Re: [Gmod-ajax] Perl lib version question

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

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
>>
>>
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>