Re: [Gmod-ajax] Perl lib version question

[Colin <col...@gm...>]

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
> >>
> >
>