[Gmod-help] Re: [Gmod-gbrowse] Session lock-type error

joseph franklin joseph.franklin at yale.edu
Tue Jul 28 09:27:11 EDT 2009 

Because the CVS source wasn't building properly, I downloaded 1.996  
directly from CPAN, and that installed properly and recovered the  
browser, though for some reason I had to go into the source config to  
manually point to the (normally default) CSS file, as it wasn't  
loading normally.



On 27 Jul 2009, at 17:34, Dave Clements, GMOD Help Desk wrote:

> Hi Joe,
>
> Is the browser window empty, or is it displaying something? If it is
> displaying something, a screenshot might help.
>
> I don't know what is going on with the errors.  A lot of the code in
> HTML.pm that is generating the warnings are $self->tr('SOME_KEY')
> calls, which means their is some problem with the language
> translation.  I believe SOME_KEY is supposed to look up the value to
> display in your local language (English, I'm guessing), but all calls
> like that are returning nulls.
>
> Does anybody have any idea why just the translations would have
> problems?  Is your conf/languages directory readable?
>
> Normally, I'd also suggest reinstalling from CVS, but this doesn't
> feel like the kind of problem that might be fixed by that.
>
> Dave C.
>
>
>
>
> On Mon, Jul 27, 2009 at 1:40 PM, joseph
> franklin<joseph.franklin at yale.edu> wrote:
>> Sorry-I panicked--the unidentified lock-type errors were a result,  
>> not
>> surprisingly, of a permissions problem on the GBrowse.conf file.   
>> I've
>> fixed that, but after trying to reinstall Gbrowse-1.996 from cpan
>> (don't ask why), I have major problems--the page content appears to  
>> be
>> only partially loading, and nothing is working on the browser window.
>>
>> Below are the errors--does anyone have any ideas about resurrecting  
>> my
>> browser?
>>
>>
>> Here are the apache2 errors:
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $proposed_source in exists at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser.pm line 258.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render.pm line 864.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 474.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 478.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 482.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 483.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 485.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 486.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 500.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 500.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 1300.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 180.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $show in concatenation (.) or string at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 1573.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category in hash element at /usr/local/lib/perl/5.10.0/Bio/
>> Graphics/Browser/Render/HTML.pm line 656.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value $category_title in substitution (s///) at /usr/local/lib/perl/
>> 5.10.0/Bio/Graphics/Browser/Render/HTML.pm line 686.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in string eq at /usr/local/lib/perl/5.10.0/Bio/Graphics/ 
>> Browser/
>> Render/HTML.pm line 688.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Use of  
>> uninitialized
>> value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/ 
>> Bio/
>> Graphics/Browser/Render/HTML.pm line 987.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Odd number of
>> elements in anonymous hash at /usr/local/lib/perl/5.10.0/Bio/ 
>> Graphics/
>> Browser/Render/HTML.pm line 843.
>> [Mon Jul 27 16:35:02 2009] [error] [client xx.xx] Odd number of
>> elements in anonymous hash at /usr/local/lib/perl/5.10.0/Bio/ 
>> Graphics/
>> Browser/Render/HTML.pm line 843.
>>
>>
>> On 27 Jul 2009, at 14:27, joseph franklin wrote:
>>
>>> Hi GMOD-ers,
>>>
>>>
>>> I was tooling with the session lock settings in the GBrowse.conf  
>>> file
>>> in my GBrowse-1.996 (from cpan), because the sessions weren't  
>>> locking
>>> when gbrowse was running under mod_perl.  I returned everything to
>>> default, which was working great before:
>>> # session settings
>>> session lock type = default
>>> session driver    = driver:file;serializer:default
>>> session args      = Directory /var/tmp/gbrowse2/sessions
>>>
>>> However, I'm getting "unknown lock type" errors in my apache2 log,
>>> referring to Session.pm (see below).  I've restarted apache2 (and  
>>> the
>>> whole machine), to no avail.  There must be something I don't know
>>> about how the lock type gets set.  Is there anything I can do to
>>> return things to normal?
>>>
>>> thanks
>>> -joe
>>>
>>>
>>> error.log:
>>>
>>> [Mon Jul 27 14:17:26 2009] [error] [client XX] unknown lock type   
>>> at /
>>> usr/local/lib/perl/5.10.0/Bio/Graphics/Browser/Session.pm line 92,
>>> <DATA> line 192.
>>> [Mon Jul 27 14:17:26 2009] [error] [client XX] Premature end of  
>>> script
>>> headers: gbrowse
>>> [Mon Jul 27 14:24:57 2009] [error] [client 130.132.229.22] Odd  
>>> number
>>> of elements in hash assignment at /usr/local/lib/perl/5.10.0/Bio/
>>> Graphics/Browser/Session.pm line 28, <DATA> line 192.
>>>
>>>
>>>
>>>
>>>
>>>
>>> ________________________________
>>> Joe Franklin
>>> Department of Cell Biology
>>> Yale University School of Medicine
>>> 295 Congress Ave, BCMM 137
>>> New Haven, CT 06519
>>> USA
>>>
>>> joseph.franklin at yale.edu
>>> 407 341 3263 (cell)
>>> 203 654 7494 (google voice)
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> _______________________________________________
>>> Gmod-gbrowse mailing list
>>> Gmod-gbrowse at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>> ________________________________
>> Joe Franklin
>> Department of Cell Biology
>> Yale University School of Medicine
>> 295 Congress Ave, BCMM 137
>> New Haven, CT 06519
>> USA
>>
>> joseph.franklin at yale.edu
>> 407 341 3263 (cell)
>> 203 654 7494 (google voice)
>>
>>
>> ------------------------------------------------------------------------------
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> -- 
> * Register now for the August GMOD Meeting:
> http://gmod.org/wiki/August_2009_GMOD_Meeting
> * Please keep responses on the list!
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________________________________
Joe Franklin
Department of Cell Biology
Yale University School of Medicine
295 Congress Ave, BCMM 137
New Haven, CT 06519
USA

joseph.franklin at yale.edu
407 341 3263 (cell)
203 654 7494 (google voice)

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