[Gmod-help] Re: GBrowse/Bioperl problem
Scott Cain
cain.cshl at gmail.com
Fri Aug 29 16:59:47 EDT 2008
Hi Zhiliang,
When you do, please do a reply to all so that we know that the help
desk helped :-)
Thanks,
Scott
On Fri, Aug 29, 2008 at 4:58 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
> Hey, that error complaining about "Bio::Graphics" is gone!
>
> Now it has some other complains about some old modules... I will take care and hopefully will be able to report to you the success soon!
>
> THANKS!
>
> Zhiliang
>
> At 04:52 PM 8/29/2008 -0400, you wrote:
>>OK--now we're making progress. That tells me you have a really old
>>bioperl installed somewhere, and when you try to install GBrowse it is
>>getting the old bioperl. Try rerunning the Build install command, but
>>add the uninstall option, like this:
>>
>> sudo ./Build install --uninst 1
>>
>>which will remove old bioperl modules from where ever they are. If
>>that doesn't work (ie, the perl command still doesn't find the right
>>Bio::Graphics::Panel), double check that you really have bioperl-live
>>and not something else (I don't really know what that something else
>>might be--I'm running out of options :-)
>>
>>Oh, and the thing about symlinks doesn't have anything to do with
>>this. It is trying (and probably succeeding) to make a symlink for a
>>script it is installing so it can be excuted with either its real name
>>or the linked name. It says "trying" because it doesn't work under
>>Windows.
>>
>>Scott
>>
>>
>>On Fri, Aug 29, 2008 at 4:45 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>> Scott,
>>>
>>> I am sorry, I had an alias 'perl -p -i.bak -e' on.
>>>
>>> Now it says:
>>>> perl -MBio::Graphics::Panel -e 'print Bio::Graphics::Panel->api_version'
>>> Can't locate object method "api_version" via package "Bio::Graphics::Panel" at -e line 1.
>>>
>>> I have sent you a mail about the "Bio::Graphics" locations... perhaps on this system (linux) some symbolic links are missing? - Because I notice at the end of "./Build install" there is a line:
>>>
>>> /usr/local/bin/perl maintenance/symlink_script.pl
>>> Will try to install symlinks to /usr/local/bin
>>>
>>> Not sure what does "will try to" mean, and links from where to where...
>>>
>>> Zhiliang
>>>
>>> At 04:19 PM 8/29/2008 -0400, you wrote:
>>>>Hi Zhiliang,
>>>>
>>>>Did you copy and paste that command? I just checked it on both my
>>>>Ubuntu and Mac OS 10.5 computers and it gives the expected answer
>>>>("1.7", but with no line feed, so it looked like this: "1.7sloan:~
>>>>cain$", where the command prompt is "sloan:~ cain$"). Since you are
>>>>installing in /usr/local, I would expect to find the bioperl modules
>>>>in /usr/local/lib/perl/5.8.8/Bio/ or similar.
>>>>
>>>>Scott
>>>>
>>>>
>>>>On Fri, Aug 29, 2008 at 4:13 PM, Zhiliang Hu <zhu at iastate.edu> wrote:
>>>>> Thank Scott - that's a useful info!
>>>>>
>>>>> This command line produced an error:
>>>>>> perl -MBio::Graphics::Panel -e 'print Bio::Graphics::Panel->api_version'
>>>>>
>>>>> syntax error at -e line 2, near "MBio::Graphics::Panel
>>>>> print"
>>>>> Execution of -e aborted due to compilation errors.
>>>>>
>>>>>
>>>>> On the installation -- I do find over 60+ bioperl programs got copied to /usr/local/bin/bp_* today.
>>>>>
>>>>> I will look into if the "Bio::Graphics" parts got into the system locations...
>>>>>
>>>>> Zhiliang
>>>>>
>>>>>
>>>>> At 02:35 PM 8/29/2008 -0400, Scott Cain wrote:
>>>>>>The message about "Bio::Graphics version 0" means that the GBrowse
>>>>>>installer couldn't find bioperl at all. Are you sure you installed
>>>>>>it? Is it in the normal path for perl? There is no separate
>>>>>>installer for Bio::Graphics; it is part of bioperl. What happens if
>>>>>>you do this on the command line:
>>>>>>
>>>>>> perl -MBio::Graphics::Panel -e 'print Bio::Graphics::Panel->api_version'
>>>>>>
>>>>>>Scott
>>>>>>
>>>>>>
>>>>>>On Fri, Aug 29, 2008 at 2:16 PM, 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>--
>>>>>>------------------------------------------------------------------------
>>>>>>Scott Cain, Ph. D. cain.cshl at gmail.com
>>>>>>GMOD Coordinator (http://gmod.org/) 216-392-3087
>>>>>>Cold Spring Harbor Laboratory
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>--
>>>>------------------------------------------------------------------------
>>>>Scott Cain, Ph. D. cain.cshl at gmail.com
>>>>GMOD Coordinator (http://gmod.org/) 216-392-3087
>>>>Cold Spring Harbor Laboratory
>>>
>>>
>>
>>
>>
>>--
>>------------------------------------------------------------------------
>>Scott Cain, Ph. D. cain.cshl at gmail.com
>>GMOD Coordinator (http://gmod.org/) 216-392-3087
>>Cold Spring Harbor Laboratory
>
>
--
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl at gmail.com
GMOD Coordinator (http://gmod.org/) 216-392-3087
Cold Spring Harbor Laboratory
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