error to reinstall GBrowse v2

[Biliards]

Hi all,

After good installation in server test, where apache gbrowse
configuration works and modperl and/or modfcgi works with demo
databases, I reinstall gbrowse v2 in our site server: I used new
server, I install all and my principal pipeline was:

* install prerequisites about
http://gmod.org/wiki/GBrowse_2.0_Prerequisites without Bio/Graphics
package
* export CVSROOT=:pserver:anonymous@...:/cvsroot/gmod
* cvs co Generic-Genome-Browser
* cvs update -d
* iter that start with 'perl Build.PL'

after restart apache, I have got bottom errors log when I run
http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/
I attached my apache gbrowse configuration file.

Invalid source  at
/usr/local/lib/perl/5.10.0/Bio/Graphics/Browser/Render.pm line 54
Status: 302 Found
Location: /vitis_vinifera_8x/

Set-Cookie: gbrowse_sess=9065e1cd04f56f8e3a41d7437a20e682; path=/;
expires=Fri, 03-Jul-2009 13:26:13 GMT
Date: Wed, 03 Jun 2009 13:26:13 GMT
Cache-control: no-cache
Content-Type: text/html; charset=ISO-8859-1

..html gbrowse page content...

[Wed Jun 03 15:26:13 2009] [warn] (104)Connection reset by peer:
mod_fcgid: read data from fastcgi server error.
[Wed Jun 03 15:26:13 2009] [error] [client 192.168.20.79] Premature
end of script headers: gbrowse, referer:
http://gbrowse.cribi.unipd.it/
[Wed Jun 03 15:26:19 2009] [notice] mod_fcgid: process
/usr/lib/cgi-bin/public/gbrowse(29584) exit(communication error),
terminated by calling exit(), return code: 0

When I run http://gbrowse.cribi.unipd.it/mpublic/gbrowse/vitis_vinifera_8x/
I obtain other apache errors:

[Wed Jun 03 15:41:26 2009] [error] [client 192.168.20.79] failed to
resolve handler `ModPerl::Registry': Can't locate loadable object for
module Apache2::ServerUtil in @INC (@INC contains: /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl . /etc/apache2) at
/usr/lib/perl5/Apache2/XSLoader.pm line 31\nCompilation failed in
require at /usr/lib/perl5/ModPerl/RegistryCooker.pm line 30.\nBEGIN
failed--compilation aborted at
/usr/lib/perl5/ModPerl/RegistryCooker.pm line 30.\nCompilation failed
in require at (eval 3) line 3.\n\t...propagated at
/usr/share/perl/5.10/base.pm line 92.\nBEGIN failed--compilation
aborted at /usr/lib/perl5/ModPerl/Registry.pm line 26.\nCompilation
failed in require at (eval 2) line 3.\n

Instead, when I run
http://gbrowse.cribi.unipd.it/fpublic/gbrowse/vitis_vinifera_8x/ I
have got this apache error log:

[Wed Jun 03 15:43:11 2009] [error] [client 192.168.20.79] File does
not exist: /usr/lib/cgi-bin/public/gbrowse/vitis_vinifera_8x/

Have you got any ideas about this errors log?
Best,
Alessandra.


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[zph]

On Wed, 3 Jun 2009, Alessandra wrote:
[snip]
[Wed Jun 03 15:41:26 2009] [error] [client 192.168.20.79] failed to
resolve handler `ModPerl::Registry': Can't locate loadable object for
module Apache2::ServerUtil in @INC (@INC contains: /etc/perl
[snip]

This means the perl module Apache2::ServerUtil isn't installed
on your server or cannot be found at run time.

Regards,

Zong-Pei


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[Biliards]

I don't understand because if I run command line:
perl -MCPAN -e 'install Apache2::ServerUtil'

CPAN: Storable loaded ok (v2.18)
Going to read /root/.cpan/Metadata
  Database was generated on Wed, 03 Jun 2009 01:29:51 GMT
CPAN: YAML loaded ok (v0.66)
Going to read /root/.cpan/build/
............................................................................DONE
Found 1 old build, restored the state of 1
Apache2::ServerUtil is up to date (2.000004).

and idem about I run:
locate Apache2/ServerUtil

/usr/lib/perl5/Apache2/ServerUtil.pm

Ale.

On Wed, Jun 3, 2009 at 5:49 PM,  <zph@...> wrote:

> On Wed, 3 Jun 2009, Alessandra wrote:
> [snip]
> [Wed Jun 03 15:41:26 2009] [error] [client 192.168.20.79] failed to
> resolve handler `ModPerl::Registry': Can't locate loadable object for
> module Apache2::ServerUtil in @INC (@INC contains: /etc/perl
> [snip]
>
> This means the perl module Apache2::ServerUtil isn't installed
> on your server or cannot be found at run time.
>
> Regards,
>
> Zong-Pei
>
>

--
 Alessandra Bilardi, Ph. D.
----
 CRIBI, University of Padova, Italy
 Via Ugo Bassi, 58/B - 35121 Padova
 Tel [phone] Fax [phone]
  http://www.linkedin.com/in/bilardi
----
La semplicità è la più alta forma di perfezione (Leonardo Da Vinci)
Keep simple, stupid (KISS, IT)
----

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[Biliards]

Hi all,
I test and reinstall all in two server. I'm using cvs version and I
have got similar results:

* gbrowse works very good with these url:
http://gbrowse.cribi.unipd.it/demo/gbrowse/yeast/
http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/

* these errors with these url:
http://gbrowse.cribi.unipd.it/mdemo/gbrowse/yeast/

alternative error when I run different databases set..

[Thu Jun 04 00:36:10 2009] [error] [client 147.162.3.222] failed to
resolve handler `ModPerl::Registry': Attempt to reload
ModPerl/Registry.pm aborted.\nCompilation failed in require at (eval
4) line 3.\n

..or I rerun egual databases set

[Thu Jun 04 00:36:19 2009] [error] [client 147.162.3.222] failed to
resolve handler `ModPerl::Registry': Can't locate loadable object for
module Apache2::ServerUtil in @INC (@INC contains: /etc/perl
/usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5
/usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10
/usr/local/lib/site_perl . /etc/apache2) at
/usr/lib/perl5/Apache2/XSLoader.pm line 31\nCompilation failed in
require at /usr/lib/perl5/ModPerl/RegistryCooker.pm line 30.\nBEGIN
failed--compilation aborted at
/usr/lib/perl5/ModPerl/RegistryCooker.pm line 30.\nCompilation failed
in require at (eval 3) line 3.\n\t...propagated at
/usr/share/perl/5.10/base.pm line 92.\nBEGIN failed--compilation
aborted at /usr/lib/perl5/ModPerl/Registry.pm line 26.\nCompilation
failed in require at (eval 2) line 3.\n

* these errors with these url:
http://gbrowse.cribi.unipd.it/fdemo/gbrowse/yeast/

Invalid source  at
/usr/local/lib/perl/5.10.0/Bio/Graphics/Browser/Render.pm line 54
Status: 302 Found
Location: /yeast/

Set-Cookie: gbrowse_sess=755803d9290c97b00a7fb30f1b14f516; path=/;
expires=Fri, 03-Jul-2009 22:39:58 GMT
Date: Wed, 03 Jun 2009 22:39:58 GMT
Cache-control: no-cache
Content-Type: text/html; charset=ISO-8859-1

<!DOCTYPE html
...
</html>[Thu Jun 04 00:39:58 2009] [warn] (104)Connection reset by
peer: mod_fcgid: read data from fastcgi server error.
[Thu Jun 04 00:39:58 2009] [error] [client 147.162.3.222] Premature
end of script headers: gbrowse
[Thu Jun 04 00:39:59 2009] [notice] mod_fcgid: process
/usr/lib/cgi-bin/public/gbrowse(13915) exit(communication error),
terminated by calling exit(), return code: 0

I have got last version about:

Bio::Graphics::Browser is up to date (1.994).
Apache2::ServerUtil is up to date (2.000004).

Have you got any ideas about these errors?

Best,
Alessandra.


On Wed, Jun 3, 2009 at 6:48 PM, Alessandra <alessandra.bilardi@...> wrote:

> I don't understand because if I run command line:
> perl -MCPAN -e 'install Apache2::ServerUtil'
>
> CPAN: Storable loaded ok (v2.18)
> Going to read /root/.cpan/Metadata
>  Database was generated on Wed, 03 Jun 2009 01:29:51 GMT
> CPAN: YAML loaded ok (v0.66)
> Going to read /root/.cpan/build/
> ............................................................................DONE
> Found 1 old build, restored the state of 1
> Apache2::ServerUtil is up to date (2.000004).
>
> and idem about I run:
> locate Apache2/ServerUtil
>
> /usr/lib/perl5/Apache2/ServerUtil.pm
>
> Ale.
>
> On Wed, Jun 3, 2009 at 5:49 PM,  <zph@...> wrote:
>> On Wed, 3 Jun 2009, Alessandra wrote:
>> [snip]
>> [Wed Jun 03 15:41:26 2009] [error] [client 192.168.20.79] failed to
>> resolve handler `ModPerl::Registry': Can't locate loadable object for
>> module Apache2::ServerUtil in @INC (@INC contains: /etc/perl
>> [snip]
>>
>> This means the perl module Apache2::ServerUtil isn't installed
>> on your server or cannot be found at run time.
>>
>> Regards,
>>
>> Zong-Pei
>>
>>
>
>
>
> --
>  Alessandra Bilardi, Ph. D.
> ----
>  CRIBI, University of Padova, Italy
>  Via Ugo Bassi, 58/B - 35121 Padova
>  Tel [phone] Fax [phone]
>  http://www.linkedin.com/in/bilardi
> ----
> La semplicità è la più alta forma di perfezione (Leonardo Da Vinci)
> Keep simple, stupid (KISS, IT)
> ----
>

--
 Alessandra Bilardi, Ph. D.
----
 CRIBI, University of Padova, Italy
 Via Ugo Bassi, 58/B - 35121 Padova
 Tel [phone] Fax [phone]
  http://www.linkedin.com/in/bilardi
----
La semplicità è la più alta forma di perfezione (Leonardo Da Vinci)
Keep simple, stupid (KISS, IT)
----

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
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Gmod-gbrowse@...
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[zph]

What happens if mod_perl is turned off?

Are there more than one version of Perl on the server? And
which perl is used by GBrowse?



On Wed, 3 Jun 2009, Alessandra wrote:

I don't understand because if I run command line:
perl -MCPAN -e 'install Apache2::ServerUtil'

CPAN: Storable loaded ok (v2.18)
Going to read /root/.cpan/Metadata
  Database was generated on Wed, 03 Jun 2009 01:29:51 GMT
CPAN: YAML loaded ok (v0.66)
Going to read /root/.cpan/build/
............................................................................DONE
Found 1 old build, restored the state of 1
Apache2::ServerUtil is up to date (2.000004).

and idem about I run:
locate Apache2/ServerUtil

/usr/lib/perl5/Apache2/ServerUtil.pm

Ale.

On Wed, Jun 3, 2009 at 5:49 PM,  <zph@...> wrote:

> On Wed, 3 Jun 2009, Alessandra wrote:
> [snip]
> [Wed Jun 03 15:41:26 2009] [error] [client 192.168.20.79] failed to
> resolve handler `ModPerl::Registry': Can't locate loadable object for
> module Apache2::ServerUtil in @INC (@INC contains: /etc/perl
> [snip]
>
> This means the perl module Apache2::ServerUtil isn't installed
> on your server or cannot be found at run time.
>
> Regards,
>
> Zong-Pei

[snip]


------------------------------------------------------------------------------
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[Biliards]

I commented line
LoadModule perl_module /usr/lib/apache2/modules/mod_perl.so

in /etc/apache2/mods-available/perl.load

and I obtain only normal error about page not found when I request
http://gbrowse.cribi.unipd.it/mpublic/gbrowse/vitis_vinifera_8x/

other apache errors log about fpublic are egual.

I have got two directory about perl:

/usr/local/lib/perl/5.10.0/
and /usr/local/share/perl/5.10.0/
but I checked these directories and there are not file in each
directories: there are not file double.

>-------------------------------------------<
others apache error log
>-------------------------------------------<

I'm testing gbrowse mysql databases that they works with gbrowse v1.69
(db_adaptor=Bio::DB::GFF), as
http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/

and if I click one track for gbrowse_details page, I obtain page with
this warning:
"Requested feature not found in database."

instead, when I test others databases with
db_adaptor=Bio::DB::SeqFeature::Store (there are private, with pw, but
if it is important I could create example gbrowse for you) this I
obtain apache error log:

"my" variable $name masks earlier declaration in same scope at (eval
107) line 3.
"my" variable $name masks earlier declaration in same scope at (eval
112) line 3.

Alessandra.



On Thu, Jun 4, 2009 at 4:40 PM, <zph@...> wrote:

>
> What happens if mod_perl is turned off?
>
> Are there more than one version of Perl on the server? And
> which perl is used by GBrowse?
>
>
>
> On Wed, 3 Jun 2009, Alessandra wrote:
>
> I don't understand because if I run command line:
> perl -MCPAN -e 'install Apache2::ServerUtil'
>
> CPAN: Storable loaded ok (v2.18)
> Going to read /root/.cpan/Metadata
>  Database was generated on Wed, 03 Jun 2009 01:29:51 GMT
> CPAN: YAML loaded ok (v0.66)
> Going to read /root/.cpan/build/
> ............................................................................DONE
> Found 1 old build, restored the state of 1
> Apache2::ServerUtil is up to date (2.000004).
>
> and idem about I run:
> locate Apache2/ServerUtil
>
> /usr/lib/perl5/Apache2/ServerUtil.pm
>
> Ale.
>
> On Wed, Jun 3, 2009 at 5:49 PM,  <zph@...> wrote:
>> On Wed, 3 Jun 2009, Alessandra wrote:
>> [snip]
>> [Wed Jun 03 15:41:26 2009] [error] [client 192.168.20.79] failed to
>> resolve handler `ModPerl::Registry': Can't locate loadable object for
>> module Apache2::ServerUtil in @INC (@INC contains: /etc/perl
>> [snip]
>>
>> This means the perl module Apache2::ServerUtil isn't installed
>> on your server or cannot be found at run time.
>>
>> Regards,
>>
>> Zong-Pei
> [snip]
>
>

--
 Alessandra Bilardi, Ph. D.
----
 CRIBI, University of Padova, Italy
 Via Ugo Bassi, 58/B - 35121 Padova
 Tel [phone] Fax [phone]
  http://www.linkedin.com/in/bilardi
----
La semplicità è la più alta forma di perfezione (Leonardo Da Vinci)
Keep simple, stupid (KISS, IT)
----

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
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[zph]

Hi,

Your experiment shows that Apache cannot find some required
modules at run time on your server. It's also possible that
your

  /usr/lib/apache2/modules/mod_perl.so

doesn't work with other modules because of the version
mismatch. Please make sure that the mod_perl is right for
perl 5.10.0 and the Apache server. Because mod_perl must be
for a specific Perl *and* Apache version.

I've just successfully installed GBrowse 1.994, and it runs
with mod_perl

  https://slave.molbiol.ox.ac.uk/mgb2/gbrowse/yeast/

or without mod_perl
  https://slave.molbiol.ox.ac.uk/cgi-bin/gbrowse/yeast/

We use httpd-2.2.9-1.fc8 perl-5.8.8-41.fc8 and
mod_perl-2.0.3-14, all from Fedora Core 8 distribution.

After installing all the required packages, we've configured
GBrowse as follows

perl Build.PL --apachemodules=/usr/lib64/httpd/modules \
              --cgibin=/wwwdata/gbrowse-2.0a/cgi-bin \
              --conf=/wwwdata/gbrowse-2.0a/conf \
              --htdocs=/wwwdata/gbrowse-2.0a/htdocs \
              --databases=/wwwdata/gbrowse-2.0a/databases \
              --tmp=/tmp/gbrowse2 \
              --portdemo=8080 \
              --wwwuser=nobody

And below are some relevant entries in Apache configuration
gbrowse2.conf:

ScriptAlias  "/cgi-bin"   "/wwwdata/gbrowse-2.0a/cgi-bin/gb2"
ScriptAlias  "/mgb2"      "/wwwdata/gbrowse-2.0a/cgi-bin/gb2"

<IfModule mod_perl.c>
   PerlModule ModPerl::Registry

   <Location /mgb2>
     SetHandler perl-script
     PerlResponseHandler ModPerl::Registry
     PerlOptions +ParseHeaders
   </Location>
</IfModule>

Hope this encourages you to examine your site installation
and configuration closely to solve the problem. Sorry I cannot
answer other questions you've raised.

Regards,

Zong-Pei


On Mon, 8 Jun 2009, Alessandra wrote:
Date: Mon, 8 Jun 2009 14:37:01 +0200
From: Alessandra <alessandra.bilardi@...>
To: zph@...
Cc: GMOD GBrowse List <gmod-gbrowse@...>
Subject: Re: [Gmod-gbrowse] error to reinstall GBrowse v2

I commented line
LoadModule perl_module /usr/lib/apache2/modules/mod_perl.so

in /etc/apache2/mods-available/perl.load

and I obtain only normal error about page not found when I request
http://gbrowse.cribi.unipd.it/mpublic/gbrowse/vitis_vinifera_8x/

other apache errors log about fpublic are egual.

I have got two directory about perl:

/usr/local/lib/perl/5.10.0/
and /usr/local/share/perl/5.10.0/
but I checked these directories and there are not file in each
directories: there are not file double.

>-------------------------------------------<
others apache error log
>-------------------------------------------<

I'm testing gbrowse mysql databases that they works with gbrowse v1.69
(db_adaptor=Bio::DB::GFF), as
http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/

and if I click one track for gbrowse_details page, I obtain page with
this warning:
"Requested feature not found in database."

instead, when I test others databases with
db_adaptor=Bio::DB::SeqFeature::Store (there are private, with pw, but
if it is important I could create example gbrowse for you) this I
obtain apache error log:

"my" variable $name masks earlier declaration in same scope at (eval
107) line 3.
"my" variable $name masks earlier declaration in same scope at (eval
112) line 3.

Alessandra.

[snip]

------------------------------------------------------------------------------
OpenSolaris 2009.06 is a cutting edge operating system for enterprises
looking to deploy the next generation of Solaris that includes the latest
innovations from Sun and the OpenSource community. Download a copy and
enjoy capabilities such as Networking, Storage and Virtualization.
Go to: http://p.sf.net/sfu/opensolaris-get
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
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[Biliards]

Dear Zong-Pei,
Thank you so much for all of your help.
I resolved the modperl problem (one down, two to go).

* I'm using debian lenny system, perl, v5.10.0 built for
x86_64-linux-gnu-thread-multi and last version about
libapache2-mod-perl2
* I commented line LoadModule perl_module /usr/lib/apache2/modules/mod_perl.so
in /etc/apache2/mods-available/perl.load
* I add line PerlModule ModPerl::Registry inner <IfModule mod_perl.c>
in gbrowse2.conf

I don't know very well apache config because I don't understand the solution.
Thank you very much.

Best,
Alessandra.

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