[Gmod-help] Re: [Gmod-gbrowse] Session lock-type error
joseph franklin
joseph.franklin at yale.edu
Mon Jul 27 17:59:50 EDT 2009
Thanks Dave,
I've attached a screen-shot. Note that much of the contents load, and
some things work, such as making PDFs or links to individual images
(indicating that some rendering is working). However, navigation
doesn't work and rendered tracks don't appear, and the page styling
(which should be the default transparent CSS) is defective.
I actually tried the CVS install and got this error:
Can't copy('cgi-bin/README', 'blib/cgi-bin/README'): No such file or
directory at /usr/share/perl/5.10/Module/Build/Base.pm line 4191,
<GEN73> line 27.
I'm not sure what I'm looking for with the conf/languages directory--I
haven't done anything with that (that I know of).
I clearly did something bad, and I'm willing to do pretty much
whatever is necessary to get this back online, if anyone has any
thoughts.
Thanks again,
joe
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Picture 16.png
Type: image/png
Size: 182878 bytes
Desc: not available
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20090727/bec16b5a/attachment.png>
-------------- next part --------------
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!
> * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
More information about the Gmod-help
mailing list