 0,
>>>        'DB_File::Lock'            => 0,
>>>        'DBI'                      => 0,
>>>        'DBD::mysql'               => 0,
>>>        'DBD::Pg'                  => 0,
>>>        'DBD::SQLite'              => 0,
>>>        'Digest::SHA'              => 0,
>>>        'FCGI'                     => 0,
>>>        'File::NFSLock'            => 0,
>>>        'GD::SVG'                  => 0,
>>>        'Math::BigInt'             => 0,
>>>        'Net::OpenID::Consumer'    => 0,
>>>        'Net::SMTP::SSL'           => 0,
>>>        $] <= 5.008 ? ('Safe::World'  => 0)
>>>                    : ()               ,
>>>        'Template'                 => 2.20,
>>>        'Term::ReadKey'            => 0,
>>>    },
>>>
>>>
>>>
>>> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>>>
>>>> David Jeang
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 1:41 PM
>>>> To: Jeang, David - ARS
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> This is pretty important:
>>>>
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/5.8.8
>>>> .) at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graph
>>>> i
>>>> c
>>>> s/Browser2/SendMail.pm
>>>> line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>>>> failed--compilation aborted at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graph
>>>> i
>>>> c
>>>> s/Browser2/SendMail.pm
>>>> line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
>>>> failed in require at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graph
>>>> i
>>>> c
>>>> s/Browser2/Action.pm
>>>> line 11.
>>>>
>>>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>>>> If that's not installed, chances are other things aren't as well.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>>>
>>>>> There are a ton of logs here though, I'm not sure which one to look at.
>>>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>>>> Just guessing, but this is the log for error:
>>>>>
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>>>> pm in @INC (@INC contains:
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>>>> /perl5/5.8.8 .) at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>>>> o/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>>>> failed--compilatio n aborted at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>>> hics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation
>>>>> failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>>>> [client 10.12.20.67] File does not exist:
>>>>> /var/www/drupal/favicon.ico [Tue Jun
>>>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>> be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serv
>>>>> e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be passed
>>>>> by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on line 14,
>>>>> referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&serv
>>>>> e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>>> assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>> be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be passed by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&se
>>>>> r
>>>>> v
>>>>> e
>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be passed by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&se
>>>>> r
>>>>> v
>>>>> e
>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  O
>>>>>
>>>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>>>> David Jeang
>>>>>
>>>>> -----Original Message-----
>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>>>> To: Jeang, David - ARS
>>>>> Cc: Gbrowse (E-mail)
>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>
>>>>> Hi David,
>>>>>
>>>>> Please keep the GBrowse mailing list cc'ed.
>>>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>> On closer inspection, there is var/log/httpd,
>>>>>>
>>>>>> But I'm denied access....
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>>>> To: Jeang, David - ARS
>>>>>> Cc: [hidden email]
>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>> I've installed Gbrowse 2.49 on the local server, and am trying to
>>>>>>> connect to a chado database on the same server.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> This is how I set the conf file for Gbrowse
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> [GENERAL]
>>>>>>>
>>>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>>>
>>>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>>>
>>>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>>>
>>>>>>>                      -user tripaldemo
>>>>>>>
>>>>>>>                      -pass tripal2demo
>>>>>>>
>>>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>>>
>>>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>>>> environment variable GBROWSE_CONF
>>>>>>>
>>>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>>>
>>>>>>> url_base               = /gbrowse2
>>>>>>>
>>>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>>>
>>>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>>>
>>>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>>>
>>>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> However, when I try to access the link:
>>>>>>>
>>>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I get:
>>>>>>>
>>>>>>> Internal Server Error
>>>>>>>
>>>>>>> The server encountered an internal error or misconfiguration and
>>>>>>> was unable to complete your request.
>>>>>>>
>>>>>>> Please contact the server administrator, root@localhost and
>>>>>>> inform them of the time the error occurred, and anything you
>>>>>>> might have done that may have caused the error.
>>>>>>>
>>>>>>> More information about this error may be available in the server error log.
>>>>>>>
>>>>>>> ________________________________
>>>>>>>
>>>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I'm at a dead end, the configurations are right, and I even
>>>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> David Jeang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> This electronic message contains information generated by the
>>>>>>> USDA solely for the intended recipients. Any unauthorized
>>>>>>> interception of this message or the use or disclosure of the
>>>>>>> information it contains may violate the law and subject the
>>>>>>> violator to civil or criminal penalties. If you believe you have
>>>>>>> received this message in error, please notify the sender and delete the email immediately.
>>>>>>>
>>>>>>> -----------------------------------------------------------------
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> --------
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>>>>>> -- 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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>>>>> --
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>>>>> -
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>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> --------------------------------------------------------------------
>>>> -
>>>> -
>>>> -- 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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>>> ---------------------------------------------------------------------
>>> -
>>> -- 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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>>
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>> --
>> ----------------------------------------------------------------------
>> -- 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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>
>
> --
> ------------------------------------------------------------------------
> 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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Ontario Institute for Cancer Research

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Re: trying to connect to chado database

Jeang, David - ARS
I found it in opt/ActivePerl-5.12/lib/Digest/SHA.PM

What should I do now?


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 3:06 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Nope: you're looking for SHA.pm in a directory called Digest.

On Tue, Jun 26, 2012 at 3:01 PM, Jeang, David - ARS <[hidden email]> wrote:

> Just double checking, the file I'm looking for is DigestSHA.pm?
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 3:00 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> HI David,
>
> The same error about Digest/SHA.pm?  That means it didn't get installed correctly or in a place that apache can find it.  Where is it?
>
> Scott
>
>
> On Tue, Jun 26, 2012 at 2:46 PM, Jeang, David - ARS <[hidden email]> wrote:
>> No, I'm getting the same error unless I'm doing it wrong.
>>
>> It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 2:42 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> Hi David,
>>
>> You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> I have this when I run the Build. What do I do to install them?
>>>
>>> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
>>> prerequisites...
>>>  recommends:
>>>    *  Bio::DB::BigFile is not installed
>>>    *  Bio::DB::Sam is not installed
>>>    *  Net::OpenID::Consumer is not installed
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 2:17 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>>>
>>> Scott
>>>
>>>    requires     => {
>>>        'perl'                => '5.008',
>>>        'Bio::Root::Version'  => '1.0069',
>>>        'Bio::Graphics'       => '2.28',
>>>        'CGI::Session'        => '4.02',
>>>        'Digest::MD5'         => 0,
>>>        'ExtUtils::CBuilder'  => 0,
>>>        'File::Temp'          => 0,
>>>        'GD'                  => '2.07',
>>>        'Text::ParseWords'    => '3.27',
>>>        'IO::String'          => 0,
>>>        'JSON'                => 0,
>>>        'LWP'                 => 0,
>>>        'Statistics::Descriptive'  => 0,
>>>        'Storable'            => 0,
>>>        'Time::HiRes'         => 0,
>>>        'Digest::SHA'         => 0,
>>>        'Date::Parse'         => 0,
>>>        'Term::ReadKey'       => 0,
>>>    },
>>>    build_requires => {'Capture::Tiny'       => 0,},
>>>    recommends  => {
>>>        'Bio::Das'                 => 0,
>>>        'Bio::DB::Sam'             => 1.20,
>>>        'Bio::DB::BigFile'         => 1.00,
>>>        'Crypt::SSLeay'            => 0,
>>>        'DB_File::Lock'            => 0,
>>>        'DBI'                      => 0,
>>>        'DBD::mysql'               => 0,
>>>        'DBD::Pg'                  => 0,
>>>        'DBD::SQLite'              => 0,
>>>        'Digest::SHA'              => 0,
>>>        'FCGI'                     => 0,
>>>        'File::NFSLock'            => 0,
>>>        'GD::SVG'                  => 0,
>>>        'Math::BigInt'             => 0,
>>>        'Net::OpenID::Consumer'    => 0,
>>>        'Net::SMTP::SSL'           => 0,
>>>        $] <= 5.008 ? ('Safe::World'  => 0)
>>>                    : ()               ,
>>>        'Template'                 => 2.20,
>>>        'Term::ReadKey'            => 0,
>>>    },
>>>
>>>
>>>
>>> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>>>
>>>> David Jeang
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 1:41 PM
>>>> To: Jeang, David - ARS
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> This is pretty important:
>>>>
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>>>> /usr/lib/perl5/5.8.8
>>>> .) at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>> h
>>>> i
>>>> c
>>>> s/Browser2/SendMail.pm
>>>> line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>>>> failed--compilation aborted at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>> h
>>>> i
>>>> c
>>>> s/Browser2/SendMail.pm
>>>> line 8.
>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
>>>> failed in require at
>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>> h
>>>> i
>>>> c
>>>> s/Browser2/Action.pm
>>>> line 11.
>>>>
>>>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>>>> If that's not installed, chances are other things aren't as well.
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>>>
>>>>> There are a ton of logs here though, I'm not sure which one to look at.
>>>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>>>> Just guessing, but this is the log for error:
>>>>>
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>>>> pm in @INC (@INC contains:
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>>>> /perl5/5.8.8 .) at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>>>> o/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>>>> failed--compilatio n aborted at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>> p
>>>>> hics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67]
>>>>> Compilation failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>>>> [client 10.12.20.67] File does not exist:
>>>>> /var/www/drupal/favicon.ico [Tue Jun
>>>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>> be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&ser
>>>>> v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>>> passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on
>>>>> line 14,
>>>>> referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&ser
>>>>> v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>>> assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>> be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be passed by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&s
>>>>> e
>>>>> r
>>>>> v
>>>>> e
>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be passed by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&s
>>>>> e
>>>>> r
>>>>> v
>>>>> e
>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  Only variables should be assigned by reference in
>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>> 23,
>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>>> Standards:  O
>>>>>
>>>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>>>> David Jeang
>>>>>
>>>>> -----Original Message-----
>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>>>> To: Jeang, David - ARS
>>>>> Cc: Gbrowse (E-mail)
>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>
>>>>> Hi David,
>>>>>
>>>>> Please keep the GBrowse mailing list cc'ed.
>>>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>> On closer inspection, there is var/log/httpd,
>>>>>>
>>>>>> But I'm denied access....
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>>>> To: Jeang, David - ARS
>>>>>> Cc: [hidden email]
>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>> I've installed Gbrowse 2.49 on the local server, and am trying
>>>>>>> to connect to a chado database on the same server.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> This is how I set the conf file for Gbrowse
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> [GENERAL]
>>>>>>>
>>>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>>>
>>>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>>>
>>>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>>>
>>>>>>>                      -user tripaldemo
>>>>>>>
>>>>>>>                      -pass tripal2demo
>>>>>>>
>>>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>>>
>>>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>>>> environment variable GBROWSE_CONF
>>>>>>>
>>>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>>>
>>>>>>> url_base               = /gbrowse2
>>>>>>>
>>>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>>>
>>>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>>>
>>>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>>>
>>>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> However, when I try to access the link:
>>>>>>>
>>>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I get:
>>>>>>>
>>>>>>> Internal Server Error
>>>>>>>
>>>>>>> The server encountered an internal error or misconfiguration and
>>>>>>> was unable to complete your request.
>>>>>>>
>>>>>>> Please contact the server administrator, root@localhost and
>>>>>>> inform them of the time the error occurred, and anything you
>>>>>>> might have done that may have caused the error.
>>>>>>>
>>>>>>> More information about this error may be available in the server error log.
>>>>>>>
>>>>>>> ________________________________
>>>>>>>
>>>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I'm at a dead end, the configurations are right, and I even
>>>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> David Jeang
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> This electronic message contains information generated by the
>>>>>>> USDA solely for the intended recipients. Any unauthorized
>>>>>>> interception of this message or the use or disclosure of the
>>>>>>> information it contains may violate the law and subject the
>>>>>>> violator to civil or criminal penalties. If you believe you have
>>>>>>> received this message in error, please notify the sender and delete the email immediately.
>>>>>>>
>>>>>>> ----------------------------------------------------------------
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> --------
>>>>>>> Live Security Virtual Conference Exclusive live event will cover
>>>>>>> all the ways today's security and threat landscape has changed
>>>>>>> and how IT managers can respond.
>>>>>>> Discussions will include endpoint security, mobile security and
>>>>>>> the latest in malware threats.
>>>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>> _______________________________________________
>>>>>>> Gmod-gbrowse mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> -----------------------------------------------------------------
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> -
>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>
>
>
>
> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
>



--
------------------------------------------------------------------------
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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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Scott Cain
Hi David,

Hmm, ActivePerl on Linux.  Pretty sure that's the first time I've seen that :-)

You need to set the PERL5LIB environment variable in your apache
config; hopefully you have mod_env available.  Locate your httpd.conf
file; it's probably in /etc/apache2.  To the bottom of it, add

SetEnv PERL5LIB /opt/ActivePerl-5.12

and restart apache (of course, you have to be in a root shell to do
all of that).  I assumed that you were missing the leading / in your
path, so I added it in.

Scott


On Tue, Jun 26, 2012 at 3:19 PM, Jeang, David - ARS
<[hidden email]> wrote:

> I found it in opt/ActivePerl-5.12/lib/Digest/SHA.PM
>
> What should I do now?
>
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 3:06 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Nope: you're looking for SHA.pm in a directory called Digest.
>
> On Tue, Jun 26, 2012 at 3:01 PM, Jeang, David - ARS <[hidden email]> wrote:
>> Just double checking, the file I'm looking for is DigestSHA.pm?
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 3:00 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> HI David,
>>
>> The same error about Digest/SHA.pm?  That means it didn't get installed correctly or in a place that apache can find it.  Where is it?
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 2:46 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> No, I'm getting the same error unless I'm doing it wrong.
>>>
>>> It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 2:42 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I have this when I run the Build. What do I do to install them?
>>>>
>>>> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
>>>> prerequisites...
>>>>  recommends:
>>>>    *  Bio::DB::BigFile is not installed
>>>>    *  Bio::DB::Sam is not installed
>>>>    *  Net::OpenID::Consumer is not installed
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 2:17 PM
>>>> To: Jeang, David - ARS
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> Hi David,
>>>>
>>>> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>>>>
>>>> Scott
>>>>
>>>>    requires     => {
>>>>        'perl'                => '5.008',
>>>>        'Bio::Root::Version'  => '1.0069',
>>>>        'Bio::Graphics'       => '2.28',
>>>>        'CGI::Session'        => '4.02',
>>>>        'Digest::MD5'         => 0,
>>>>        'ExtUtils::CBuilder'  => 0,
>>>>        'File::Temp'          => 0,
>>>>        'GD'                  => '2.07',
>>>>        'Text::ParseWords'    => '3.27',
>>>>        'IO::String'          => 0,
>>>>        'JSON'                => 0,
>>>>        'LWP'                 => 0,
>>>>        'Statistics::Descriptive'  => 0,
>>>>        'Storable'            => 0,
>>>>        'Time::HiRes'         => 0,
>>>>        'Digest::SHA'         => 0,
>>>>        'Date::Parse'         => 0,
>>>>        'Term::ReadKey'       => 0,
>>>>    },
>>>>    build_requires => {'Capture::Tiny'       => 0,},
>>>>    recommends  => {
>>>>        'Bio::Das'                 => 0,
>>>>        'Bio::DB::Sam'             => 1.20,
>>>>        'Bio::DB::BigFile'         => 1.00,
>>>>        'Crypt::SSLeay'            => 0,
>>>>        'DB_File::Lock'            => 0,
>>>>        'DBI'                      => 0,
>>>>        'DBD::mysql'               => 0,
>>>>        'DBD::Pg'                  => 0,
>>>>        'DBD::SQLite'              => 0,
>>>>        'Digest::SHA'              => 0,
>>>>        'FCGI'                     => 0,
>>>>        'File::NFSLock'            => 0,
>>>>        'GD::SVG'                  => 0,
>>>>        'Math::BigInt'             => 0,
>>>>        'Net::OpenID::Consumer'    => 0,
>>>>        'Net::SMTP::SSL'           => 0,
>>>>        $] <= 5.008 ? ('Safe::World'  => 0)
>>>>                    : ()               ,
>>>>        'Template'                 => 2.20,
>>>>        'Term::ReadKey'            => 0,
>>>>    },
>>>>
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>>>>
>>>>> David Jeang
>>>>>
>>>>> -----Original Message-----
>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>> Sent: Tuesday, June 26, 2012 1:41 PM
>>>>> To: Jeang, David - ARS
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>
>>>>> This is pretty important:
>>>>>
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/5.8.8
>>>>> .) at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/SendMail.pm
>>>>> line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>>>>> failed--compilation aborted at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/SendMail.pm
>>>>> line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation
>>>>> failed in require at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Grap
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/Action.pm
>>>>> line 11.
>>>>>
>>>>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>>>>> If that's not installed, chances are other things aren't as well.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>>>>
>>>>>> There are a ton of logs here though, I'm not sure which one to look at.
>>>>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>>>>> Just guessing, but this is the log for error:
>>>>>>
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>>>>> pm in @INC (@INC contains:
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>>>>> /perl5/5.8.8 .) at
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>>>>> o/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>>>>> failed--compilatio n aborted at
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>>> p
>>>>>> hics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67]
>>>>>> Compilation failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>>>>> [client 10.12.20.67] File does not exist:
>>>>>> /var/www/drupal/favicon.ico [Tue Jun
>>>>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>>>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&ser
>>>>>> v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>>>> passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php on
>>>>>> line 14,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&ser
>>>>>> v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error] [client
>>>>>> 10.12.20.67] PHP Strict Standards:  Only variables should be
>>>>>> assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP Strict
>>>>>> Standards:  Only variables should be passed by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>>>> Standards:  Only variables should be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&s
>>>>>> e
>>>>>> r
>>>>>> v
>>>>>> e
>>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP Strict
>>>>>> Standards:  Only variables should be passed by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&s
>>>>>> e
>>>>>> r
>>>>>> v
>>>>>> e
>>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>>>> Standards:  Only variables should be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP Strict
>>>>>> Standards:  O
>>>>>>
>>>>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>>>>> David Jeang
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>>>>> To: Jeang, David - ARS
>>>>>> Cc: Gbrowse (E-mail)
>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> Please keep the GBrowse mailing list cc'ed.
>>>>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>> On closer inspection, there is var/log/httpd,
>>>>>>>
>>>>>>> But I'm denied access....
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>>>>> To: Jeang, David - ARS
>>>>>>> Cc: [hidden email]
>>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>>
>>>>>>> Hi David,
>>>>>>>
>>>>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>>> I've installed Gbrowse 2.49 on the local server, and am trying
>>>>>>>> to connect to a chado database on the same server.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> This is how I set the conf file for Gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [GENERAL]
>>>>>>>>
>>>>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>>>>
>>>>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>>>>
>>>>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>>>>
>>>>>>>>                      -user tripaldemo
>>>>>>>>
>>>>>>>>                      -pass tripal2demo
>>>>>>>>
>>>>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>>>>
>>>>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>>>>> environment variable GBROWSE_CONF
>>>>>>>>
>>>>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>>>>
>>>>>>>> url_base               = /gbrowse2
>>>>>>>>
>>>>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>>>>
>>>>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>>>>
>>>>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>>>>
>>>>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> However, when I try to access the link:
>>>>>>>>
>>>>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I get:
>>>>>>>>
>>>>>>>> Internal Server Error
>>>>>>>>
>>>>>>>> The server encountered an internal error or misconfiguration and
>>>>>>>> was unable to complete your request.
>>>>>>>>
>>>>>>>> Please contact the server administrator, root@localhost and
>>>>>>>> inform them of the time the error occurred, and anything you
>>>>>>>> might have done that may have caused the error.
>>>>>>>>
>>>>>>>> More information about this error may be available in the server error log.
>>>>>>>>
>>>>>>>> ________________________________
>>>>>>>>
>>>>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I'm at a dead end, the configurations are right, and I even
>>>>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> David Jeang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> This electronic message contains information generated by the
>>>>>>>> USDA solely for the intended recipients. Any unauthorized
>>>>>>>> interception of this message or the use or disclosure of the
>>>>>>>> information it contains may violate the law and subject the
>>>>>>>> violator to civil or criminal penalties. If you believe you have
>>>>>>>> received this message in error, please notify the sender and delete the email immediately.
>>>>>>>>
>>>>>>>> ----------------------------------------------------------------
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> --------
>>>>>>>> Live Security Virtual Conference Exclusive live event will cover
>>>>>>>> all the ways today's security and threat landscape has changed
>>>>>>>> and how IT managers can respond.
>>>>>>>> Discussions will include endpoint security, mobile security and
>>>>>>>> the latest in malware threats.
>>>>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> -----------------------------------------------------------------
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> -------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> --------------------------------------------------------------------
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ---------------------------------------------------------------------
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------------
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>>
>>
>>
>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net GMOD Coordinator (http://gmod.org/)                     216-392-3087 Ontario Institute for Cancer Research
>
>



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

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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Re: trying to connect to chado database

Jeang, David - ARS
There is no apache2 folder in etc, but I did find /etc/httpd/conf/httpd.conf

Is that correct?

And what's the command to reset Apache in the command terminal?

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 3:38 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

Hmm, ActivePerl on Linux.  Pretty sure that's the first time I've seen that :-)

You need to set the PERL5LIB environment variable in your apache config; hopefully you have mod_env available.  Locate your httpd.conf file; it's probably in /etc/apache2.  To the bottom of it, add

SetEnv PERL5LIB /opt/ActivePerl-5.12

and restart apache (of course, you have to be in a root shell to do all of that).  I assumed that you were missing the leading / in your path, so I added it in.

Scott


On Tue, Jun 26, 2012 at 3:19 PM, Jeang, David - ARS <[hidden email]> wrote:

> I found it in opt/ActivePerl-5.12/lib/Digest/SHA.PM
>
> What should I do now?
>
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 3:06 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Nope: you're looking for SHA.pm in a directory called Digest.
>
> On Tue, Jun 26, 2012 at 3:01 PM, Jeang, David - ARS <[hidden email]> wrote:
>> Just double checking, the file I'm looking for is DigestSHA.pm?
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 3:00 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> HI David,
>>
>> The same error about Digest/SHA.pm?  That means it didn't get installed correctly or in a place that apache can find it.  Where is it?
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 2:46 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> No, I'm getting the same error unless I'm doing it wrong.
>>>
>>> It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 2:42 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I have this when I run the Build. What do I do to install them?
>>>>
>>>> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
>>>> prerequisites...
>>>>  recommends:
>>>>    *  Bio::DB::BigFile is not installed
>>>>    *  Bio::DB::Sam is not installed
>>>>    *  Net::OpenID::Consumer is not installed
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 2:17 PM
>>>> To: Jeang, David - ARS
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> Hi David,
>>>>
>>>> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>>>>
>>>> Scott
>>>>
>>>>    requires     => {
>>>>        'perl'                => '5.008',
>>>>        'Bio::Root::Version'  => '1.0069',
>>>>        'Bio::Graphics'       => '2.28',
>>>>        'CGI::Session'        => '4.02',
>>>>        'Digest::MD5'         => 0,
>>>>        'ExtUtils::CBuilder'  => 0,
>>>>        'File::Temp'          => 0,
>>>>        'GD'                  => '2.07',
>>>>        'Text::ParseWords'    => '3.27',
>>>>        'IO::String'          => 0,
>>>>        'JSON'                => 0,
>>>>        'LWP'                 => 0,
>>>>        'Statistics::Descriptive'  => 0,
>>>>        'Storable'            => 0,
>>>>        'Time::HiRes'         => 0,
>>>>        'Digest::SHA'         => 0,
>>>>        'Date::Parse'         => 0,
>>>>        'Term::ReadKey'       => 0,
>>>>    },
>>>>    build_requires => {'Capture::Tiny'       => 0,},
>>>>    recommends  => {
>>>>        'Bio::Das'                 => 0,
>>>>        'Bio::DB::Sam'             => 1.20,
>>>>        'Bio::DB::BigFile'         => 1.00,
>>>>        'Crypt::SSLeay'            => 0,
>>>>        'DB_File::Lock'            => 0,
>>>>        'DBI'                      => 0,
>>>>        'DBD::mysql'               => 0,
>>>>        'DBD::Pg'                  => 0,
>>>>        'DBD::SQLite'              => 0,
>>>>        'Digest::SHA'              => 0,
>>>>        'FCGI'                     => 0,
>>>>        'File::NFSLock'            => 0,
>>>>        'GD::SVG'                  => 0,
>>>>        'Math::BigInt'             => 0,
>>>>        'Net::OpenID::Consumer'    => 0,
>>>>        'Net::SMTP::SSL'           => 0,
>>>>        $] <= 5.008 ? ('Safe::World'  => 0)
>>>>                    : ()               ,
>>>>        'Template'                 => 2.20,
>>>>        'Term::ReadKey'            => 0,
>>>>    },
>>>>
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>>>>
>>>>> David Jeang
>>>>>
>>>>> -----Original Message-----
>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>> Sent: Tuesday, June 26, 2012 1:41 PM
>>>>> To: Jeang, David - ARS
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>
>>>>> This is pretty important:
>>>>>
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/5.8.8
>>>>> .) at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>> p
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/SendMail.pm
>>>>> line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>>>>> failed--compilation aborted at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>> p
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/SendMail.pm
>>>>> line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67]
>>>>> Compilation failed in require at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>> p
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/Action.pm
>>>>> line 11.
>>>>>
>>>>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>>>>> If that's not installed, chances are other things aren't as well.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>>>>
>>>>>> There are a ton of logs here though, I'm not sure which one to look at.
>>>>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>>>>> Just guessing, but this is the log for error:
>>>>>>
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>>>>> pm in @INC (@INC contains:
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>>>>> /perl5/5.8.8 .) at
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>>>>> o/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>>>>> failed--compilatio n aborted at
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gr
>>>>>> a
>>>>>> p
>>>>>> hics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67]
>>>>>> Compilation failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>>>>> [client 10.12.20.67] File does not exist:
>>>>>> /var/www/drupal/favicon.ico [Tue Jun
>>>>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>>>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&se
>>>>>> r v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php
>>>>>> on line 14,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&se
>>>>>> r v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be passed by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&
>>>>>> s
>>>>>> e
>>>>>> r
>>>>>> v
>>>>>> e
>>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be passed by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&
>>>>>> s
>>>>>> e
>>>>>> r
>>>>>> v
>>>>>> e
>>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  O
>>>>>>
>>>>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>>>>> David Jeang
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>>>>> To: Jeang, David - ARS
>>>>>> Cc: Gbrowse (E-mail)
>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> Please keep the GBrowse mailing list cc'ed.
>>>>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>> On closer inspection, there is var/log/httpd,
>>>>>>>
>>>>>>> But I'm denied access....
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>>>>> To: Jeang, David - ARS
>>>>>>> Cc: [hidden email]
>>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>>
>>>>>>> Hi David,
>>>>>>>
>>>>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>>> I've installed Gbrowse 2.49 on the local server, and am trying
>>>>>>>> to connect to a chado database on the same server.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> This is how I set the conf file for Gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [GENERAL]
>>>>>>>>
>>>>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>>>>
>>>>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>>>>
>>>>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>>>>
>>>>>>>>                      -user tripaldemo
>>>>>>>>
>>>>>>>>                      -pass tripal2demo
>>>>>>>>
>>>>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>>>>
>>>>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>>>>> environment variable GBROWSE_CONF
>>>>>>>>
>>>>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>>>>
>>>>>>>> url_base               = /gbrowse2
>>>>>>>>
>>>>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>>>>
>>>>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>>>>
>>>>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>>>>
>>>>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> However, when I try to access the link:
>>>>>>>>
>>>>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I get:
>>>>>>>>
>>>>>>>> Internal Server Error
>>>>>>>>
>>>>>>>> The server encountered an internal error or misconfiguration
>>>>>>>> and was unable to complete your request.
>>>>>>>>
>>>>>>>> Please contact the server administrator, root@localhost and
>>>>>>>> inform them of the time the error occurred, and anything you
>>>>>>>> might have done that may have caused the error.
>>>>>>>>
>>>>>>>> More information about this error may be available in the server error log.
>>>>>>>>
>>>>>>>> ________________________________
>>>>>>>>
>>>>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I'm at a dead end, the configurations are right, and I even
>>>>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> David Jeang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> This electronic message contains information generated by the
>>>>>>>> USDA solely for the intended recipients. Any unauthorized
>>>>>>>> interception of this message or the use or disclosure of the
>>>>>>>> information it contains may violate the law and subject the
>>>>>>>> violator to civil or criminal penalties. If you believe you
>>>>>>>> have received this message in error, please notify the sender and delete the email immediately.
>>>>>>>>
>>>>>>>> ---------------------------------------------------------------
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> --------
>>>>>>>> Live Security Virtual Conference Exclusive live event will
>>>>>>>> cover all the ways today's security and threat landscape has
>>>>>>>> changed and how IT managers can respond.
>>>>>>>> Discussions will include endpoint security, mobile security and
>>>>>>>> the latest in malware threats.
>>>>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ----------------------------------------------------------------
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> -----------------------------------------------------------------
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> -
>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>>
>>
>>
>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



--
------------------------------------------------------------------------
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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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: trying to connect to chado database

Jeang, David - ARS
In reply to this post by Scott Cain
Ok, the file is modified, what command do I give at the root to restart apache?

-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Tuesday, June 26, 2012 3:38 PM
To: Jeang, David - ARS
Cc: [hidden email]
Subject: Re: [Gmod-gbrowse] trying to connect to chado database

Hi David,

Hmm, ActivePerl on Linux.  Pretty sure that's the first time I've seen that :-)

You need to set the PERL5LIB environment variable in your apache config; hopefully you have mod_env available.  Locate your httpd.conf file; it's probably in /etc/apache2.  To the bottom of it, add

SetEnv PERL5LIB /opt/ActivePerl-5.12

and restart apache (of course, you have to be in a root shell to do all of that).  I assumed that you were missing the leading / in your path, so I added it in.

Scott


On Tue, Jun 26, 2012 at 3:19 PM, Jeang, David - ARS <[hidden email]> wrote:

> I found it in opt/ActivePerl-5.12/lib/Digest/SHA.PM
>
> What should I do now?
>
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, June 26, 2012 3:06 PM
> To: Jeang, David - ARS
> Cc: [hidden email]
> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>
> Nope: you're looking for SHA.pm in a directory called Digest.
>
> On Tue, Jun 26, 2012 at 3:01 PM, Jeang, David - ARS <[hidden email]> wrote:
>> Just double checking, the file I'm looking for is DigestSHA.pm?
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Tuesday, June 26, 2012 3:00 PM
>> To: Jeang, David - ARS
>> Cc: [hidden email]
>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>
>> HI David,
>>
>> The same error about Digest/SHA.pm?  That means it didn't get installed correctly or in a place that apache can find it.  Where is it?
>>
>> Scott
>>
>>
>> On Tue, Jun 26, 2012 at 2:46 PM, Jeang, David - ARS <[hidden email]> wrote:
>>> No, I'm getting the same error unless I'm doing it wrong.
>>>
>>> It is http://i5k.nal.usda.gov/cgi-bin/gbrowse/yeast by default right?
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]]
>>> Sent: Tuesday, June 26, 2012 2:42 PM
>>> To: Jeang, David - ARS
>>> Cc: [hidden email]
>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>
>>> Hi David,
>>>
>>> You don't need those right now (that's while they're labeled "recommends").  Can you access the built in yeast database now?
>>>
>>> Scott
>>>
>>>
>>> On Tue, Jun 26, 2012 at 2:25 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>> I have this when I run the Build. What do I do to install them?
>>>>
>>>> [djeang@metagenomics GBrowse-2.49]$ sudo perl Build.PL Checking
>>>> prerequisites...
>>>>  recommends:
>>>>    *  Bio::DB::BigFile is not installed
>>>>    *  Bio::DB::Sam is not installed
>>>>    *  Net::OpenID::Consumer is not installed
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]]
>>>> Sent: Tuesday, June 26, 2012 2:17 PM
>>>> To: Jeang, David - ARS
>>>> Cc: [hidden email]
>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>
>>>> Hi David,
>>>>
>>>> How did you install GBrowse?  It should have warned you that there were missing prereqs.  I'll put the list at the end of this email, but really the easiest way to see if there are prereqs missing is to run perl Build.PL again.
>>>>
>>>> Scott
>>>>
>>>>    requires     => {
>>>>        'perl'                => '5.008',
>>>>        'Bio::Root::Version'  => '1.0069',
>>>>        'Bio::Graphics'       => '2.28',
>>>>        'CGI::Session'        => '4.02',
>>>>        'Digest::MD5'         => 0,
>>>>        'ExtUtils::CBuilder'  => 0,
>>>>        'File::Temp'          => 0,
>>>>        'GD'                  => '2.07',
>>>>        'Text::ParseWords'    => '3.27',
>>>>        'IO::String'          => 0,
>>>>        'JSON'                => 0,
>>>>        'LWP'                 => 0,
>>>>        'Statistics::Descriptive'  => 0,
>>>>        'Storable'            => 0,
>>>>        'Time::HiRes'         => 0,
>>>>        'Digest::SHA'         => 0,
>>>>        'Date::Parse'         => 0,
>>>>        'Term::ReadKey'       => 0,
>>>>    },
>>>>    build_requires => {'Capture::Tiny'       => 0,},
>>>>    recommends  => {
>>>>        'Bio::Das'                 => 0,
>>>>        'Bio::DB::Sam'             => 1.20,
>>>>        'Bio::DB::BigFile'         => 1.00,
>>>>        'Crypt::SSLeay'            => 0,
>>>>        'DB_File::Lock'            => 0,
>>>>        'DBI'                      => 0,
>>>>        'DBD::mysql'               => 0,
>>>>        'DBD::Pg'                  => 0,
>>>>        'DBD::SQLite'              => 0,
>>>>        'Digest::SHA'              => 0,
>>>>        'FCGI'                     => 0,
>>>>        'File::NFSLock'            => 0,
>>>>        'GD::SVG'                  => 0,
>>>>        'Math::BigInt'             => 0,
>>>>        'Net::OpenID::Consumer'    => 0,
>>>>        'Net::SMTP::SSL'           => 0,
>>>>        $] <= 5.008 ? ('Safe::World'  => 0)
>>>>                    : ()               ,
>>>>        'Template'                 => 2.20,
>>>>        'Term::ReadKey'            => 0,
>>>>    },
>>>>
>>>>
>>>>
>>>> On Tue, Jun 26, 2012 at 2:10 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>> Could I have a full list based on the error logs, and where and how to install them? If it's not too much trouble.
>>>>>
>>>>> David Jeang
>>>>>
>>>>> -----Original Message-----
>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>> Sent: Tuesday, June 26, 2012 1:41 PM
>>>>> To: Jeang, David - ARS
>>>>> Cc: [hidden email]
>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>
>>>>> This is pretty important:
>>>>>
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains:
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl
>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
>>>>> /usr/lib/perl5/5.8.8
>>>>> .) at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>> p
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/SendMail.pm
>>>>> line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN
>>>>> failed--compilation aborted at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>> p
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/SendMail.pm
>>>>> line 8.
>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67]
>>>>> Compilation failed in require at
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gra
>>>>> p
>>>>> h
>>>>> i
>>>>> c
>>>>> s/Browser2/Action.pm
>>>>> line 11.
>>>>>
>>>>> It means that Digest::SHA, a perl module that is a prereq for GBrowse, isn't installed (at least not in a place that GBrowse can find it).
>>>>> If that's not installed, chances are other things aren't as well.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, Jun 26, 2012 at 1:37 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>> I've managed to use a root login through a shell account in putty, risky, but doable.
>>>>>>
>>>>>> There are a ton of logs here though, I'm not sure which one to look at.
>>>>>> I've got ssl_error log, error log, access log, ssl_access log, ssl_request log, mgdb_access log, and there are 5 of each too.
>>>>>> Just guessing, but this is the log for error:
>>>>>>
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.
>>>>>> pm in @INC (@INC contains:
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>>>> multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl
>>>>>> /usr/lib64/perl5/v endor_perl/5.8.8/x86_64-linux-thread-multi
>>>>>> /usr/lib/perl5/vendor_perl/5.8.8 /usr /lib/perl5/vendor_perl
>>>>>> /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib
>>>>>> /perl5/5.8.8 .) at
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bi
>>>>>> o/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN
>>>>>> failed--compilatio n aborted at
>>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Gr
>>>>>> a
>>>>>> p
>>>>>> hics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67]
>>>>>> Compilation failed in re quire at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 09:50:39 2012] [error]
>>>>>> [client 10.12.20.67] File does not exist:
>>>>>> /var/www/drupal/favicon.ico [Tue Jun
>>>>>> 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist:
>>>>>> /var/www/drupal/favicon.ico [Tue Jun 26 09:50:39 2012] [error] [client 10.12.20.67] File does not exist: /var/www/drupal/favicon.ico [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 09:51:47 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:28 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:07:29 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:18:26 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&se
>>>>>> r v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be passed by reference in /var/www/phpPgAdmin-5.0.4/redirect.php
>>>>>> on line 14,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=server&se
>>>>>> r v e r = %3A5432%3Aallow [Tue Jun 26 10:18:26 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Can't locate Digest/SHA.pm in @INC (@INC contains: /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5.8.8 .) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/SendMail.pm line 8.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Action.pm line 11.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 18.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at (eval 47) line 3.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] \t...propagated at /usr/lib/perl5/5.8.8/base.pm line 85.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render/HTML.pm line 5.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Compilation failed in require at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] BEGIN failed--compilation aborted at /var/www/cgi-bin/gb2/gbrowse line 12.
>>>>>> [Tue Jun 26 10:19:28 2012] [error] [client 10.12.20.67] Premature
>>>>>> end of script headers: gbrowse [Tue Jun 26 10:26:49 2012] [error]
>>>>>> [client 10.12.20.67] PHP Strict Standards:  Only variables should
>>>>>> be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>>> [Tue Jun 26 10:26:49 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be passed by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php
>>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&
>>>>>> s
>>>>>> e
>>>>>> r
>>>>>> v
>>>>>> e
>>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>>> [Tue Jun 26 10:27:00 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be passed by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/redirect.php on line 14, referer:
>>>>>> http://i5k.nal.usda.gov/phppgadmin/redirect.php?subject=database&
>>>>>> s
>>>>>> e
>>>>>> r
>>>>>> v
>>>>>> e
>>>>>> r=%3A5432%3Aallow&database=tripal&
>>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  Only variables should be assigned by reference in
>>>>>> /var/www/phpPgAdmin-5.0.4/classes/database/Connection.php on line
>>>>>> 23,
>>>>>> referer: http://i5k.nal.usda.gov/phppgadmin/browser.php
>>>>>> [Tue Jun 26 10:27:03 2012] [error] [client 10.12.20.67] PHP
>>>>>> Strict
>>>>>> Standards:  O
>>>>>>
>>>>>> I'm not sure which errors are relevant since I've tried re-editing the configuration a few times today.
>>>>>> David Jeang
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>> Sent: Tuesday, June 26, 2012 12:35 PM
>>>>>> To: Jeang, David - ARS
>>>>>> Cc: Gbrowse (E-mail)
>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>
>>>>>> Hi David,
>>>>>>
>>>>>> Please keep the GBrowse mailing list cc'ed.
>>>>>> Debugging this without access to the error log will be essentially impossible.  Please bug whoever you have to to get access.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Tue, Jun 26, 2012 at 12:08 PM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>> On closer inspection, there is var/log/httpd,
>>>>>>>
>>>>>>> But I'm denied access....
>>>>>>>
>>>>>>> -----Original Message-----
>>>>>>> From: Scott Cain [mailto:[hidden email]]
>>>>>>> Sent: Tuesday, June 26, 2012 12:02 PM
>>>>>>> To: Jeang, David - ARS
>>>>>>> Cc: [hidden email]
>>>>>>> Subject: Re: [Gmod-gbrowse] trying to connect to chado database
>>>>>>>
>>>>>>> Hi David,
>>>>>>>
>>>>>>> You configuration stuff looks OK.  What is the error in the error log?
>>>>>>>  It's probably in /var/httpd/log (though possibly /var/apache2/log).
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Jun 26, 2012 at 10:47 AM, Jeang, David - ARS <[hidden email]> wrote:
>>>>>>>> I've installed Gbrowse 2.49 on the local server, and am trying
>>>>>>>> to connect to a chado database on the same server.
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> This is how I set the conf file for Gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> [GENERAL]
>>>>>>>>
>>>>>>>> db_adaptor           = Bio::DB::Das::Chado
>>>>>>>>
>>>>>>>> db_args                     = -adaptor Bio::DB::Das::Chado
>>>>>>>>
>>>>>>>>                      -dsn dbi:Pg:dbname=tripal;host=localhost
>>>>>>>>
>>>>>>>>                      -user tripaldemo
>>>>>>>>
>>>>>>>>                      -pass tripal2demo
>>>>>>>>
>>>>>>>> psql=# ALTER USER tripaldemo SET search_path TO chado;
>>>>>>>>
>>>>>>>> config_base            = /etc/gbrowse2   # overridden by
>>>>>>>> environment variable GBROWSE_CONF
>>>>>>>>
>>>>>>>> htdocs_base            = /var/www/html/gbrowse2
>>>>>>>>
>>>>>>>> url_base               = /gbrowse2
>>>>>>>>
>>>>>>>> tmp_base               = /var/tmp/gbrowse2
>>>>>>>>
>>>>>>>> persistent_base        = /var/lib/gbrowse2
>>>>>>>>
>>>>>>>> userdata_base          = /var/lib/gbrowse2/userdata
>>>>>>>>
>>>>>>>> db_base                = /var/www/cgi-bin/gb2/gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> However, when I try to access the link:
>>>>>>>>
>>>>>>>> http://i5k.nal.usda.gov/cgi-bin/gb2/gbrowse
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I get:
>>>>>>>>
>>>>>>>> Internal Server Error
>>>>>>>>
>>>>>>>> The server encountered an internal error or misconfiguration
>>>>>>>> and was unable to complete your request.
>>>>>>>>
>>>>>>>> Please contact the server administrator, root@localhost and
>>>>>>>> inform them of the time the error occurred, and anything you
>>>>>>>> might have done that may have caused the error.
>>>>>>>>
>>>>>>>> More information about this error may be available in the server error log.
>>>>>>>>
>>>>>>>> ________________________________
>>>>>>>>
>>>>>>>> Apache/2.2.3 (CentOS) Server at i5k.nal.usda.gov Port 80
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> I'm at a dead end, the configurations are right, and I even
>>>>>>>> accounted for PostgreSQL creating a separate path to chado. What am I missing?
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> David Jeang
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> This electronic message contains information generated by the
>>>>>>>> USDA solely for the intended recipients. Any unauthorized
>>>>>>>> interception of this message or the use or disclosure of the
>>>>>>>> information it contains may violate the law and subject the
>>>>>>>> violator to civil or criminal penalties. If you believe you
>>>>>>>> have received this message in error, please notify the sender and delete the email immediately.
>>>>>>>>
>>>>>>>> ---------------------------------------------------------------
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> -
>>>>>>>> --------
>>>>>>>> Live Security Virtual Conference Exclusive live event will
>>>>>>>> cover all the ways today's security and threat landscape has
>>>>>>>> changed and how IT managers can respond.
>>>>>>>> Discussions will include endpoint security, mobile security and
>>>>>>>> the latest in malware threats.
>>>>>>>> http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-gbrowse mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ----------------------------------------------------------------
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -
>>>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> -----------------------------------------------------------------
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -
>>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------
>>>>> -
>>>>> -
>>>>> -
>>>>> -
>>>>> -- Scott Cain, Ph. D.                                   scott at
>>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> -
>>>> -
>>>> -
>>>> -- Scott Cain, Ph. D.                                   scott at
>>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>>> 216-392-3087 Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> --------------------------------------------------------------------
>>> -
>>> -
>>> -- Scott Cain, Ph. D.                                   scott at
>>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>>> 216-392-3087 Ontario Institute for Cancer Research
>>>
>>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------------
>> -
>> -- Scott Cain, Ph. D.                                   scott at
>> scottcain dot net GMOD Coordinator (http://gmod.org/)
>> 216-392-3087 Ontario Institute for Cancer Research
>>
>>
>>
>>
>>
>> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
>>
>
>
>
> --
> ----------------------------------------------------------------------
> -- Scott Cain, Ph. D.                                   scott at
> scottcain dot net GMOD Coordinator (http://gmod.org/)                    
> 216-392-3087 Ontario Institute for Cancer Research
>
>



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



------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-gbrowse mailing list
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123