[GMOD-devel] FW: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

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[GMOD-devel] FW: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

Jayaraman, Pushkala
FW: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

Hello People,
I need some help! Im trying to help my Sys-Admin install Gbrowse2 on our server. But then we seem to receive these errors: Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

we have even upgraded to the latest of the Bio::Graphics versions and yet we find the same errors even in the Install:

 


NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09). 



Please Help....
Thanks,
Pushkala Jayaraman
Programmer Analyst II
Rat Genome Database
Medical College of Wisconsin, Wauwatosa, WI



-----Original Message-----
From: Brodie, Kent [[hidden email]]
Sent: Mon 5/17/2010 4:26 PM
To: Jayaraman, Pushkala
Subject: RE: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

I have upgraded Bio::Graphics to 2.09.



Same errors.   I see the errors in the gbrowse install too::







NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09).



                                               





From: Jayaraman, Pushkala [[hidden email]]
Sent: Monday, May 17, 2010 3:45 PM
To: Brodie, Kent
Subject: FW: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



Hello  Kent,

It seems that this problem is an out-of-date Bio::Graphics version.



Pushkala



From: Lincoln Stein [[hidden email]]
Sent: Monday, May 17, 2010 3:41 PM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



The problem is an out-of-date Bio::Graphics. The install should have complained that you need a more recent version. Please install Bio::Graphics version 2.09.



Lincoln

On Mon, May 17, 2010 at 4:31 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

We finally have Gbrowse2 installed on Solaris. And we even got to the part where we get this link to test on our browser:

http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast



But this link led to a blank page and a 500 internal server error on our browser.

The apache logs give us this:





[Mon May 17 15:13:58 2010] [error] [client 141.106.161.52] File does not exist: /rgd_home/3.0/WWW/fgb2, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Invalid source yeast_renderfarm at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm line 61, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:15:15 2010] [info] [client 127.0.0.1] (32)Broken pipe: core_output_filter: writing data to the network





We are currently installing this on a Solaris system. Please help me figure out this error..





Thanks,

Pushkala


------------------------------------------------------------------------------


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Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



------------------------------------------------------------------------------


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Re: [GMOD-devel] [Gmod-gbrowse] FW: Help with Gbrowse2.0 on Solaris

Lincoln Stein
Hi,

This is still a problem with the wrong Bio::Graphics version. Perhaps you have Bio::Graphics installed in two different places and the old one has priority over the new one in the perl library path?

Could you run the following command:

perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '

do it first when running under your own account and then when running as root. If the right version of Bio::Graphics is in the library path, then it will print out 2.09 each time.

Lincoln

On Tue, May 18, 2010 at 8:42 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello People,
I need some help! Im trying to help my Sys-Admin install Gbrowse2 on our server. But then we seem to receive these errors: Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

we have even upgraded to the latest of the Bio::Graphics versions and yet we find the same errors even in the Install:

 


NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09). 



Please Help....
Thanks,
Pushkala Jayaraman
Programmer Analyst II
Rat Genome Database
Medical College of Wisconsin, Wauwatosa, WI



-----Original Message-----
From: Brodie, Kent [[hidden email]]
Sent: Mon 5/17/2010 4:26 PM
To: Jayaraman, Pushkala
Subject: RE: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

I have upgraded Bio::Graphics to 2.09.



Same errors.   I see the errors in the gbrowse install too::







NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09).



                                               





From: Jayaraman, Pushkala [[hidden email]]
Sent: Monday, May 17, 2010 3:45 PM
To: Brodie, Kent
Subject: FW: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



Hello  Kent,

It seems that this problem is an out-of-date Bio::Graphics version.





Pushkala



From: Lincoln Stein [[hidden email]]
Sent: Monday, May 17, 2010 3:41 PM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



The problem is an out-of-date Bio::Graphics. The install should have complained that you need a more recent version. Please install Bio::Graphics version 2.09.



Lincoln

On Mon, May 17, 2010 at 4:31 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

We finally have Gbrowse2 installed on Solaris. And we even got to the part where we get this link to test on our browser:

http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast



But this link led to a blank page and a 500 internal server error on our browser.

The apache logs give us this:





[Mon May 17 15:13:58 2010] [error] [client 141.106.161.52] File does not exist: /rgd_home/3.0/WWW/fgb2, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Invalid source yeast_renderfarm at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm line 61, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:15:15 2010] [info] [client 127.0.0.1] (32)Broken pipe: core_output_filter: writing data to the network





We are currently installing this on a Solaris system. Please help me figure out this error..





Thanks,

Pushkala


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>



------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------


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Re: [GMOD-devel] [Gmod-gbrowse] FW: Help with Gbrowse2.0 on Solaris

Jayaraman, Pushkala

You were right Lincoln, it was a matter of multiple Bio::Graphics  version.. It works now..

Thank you..

J

I see that there are individual track download buttons.. sweet! J I didn’t have it in the Gbrowse2 I had initially downloaded in February.. is that a feature we can switch on and off..?

 

Pushkala

 

From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 8:49 AM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] FW: Help with Gbrowse2.0 on Solaris

 

Hi,

 

This is still a problem with the wrong Bio::Graphics version. Perhaps you have Bio::Graphics installed in two different places and the old one has priority over the new one in the perl library path?

 

Could you run the following command:

 

perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '

 

do it first when running under your own account and then when running as root. If the right version of Bio::Graphics is in the library path, then it will print out 2.09 each time.

 

Lincoln

 

On Tue, May 18, 2010 at 8:42 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello People,
I need some help! Im trying to help my Sys-Admin install Gbrowse2 on our server. But then we seem to receive these errors: Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

we have even upgraded to the latest of the Bio::Graphics versions and yet we find the same errors even in the Install:

 


NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09). 



Please Help....
Thanks,
Pushkala Jayaraman
Programmer Analyst II
Rat Genome Database
Medical College of Wisconsin, Wauwatosa, WI



-----Original Message-----
From: Brodie, Kent [[hidden email]]
Sent: Mon 5/17/2010 4:26 PM
To: Jayaraman, Pushkala
Subject: RE: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

I have upgraded Bio::Graphics to 2.09.



Same errors.   I see the errors in the gbrowse install too::







NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09).



                                               





From: Jayaraman, Pushkala [[hidden email]]
Sent: Monday, May 17, 2010 3:45 PM
To: Brodie, Kent
Subject: FW: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



Hello  Kent,

It seems that this problem is an out-of-date Bio::Graphics version.





Pushkala



From: Lincoln Stein [[hidden email]]
Sent: Monday, May 17, 2010 3:41 PM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



The problem is an out-of-date Bio::Graphics. The install should have complained that you need a more recent version. Please install Bio::Graphics version 2.09.



Lincoln

On Mon, May 17, 2010 at 4:31 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

We finally have Gbrowse2 installed on Solaris. And we even got to the part where we get this link to test on our browser:

http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast



But this link led to a blank page and a 500 internal server error on our browser.

The apache logs give us this:





[Mon May 17 15:13:58 2010] [error] [client 141.106.161.52] File does not exist: /rgd_home/3.0/WWW/fgb2, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Invalid source yeast_renderfarm at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm line 61, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:15:15 2010] [info] [client 127.0.0.1] (32)Broken pipe: core_output_filter: writing data to the network





We are currently installing this on a Solaris system. Please help me figure out this error..





Thanks,

Pushkala


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--
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Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


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Re: [GMOD-devel] [Gmod-gbrowse] FW: Help with Gbrowse2.0 on Solaris

Lincoln Stein
This is a new feature introduced in  2.06.

Lincoln

On Tue, May 18, 2010 at 11:40 AM, Jayaraman, Pushkala <[hidden email]> wrote:

You were right Lincoln, it was a matter of multiple Bio::Graphics  version.. It works now..

Thank you..

J

I see that there are individual track download buttons.. sweet! J I didn’t have it in the Gbrowse2 I had initially downloaded in February.. is that a feature we can switch on and off..?

 

Pushkala

 

From: Lincoln Stein [mailto:[hidden email]]
Sent: Tuesday, May 18, 2010 8:49 AM


To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] FW: Help with Gbrowse2.0 on Solaris

 

Hi,

 

This is still a problem with the wrong Bio::Graphics version. Perhaps you have Bio::Graphics installed in two different places and the old one has priority over the new one in the perl library path?

 

Could you run the following command:

 

perl -MBio::Graphics -e 'print $Bio::Graphics::VERSION,"\n" '

 

do it first when running under your own account and then when running as root. If the right version of Bio::Graphics is in the library path, then it will print out 2.09 each time.

 

Lincoln

 

On Tue, May 18, 2010 at 8:42 AM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello People,
I need some help! Im trying to help my Sys-Admin install Gbrowse2 on our server. But then we seem to receive these errors: Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

we have even upgraded to the latest of the Bio::Graphics versions and yet we find the same errors even in the Install:

 


NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09). 



Please Help....
Thanks,
Pushkala Jayaraman
Programmer Analyst II
Rat Genome Database
Medical College of Wisconsin, Wauwatosa, WI



-----Original Message-----
From: Brodie, Kent [[hidden email]]
Sent: Mon 5/17/2010 4:26 PM
To: Jayaraman, Pushkala
Subject: RE: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris

I have upgraded Bio::Graphics to 2.09.



Same errors.   I see the errors in the gbrowse install too::







NOTE: Run ./Build reconfig to change existing configuration.

t/01yeast.t ............... ok  

t/02.rearchitecture.t ..... 1/90 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/02.rearchitecture.t ..... Dubious, test returned 2 (wstat 512, 0x200)

Failed 49/90 subtests

t/03.render.t ............. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/03.render.t line 37.

BEGIN failed--compilation aborted at t/03.render.t line 38.

t/03.render.t ............. Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 138/138 subtests

t/04.remoteserver.t ....... 1/43 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/04.remoteserver.t ....... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 41/43 subtests

t/05.deferredrendering.t .. Can't locate object method "cachedir" via package "Bio::Graphics::FeatureFile" at t/05.deferredrendering.t line 35.

BEGIN failed--compilation aborted at t/05.deferredrendering.t line 36.

t/05.deferredrendering.t .. Dubious, test returned 2 (wstat 512, 0x200)

Failed 19/19 subtests

t/06.featuresearch.t ...... 1/26 Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/06.featuresearch.t ...... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 23/26 subtests

t/07.karyotype.t .......... Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /.cpan/build/GBrowse-2.06-DwE4Hl/t/../lib/Bio/Graphics/Browser2/DataSource.pm line 53.

t/07.karyotype.t .......... Dubious, test returned 255 (wstat 65280, 0xff00)

Failed 3/3 subtests

t/08.calign.t ............. ok  





Going to read '/.cpan/Metadata'

  Database was generated on Mon, 17 May 2010 13:34:45 GMT

Bio::Graphics is up to date (2.09).



                                               





From: Jayaraman, Pushkala [[hidden email]]
Sent: Monday, May 17, 2010 3:45 PM
To: Brodie, Kent
Subject: FW: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



Hello  Kent,

It seems that this problem is an out-of-date Bio::Graphics version.





Pushkala



From: Lincoln Stein [[hidden email]]
Sent: Monday, May 17, 2010 3:41 PM
To: Jayaraman, Pushkala
Cc: [hidden email]; [hidden email]
Subject: Re: [Gmod-gbrowse] Help with Gbrowse2.0 on Solaris



The problem is an out-of-date Bio::Graphics. The install should have complained that you need a more recent version. Please install Bio::Graphics version 2.09.



Lincoln

On Mon, May 17, 2010 at 4:31 PM, Jayaraman, Pushkala <[hidden email]> wrote:

Hello,

We finally have Gbrowse2 installed on Solaris. And we even got to the part where we get this link to test on our browser:

http://rgddev.mcw.edu/cgi-bin/gbrowse/yeast



But this link led to a blank page and a 500 internal server error on our browser.

The apache logs give us this:





[Mon May 17 15:13:58 2010] [error] [client 141.106.161.52] File does not exist: /rgd_home/3.0/WWW/fgb2, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:03 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Invalid source yeast_renderfarm at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/Render.pm line 61, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Can't locate object method "file_mtime" via package "Bio::Graphics::Browser2::DataSource" at /usr/local/lib/perl5/site_perl/5.8.8/sun4-solaris/Bio/Graphics/Browser2/DataSource.pm line 53., referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:14:49 2010] [error] [client 141.106.161.52] Premature end of script headers: gbrowse, referer: http://rgddev.mcw.edu/gbrowse2/

[Mon May 17 15:15:15 2010] [info] [client 127.0.0.1] (32)Broken pipe: core_output_filter: writing data to the network





We are currently installing this on a Solaris system. Please help me figure out this error..





Thanks,

Pushkala


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


------------------------------------------------------------------------------


_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>




--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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