[Gmod-help] Re: GBrowse/Bioperl problem

[Zhiliang Hu]

Hi Dave,

I did a usual "./Build install" (I don't think 'force' is an option there).
It seems things were copied to destinations no problem (no errors).

I am looking at how to use 'CPAN' "force install" with the local downloads...

Zhiliang


At 11:36 AM 8/29/2008 -0700, you wrote:
>Hi Zhiliang,
>
>Did you force the install of BioPerl after the failed tests?  With
>BioPerl I think 9 out of 18624 subtests failing is actually quite a
>good number.
>
>Dave C.
>
>On Fri, Aug 29, 2008 at 11:16 AM, Zhiliang Hu <zhu at iastate.edu> wrote:
>> Dave - Good to hear from you!  (Sorry that means I didn't read hard enough -- I've been struggling with bioperl-1.5.2_200 all this morning ;-)
>>
>> Now I installed "bioperl-live".  The "Build test" show few failed tests:
>>
>>   Failed 5/258 test programs. 9/18624 subtests failed.
>>
>> -- which perhaps mostly from the error I saw "Count sequence n02" or something like that. I hope this is minor.
>>
>> Now, I deleted all previous expanded "Generic-Genome-Browser-1.69" folder/files, made a trial on newly uncompressed GBrowse-1.69: "perl Makefile.PL", it complains the same:
>>
>> ----------------------------------
>> Installed Bio::Graphics version 0 is less than desired version 1.7.
>> You need to update your BioPerl installation to greater than version 1.5.2.
>>
>> Can't locate object method "api_version" via package "Bio::Graphics::Panel" at (eval 6) line 2, <STDIN> line 5.
>>        ...propagated at Makefile.PL line 266, <STDIN> line 5.
>> ----------------------------------
>>
>> I am look for separate tar ball for "Bio::Graphics" so I can do a manual install and have not found one yet...
>>
>> Will keep you updated :)
>>
>> Zhiliang
>>
>>
>> At 10:32 AM 8/29/2008 -0700, you wrote:
>>>Hi Zhiliang,
>>>
>>>It's good to hear from you!  Your e-mail caused me to look at the
>>>BioPerl page on the GMOD web site AND UPDATE IT.
>>>
>>>  http://gmod.org/wiki/BioPerl
>>>
>>>For GBrowse 1.69 you actually need BioPerl-live.  BioPerl 1.4 and
>>>1.5.2 are just too out of date.  There are pointers on the BioPerl
>>>page to the BioPerl website, or you can just download it from
>>>BioPerl.org at
>>>
>>> http://www.bioperl.org/DIST/nightly_builds/
>>>
>>>Dave C.
>>>GMOD Help Desk
>>>
>>>> From: Zhiliang Hu <zhu at iastate.edu>
>>>> Date: Thu, Aug 28, 2008 at 7:51 PM
>>>> Subject: GBrowse/Bioperl problem
>>>> To: Dave Clements <clements at nescent.org>
>>>>
>>>>
>>>> Dear Dave,
>>>>
>>>> I think this might be a small problem so I ask you directly without getting
>>>> to GMOD user group --
>>>>
>>>> I got Chado installed successfully, and came to install GBrowse.  I made
>>>> sure I installed the needed bioperl -- the latest version available:
>>>>
>>>> cpan[1]> d /bioperl/
>>>> cpan[2]> install BIRNEY/bioperl-1.4.tar.gz
>>>>
>>>> But when come to build GBrowse for install "perl Makefile.PL" (on it's
>>>> latest release v.1.69) it complains that I don't have the right bioperl:
>>>> ----------------------------------------------
>>>>                File Paths
>>>>
>>>>         CONF /usr/local/apache/conf
>>>>       HTDOCS /usr/local/apache/doc
>>>>       CGIBIN /usr/local/apache/cgi-bin
>>>>  GBROWSE_ROOT gbrowse
>>>>          LIB
>>>>          BIN
>>>>          YES
>>>>       PREFIX
>>>>        DO_XS 1
>>>>      NONROOT
>>>>      SELINUX
>>>>
>>>> (Run perl Makefile.PL -h for help on changing)
>>>> ----------------------------------------------
>>>>
>>>> Installed Bio::Graphics version 0 is less than desired version 1.7.
>>>> You need to update your BioPerl installation to greater than version 1.5.2.
>>>>
>>>> Can't locate object method "api_version" via package "Bio::Graphics::Panel"
>>>> at (eval 6) line 2, <STDIN> line 5.
>>>>        ...propagated at Makefile.PL line 266, <STDIN> line 5.
>>>> ------------------------------------------------------------
>>>>
>>>> I also checked the "Bio::Graphics" module source, and found it's bundled in
>>>> bioperl and no separate downloads available.  How may I solve this problem?
>>>>
>>>> Thanks in advance!
>>>>
>>>> Zhiliang
>>>>
>>>>
>>>>
>>>
>>>--
>>>Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>>
>>
>
>-- 
>Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback