Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

Thank you Colin!  This was an eye openning for me to cpanm... My ran of 
"cpanm Bio::Perl@1.7.2" seemed an success.

I was able to get rid of multiple "Segmentation fault (core dumped)" 
by changing the line in 'setup.sh' where perl was called with a full path: 
"have_db=`/usr/local/bin/perl -MConfig=myconfig -e".  The setup was a 
success!

Now I am getting "Segmentation fault (core dumped)" running 
"flatfile-to-json.pl", even after I changed its "#!/usr/bin/env perl" line
to "#!/usr/local/bin/perl".

Any suggestion please?

Zhiliang


On Tue, 14 Jul 2020, Colin wrote:

> Date: Tue, 14 Jul 2020 13:03:54 -0400
> From: Colin <col...@gm...>
> To: Zhiliang Hu <hu...@an...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
> If you have cpanm installed globally on your system you can try to manually
> run this command
>
> cpanm Bio::Perl@1.7.2
>
> A similar thing can likely be done with the plain cpan executable also,
> possibly this
>
> cpan CJFIELDS/BioPerl-1.007002.tar.gz
>
>
> We require 1.7.2 because later versions really significantly modified the
> BioPerl ecosystem (see changelog here
> https://github.com/bioperl/bioperl-live/blob/master/Changes)
>
>
> -Colin
>
>
> On Tue, Jul 14, 2020 at 11:59 AM Zhiliang Hu <hu...@an...> wrote:
>
>>
>> Thanks Colin for addressing the issue.  I took the path to reinstall the
>> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the
>> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>>
>> My newly downloaded JBrowse setup.sh (at a location different from
>> previous installations; on a RedHat CentOS 7 system) got complains like:
>>
>> Installing Perl prerequisites ...
>> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
>> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
>>
>> I understand it might be caused by multiple perl versions on my system but
>> by cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder
>> is there alternative ways to install "Bio::Perl@1.7.2" (actually which
>> modules?).
>>
>> I searched for old JBrowse troubleshooting and did:
>>> sudo yum groupinstall "Development Tools"
>>> sudo yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
>> and it didn't help.
>>
>> Any further suggestion please? (I know on this RH Centos7 system there are
>> perl GD, Zlib, and libpng installed but how to make the JBrowse setup know
>> where they are?)
>>
>> Zhiliang
>>
>> On Wed, 3 Jun 2020, Colin wrote:
>>
>>> Date: Wed, 3 Jun 2020 20:34:24 -0400
>>> From: Colin <col...@gm...>
>>> To: Zhiliang Hu <hu...@an...>
>>> Cc: gmod-ajax <gmo...@li...>
>>> Subject: Re: [Gmod-ajax] Perl lib version question
>>>
>>> There have been a couple people experiencing this lately. I am not
>> exactly
>>> sure why, maybe it is related people who have older versions of jbrowse
>>> upgrading to perl 5.30+.
>>>
>>> JBrowse generally installs all it's perl dependencies to a folder inside
>>> JBROWSE_ROOT/extlib
>>>
>>> I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
>>> setup.sh
>>>
>>> Here is a chat log of a user on our chat that also did these steps but it
>>> was  on macOS
>>>
>>>> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
>>>> * `sudo installer -pkg
>>>
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>> -target` - allows  Extern_H compile problem to  pass
>>>> * use `cpan` to `install JSON::XS` (for some reason the dependency won't
>>> install during setup.sh)
>>>> * run `setup.sh`
>>>
>>>
>>>
>>> -Colin
>>>
>>> On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...> wrote:
>>>
>>>> When I tried to load data to JBrowse, I got the following complain:
>>>>
>>>> Perl lib version (5.16.3) doesn't match executable
>>>> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0) at
>>>> /usr/lib64/perl5/Config.pm line 60.
>>>> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
>>>>
>>>> In cpan I did "reload cpan" and "install lib" and it says:
>>>>
>>>>    lib is up to date (0.63)
>>>>
>>>> I am at a lost as how to update my "perl lib". Any advice please?
>>>>
>>>> Zhiliang
>>>>
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>
>