Install problems..

[zacforsman]

I'm having trouble installing the perl modules on my Ubuntu server following your instructions.. I tried several alternative ways of installing the perl modules and many of them worked but the script won't run. I second Jon's suggestion of a miniconda installation... I've been fighting with this for hours. Thanks. -Zac

[zacforsman]

On Ubuntu, the packages wouldn't install with cpan Perl::Module, instead cpan install VCF (all caps) worked for all modules. However when I run
rad_haplotyper.pl I get the following error:

Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Undefined value assigned to typeglob at /usr/lib/x86_64-linux-gnu/perl5/5.22/List/MoreUtils.pm line 94.
Could not find sub 'uniq' exported by List::MoreUtils at /home/z/programs/rad_haplotyper.pl line 8.
BEGIN failed--compilation aborted at /home/z/programs/rad_haplotyper.pl line 8.

According to the perl documentation:

Undefined value assigned to typeglob
        (W misc) An undefined value was assigned to a typeglob, a la "*foo =
        undef". This does nothing. It's possible that you really mean "undef
        *foo".

Any suggestions on how to install would be most welcome. -Zac

[chollenbeck]

Hi Zac,

What errors did you get when you tried to install the modules with cpan? I don't think I've had a problem with these particular modules on Ubuntu. For example, what error do you get when you run:

cpan List::MoreUtils

[zacforsman]

I get a permissions denied error, unless I do sudo cpan List::MoreUtils...oddly, now when I enter rad_haplotyper.pl I get the help message! It suddenly looks like it works! Thanks for the help. -Zac

---

Zac H. Forsman, Ph.D. Researcher, Hawaii Institute of Marine Biology 46-007 Lilipuna Rd, Kaneohe, HI 96744 (Fedex or deliveries) Google Scholar profile: https://scholar.google.com/citations?hl=en&user=MyhFvt4AAAAJ

On Mon, Sep 4, 2017 at 3:32 AM, chollenbeck notifications@github.com wrote:

Hi Zac,

What errors did you get when you tried to install the modules with cpan? I don't think I've had a problem with these particular modules on Ubuntu. For example, what error do you get when you run:

cpan List::MoreUtils

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/chollenbeck/rad_haplotyper/issues/23#issuecomment-326964430, or mute the thread https://github.com/notifications/unsubscribe-auth/AMaBbBBX7EApxRPgKJJW_DKsv9jYxNrhks5se_wBgaJpZM4PLFIq .

[chollenbeck]

Great - glad you got it to work.