Re: [Gmod-ajax] Perl lib version question

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

I am not really sure but I wanted to revisit your other email

>As needed by new JBrowse, I installed perl 5.30 into the
/usr/local/bin/ location (my /usr/bin/ location has perl 5.16)

There is no requirement to use a new version of perl with newer versions of
JBrowse as far as I know, we should be backwards compatible with pretty old
versions of perl

Did you see something that seemed to need an upgraded perl?


-Colin

On Tue, Jul 14, 2020 at 4:10 PM Zhiliang Hu <hu...@an...> wrote:

> 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
> >>>>
> >>>
> >>
> >
>