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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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R versioning and Roary #224

Closed pjbiggs closed 5 years ago

pjbiggs commented 5 years ago

Hi,

I am using Nullarbor2 (v. 2.0.20181010; pre-Conda) installed into am Ubuntu 18.04 VM. I was using R 3.4.4 and everything was working fine. I have updated to R 3.6.1, and now my roary script is broken, and so therefore is my nullarbor:

$ roary
Can't locate Bio/Roary/CommandLine/Roary.pm in @INC (you may need to install the Bio::Roary::CommandLine::Roary module) 
............
BEGIN failed--compilation aborted at /usr/local/bin/roary line 17.

I have looked at having multiple R versions on my VM as way to sort this out. Is there a simple way to try to restore the situation by keeping my updated R version?

Thanks in advance,

Patrick

tseemann commented 5 years ago

I don't think R is the problem. The error is from Perl. I think Perl has upgraded and you've lost your local library path. You need to reinstall roary cpan Bio::Roary perhaps. This is not a Nullarbor issue. All the best!