Double size is not compatible error, no glyphs rendering, GBrowse 2.08

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Double size is not compatible error, no glyphs rendering, GBrowse 2.08

Hector Andres Urbina Saavedra
Hello all,

I just upgraded all my perl system, now running GBrowse 2.08, but glyphs
not rendering, with one of the following error messages displayed for
each track in the browser:

"Track rendering error: Server closed connection without sending any
data back" or
"Track rendering error: timeout; try viewing a smaller region" <---(that
doesn't work)

in the gbrowse_slave log we have this:

====================================
[Tue Jun  8 11:42:42 2010] [info]   [pid=9406]  [Tue Jun  8 11:42:42
2010] [info]   [pid=9402]  Forked child PID 10272
Forked child PID 10273
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10272] [Tue Jun  8 11:42:42 2010] [debug]
[pid=9402]  [Tue Jun  8 11:42:42 2010] [debug]  [pid=9406]  [Tue Jun  8
11:42:42 2010] [info]   [pid=9398]  Waiting for connection...
Waiting for connection...
Forked child PID 10274
clone_database() time: 0.000194072723388671875 s
clone_database() time: 0.000212907791137695312 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=9398]  Waiting for
connection...
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10273] Connect from 127.0.0.1
Connect from 127.0.0.1
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] clone_database() time:
0.000113010406494140625 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] Connect from 127.0.0.1
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] process_request(): read
30373 bytes
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] process_request():
setting environment
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: reading request:
0.00657892227172851562 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] process_request(): read
30364 bytes
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] process_request():
setting environment
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: reading request:
0.00659084320068359375 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] process_request():
operation = render_tracks
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] render_tracks(): thawing
parameters
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] process_request():
operation = render_tracks
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: setting
environment: 0.00047206878662109375 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] render_tracks(): thawing
parameters
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: setting
environment: 0.00045108795166015625 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] process_request(): read
30367 bytes
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] process_request():
setting environment
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: reading request:
0.00680398941040039062 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] process_request():
operation = render_tracks
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] render_tracks(): thawing
parameters
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: setting
environment: 0.000701904296875 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10274] BENCH: thawing parameters:
0.00753617286682128906 s
BENCH: thawing parameters: 0.00754094123840332031 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10274] Using cached version of arabidopsis config
data
Using cached version of arabidopsis config data
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: thawing
parameters: 0.00790119171142578125 s
Double size is not compatible at ../../lib/Storable.pm (autosplit
into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN> line 1,
at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
Double size is not compatible at ../../lib/Storable.pm (autosplit
into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN> line 1,
at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] Using cached version of
arabidopsis config data
Double size is not compatible at ../../lib/Storable.pm (autosplit
into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN> line 1,
at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
[Tue Jun  8 11:42:42 2010] [info]   [pid=9410]  [Tue Jun  8 11:42:42
2010] [info]   [pid=9402]  Forked child PID 10279
Forked child PID 10278
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10279] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10278] [Tue Jun  8 11:42:42 2010] [debug]
[pid=9410]  Waiting for connection...
...............

(and it repeats for each track)

Now I just checked if the bottom of the GBrowse web page says "version
2.08", but it still says "Generic Genome Browser version 2.00"... Have I
to do something else to get GBrowse working after each update?

Thanks,




--
Hector Urbina Saavedra
Bioinformatics Engineer
Bioinformatics Unit - Agri aquaculture Nutritional Genomic Center
Temuco - Chile
www.cgna.cl



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Re: Double size is not compatible error, no glyphs rendering, GBrowse 2.08

Lincoln Stein
Hi Hector,

Thanks for reporting this. I haven't encountered this error, but it suggests that the hardware architecture on the slaves is different than on the master server. Are the slaves running on separate machines, or perhaps different versions of Perl or the Storable library?

The version number on the bottom apparently gives the major version number (2.0) and not the minor version number. This is an omission on my part, but is probably unrelated to your issue.

Lincoln

On Tue, Jun 8, 2010 at 12:56 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
Hello all,

I just upgraded all my perl system, now running GBrowse 2.08, but glyphs
not rendering, with one of the following error messages displayed for
each track in the browser:

"Track rendering error: Server closed connection without sending any
data back" or
"Track rendering error: timeout; try viewing a smaller region" <---(that
doesn't work)

in the gbrowse_slave log we have this:

====================================
[Tue Jun  8 11:42:42 2010] [info]   [pid=9406]  [Tue Jun  8 11:42:42
2010] [info]   [pid=9402]  Forked child PID 10272
Forked child PID 10273
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10272] [Tue Jun  8 11:42:42 2010] [debug]
[pid=9402]  [Tue Jun  8 11:42:42 2010] [debug]  [pid=9406]  [Tue Jun  8
11:42:42 2010] [info]   [pid=9398]  Waiting for connection...
Waiting for connection...
Forked child PID 10274
clone_database() time: 0.000194072723388671875 s
clone_database() time: 0.000212907791137695312 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=9398]  Waiting for
connection...
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10273] Connect from 127.0.0.1
Connect from 127.0.0.1
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] clone_database() time:
0.000113010406494140625 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] Connect from 127.0.0.1
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] process_request(): read
30373 bytes
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] process_request():
setting environment
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: reading request:
0.00657892227172851562 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] process_request(): read
30364 bytes
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] process_request():
setting environment
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: reading request:
0.00659084320068359375 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] process_request():
operation = render_tracks
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] render_tracks(): thawing
parameters
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] process_request():
operation = render_tracks
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: setting
environment: 0.00047206878662109375 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] render_tracks(): thawing
parameters
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: setting
environment: 0.00045108795166015625 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] process_request(): read
30367 bytes
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] process_request():
setting environment
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: reading request:
0.00680398941040039062 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] process_request():
operation = render_tracks
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] render_tracks(): thawing
parameters
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: setting
environment: 0.000701904296875 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10274] BENCH: thawing parameters:
0.00753617286682128906 s
BENCH: thawing parameters: 0.00754094123840332031 s
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10274] Using cached version of arabidopsis config
data
Using cached version of arabidopsis config data
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: thawing
parameters: 0.00790119171142578125 s
Double size is not compatible at ../../lib/Storable.pm (autosplit
into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN> line 1,
at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
Double size is not compatible at ../../lib/Storable.pm (autosplit
into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN> line 1,
at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] Using cached version of
arabidopsis config data
Double size is not compatible at ../../lib/Storable.pm (autosplit
into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN> line 1,
at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
[Tue Jun  8 11:42:42 2010] [info]   [pid=9410]  [Tue Jun  8 11:42:42
2010] [info]   [pid=9402]  Forked child PID 10279
Forked child PID 10278
[Tue Jun  8 11:42:42 2010] [debug]  [pid=10279] [Tue Jun  8 11:42:42
2010] [debug]  [pid=10278] [Tue Jun  8 11:42:42 2010] [debug]
[pid=9410]  Waiting for connection...
...............

(and it repeats for each track)

Now I just checked if the bottom of the GBrowse web page says "version
2.08", but it still says "Generic Genome Browser version 2.00"... Have I
to do something else to get GBrowse working after each update?

Thanks,




--
Hector Urbina Saavedra
Bioinformatics Engineer
Bioinformatics Unit - Agri aquaculture Nutritional Genomic Center
Temuco - Chile
www.cgna.cl



------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-devel mailing list
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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: Double size is not compatible error, no glyphs rendering, GBrowse 2.08

Hector Andres Urbina Saavedra
Hi Lincoln,

Thank you for the answer.  We have an Intel Xeon 64 bits machine, which
is running the master and slaves.  Same version of Perl (5.12.1), same
Storable library (if you have doubts regarding this, please tell me how
to check what libraries are using master and slaves...)

Greetings,

Hector.

On Tue, 2010-06-08 at 13:50 -0400, Lincoln Stein wrote:

> Hi Hector,
>
>
> Thanks for reporting this. I haven't encountered this error, but it
> suggests that the hardware architecture on the slaves is different
> than on the master server. Are the slaves running on separate
> machines, or perhaps different versions of Perl or the Storable
> library?
>
>
> The version number on the bottom apparently gives the major version
> number (2.0) and not the minor version number. This is an omission on
> my part, but is probably unrelated to your issue.
>
>
> Lincoln
>
> On Tue, Jun 8, 2010 at 12:56 PM, Hector Andres Urbina Saavedra
> <[hidden email]> wrote:
>         Hello all,
>        
>         I just upgraded all my perl system, now running GBrowse 2.08,
>         but glyphs
>         not rendering, with one of the following error messages
>         displayed for
>         each track in the browser:
>        
>         "Track rendering error: Server closed connection without
>         sending any
>         data back" or
>         "Track rendering error: timeout; try viewing a smaller region"
>         <---(that
>         doesn't work)
>        
>         in the gbrowse_slave log we have this:
>        
>         ====================================
>         [Tue Jun  8 11:42:42 2010] [info]   [pid=9406]  [Tue Jun  8
>         11:42:42
>         2010] [info]   [pid=9402]  Forked child PID 10272
>         Forked child PID 10273
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10272] [Tue Jun  8 11:42:42 2010] [debug]
>         [pid=9402]  [Tue Jun  8 11:42:42 2010] [debug]  [pid=9406]
>          [Tue Jun  8
>         11:42:42 2010] [info]   [pid=9398]  Waiting for connection...
>         Waiting for connection...
>         Forked child PID 10274
>         clone_database() time: 0.000194072723388671875 s
>         clone_database() time: 0.000212907791137695312 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=9398]  Waiting for
>         connection...
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10273] Connect from 127.0.0.1
>         Connect from 127.0.0.1
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         clone_database() time:
>         0.000113010406494140625 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] Connect from
>         127.0.0.1
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         process_request(): read
>         30373 bytes
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         process_request():
>         setting environment
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: reading
>         request:
>         0.00657892227172851562 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         process_request(): read
>         30364 bytes
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         process_request():
>         setting environment
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: reading
>         request:
>         0.00659084320068359375 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         process_request():
>         operation = render_tracks
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         render_tracks(): thawing
>         parameters
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         process_request():
>         operation = render_tracks
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: setting
>         environment: 0.00047206878662109375 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         render_tracks(): thawing
>         parameters
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: setting
>         environment: 0.00045108795166015625 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         process_request(): read
>         30367 bytes
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         process_request():
>         setting environment
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: reading
>         request:
>         0.00680398941040039062 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         process_request():
>         operation = render_tracks
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         render_tracks(): thawing
>         parameters
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: setting
>         environment: 0.000701904296875 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10274] BENCH: thawing parameters:
>         0.00753617286682128906 s
>         BENCH: thawing parameters: 0.00754094123840332031 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10274] Using cached version of arabidopsis
>         config
>         data
>         Using cached version of arabidopsis config data
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: thawing
>         parameters: 0.00790119171142578125 s
>         Double size is not compatible at ../../lib/Storable.pm
>         (autosplit
>         into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN>
>         line 1,
>         at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
>         Double size is not compatible at ../../lib/Storable.pm
>         (autosplit
>         into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN>
>         line 1,
>         at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] Using cached
>         version of
>         arabidopsis config data
>         Double size is not compatible at ../../lib/Storable.pm
>         (autosplit
>         into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN>
>         line 1,
>         at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
>         [Tue Jun  8 11:42:42 2010] [info]   [pid=9410]  [Tue Jun  8
>         11:42:42
>         2010] [info]   [pid=9402]  Forked child PID 10279
>         Forked child PID 10278
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10279] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10278] [Tue Jun  8 11:42:42 2010] [debug]
>         [pid=9410]  Waiting for connection...
>         ...............
>        
>         (and it repeats for each track)
>        
>         Now I just checked if the bottom of the GBrowse web page says
>         "version
>         2.08", but it still says "Generic Genome Browser version
>         2.00"... Have I
>         to do something else to get GBrowse working after each update?
>        
>         Thanks,
>        
>        
>        
>        
>         --
>         Hector Urbina Saavedra
>         Bioinformatics Engineer
>         Bioinformatics Unit - Agri aquaculture Nutritional Genomic
>         Center
>         Temuco - Chile
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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: Double size is not compatible error, no glyphs rendering, GBrowse 2.08

Lincoln Stein
Hi Hector,

When you installed, did you run "./Build test" ? This should have tested the slave function and it should have failed at that point.

I'm going to send you a test script to run on the master and slave machines in a short while. We should get this sorted out quickly, I hope.

Lincoln

On Tue, Jun 8, 2010 at 2:09 PM, Hector Andres Urbina Saavedra <[hidden email]> wrote:
Hi Lincoln,

Thank you for the answer.  We have an Intel Xeon 64 bits machine, which
is running the master and slaves.  Same version of Perl (5.12.1), same
Storable library (if you have doubts regarding this, please tell me how
to check what libraries are using master and slaves...)

Greetings,

Hector.

On Tue, 2010-06-08 at 13:50 -0400, Lincoln Stein wrote:
> Hi Hector,
>
>
> Thanks for reporting this. I haven't encountered this error, but it
> suggests that the hardware architecture on the slaves is different
> than on the master server. Are the slaves running on separate
> machines, or perhaps different versions of Perl or the Storable
> library?
>
>
> The version number on the bottom apparently gives the major version
> number (2.0) and not the minor version number. This is an omission on
> my part, but is probably unrelated to your issue.
>
>
> Lincoln
>
> On Tue, Jun 8, 2010 at 12:56 PM, Hector Andres Urbina Saavedra
> <[hidden email]> wrote:
>         Hello all,
>
>         I just upgraded all my perl system, now running GBrowse 2.08,
>         but glyphs
>         not rendering, with one of the following error messages
>         displayed for
>         each track in the browser:
>
>         "Track rendering error: Server closed connection without
>         sending any
>         data back" or
>         "Track rendering error: timeout; try viewing a smaller region"
>         <---(that
>         doesn't work)
>
>         in the gbrowse_slave log we have this:
>
>         ====================================
>         [Tue Jun  8 11:42:42 2010] [info]   [pid=9406]  [Tue Jun  8
>         11:42:42
>         2010] [info]   [pid=9402]  Forked child PID 10272
>         Forked child PID 10273
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10272] [Tue Jun  8 11:42:42 2010] [debug]
>         [pid=9402]  [Tue Jun  8 11:42:42 2010] [debug]  [pid=9406]
>          [Tue Jun  8
>         11:42:42 2010] [info]   [pid=9398]  Waiting for connection...
>         Waiting for connection...
>         Forked child PID 10274
>         clone_database() time: 0.000194072723388671875 s
>         clone_database() time: 0.000212907791137695312 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=9398]  Waiting for
>         connection...
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10273] Connect from 127.0.0.1
>         Connect from 127.0.0.1
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         clone_database() time:
>         0.000113010406494140625 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] Connect from
>         127.0.0.1
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         process_request(): read
>         30373 bytes
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         process_request():
>         setting environment
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: reading
>         request:
>         0.00657892227172851562 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         process_request(): read
>         30364 bytes
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         process_request():
>         setting environment
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: reading
>         request:
>         0.00659084320068359375 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         process_request():
>         operation = render_tracks
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273]
>         render_tracks(): thawing
>         parameters
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         process_request():
>         operation = render_tracks
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] BENCH: setting
>         environment: 0.00047206878662109375 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274]
>         render_tracks(): thawing
>         parameters
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10274] BENCH: setting
>         environment: 0.00045108795166015625 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         process_request(): read
>         30367 bytes
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         process_request():
>         setting environment
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: reading
>         request:
>         0.00680398941040039062 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         process_request():
>         operation = render_tracks
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272]
>         render_tracks(): thawing
>         parameters
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: setting
>         environment: 0.000701904296875 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10274] BENCH: thawing parameters:
>         0.00753617286682128906 s
>         BENCH: thawing parameters: 0.00754094123840332031 s
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10273] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10274] Using cached version of arabidopsis
>         config
>         data
>         Using cached version of arabidopsis config data
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] BENCH: thawing
>         parameters: 0.00790119171142578125 s
>         Double size is not compatible at ../../lib/Storable.pm
>         (autosplit
>         into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN>
>         line 1,
>         at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
>         Double size is not compatible at ../../lib/Storable.pm
>         (autosplit
>         into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN>
>         line 1,
>         at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10272] Using cached
>         version of
>         arabidopsis config data
>         Double size is not compatible at ../../lib/Storable.pm
>         (autosplit
>         into ../../lib/auto/Storable/_retrieve.al) line 380, <STDIN>
>         line 1,
>         at /usr/local/lib/perl5/site_perl/5.12.1/x86_64-linux-thread-multi-ld/Bio/Graphics/Browser2/Render/Slave.pm line 285
>         [Tue Jun  8 11:42:42 2010] [info]   [pid=9410]  [Tue Jun  8
>         11:42:42
>         2010] [info]   [pid=9402]  Forked child PID 10279
>         Forked child PID 10278
>         [Tue Jun  8 11:42:42 2010] [debug]  [pid=10279] [Tue Jun  8
>         11:42:42
>         2010] [debug]  [pid=10278] [Tue Jun  8 11:42:42 2010] [debug]
>         [pid=9410]  Waiting for connection...
>         ...............
>
>         (and it repeats for each track)
>
>         Now I just checked if the bottom of the GBrowse web page says
>         "version
>         2.08", but it still says "Generic Genome Browser version
>         2.00"... Have I
>         to do something else to get GBrowse working after each update?
>
>         Thanks,
>
>
>
>
>         --
>         Hector Urbina Saavedra
>         Bioinformatics Engineer
>         Bioinformatics Unit - Agri aquaculture Nutritional Genomic
>         Center
>         Temuco - Chile
>         www.cgna.cl
>
>
>
>         ------------------------------------------------------------------------------
>         ThinkGeek and WIRED's GeekDad team up for the Ultimate
>         GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>         lucky parental unit.  See the prize list and enter to win:
>         http://p.sf.net/sfu/thinkgeek-promo
>         _______________________________________________
>         Gmod-devel mailing list
>         [hidden email]
>         https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
>
>
> --
> 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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