Undefined subroutine &AGAT::OmniscientStat::rcc_plot_from_list

[Hans-zhao831]

Hi, I installed AGAT by conda in a new env. But a report “Undefined subroutine &AGAT::OmniscientStat::rcc_plot_from_list called at /home/miniconda3/envs/agatenv/lib/site_perl/5.26.2/AGAT/OmniscientStat.pm line 169.” in the endwhen running “agat_sp_statistics.pl -gff out.gff3 -g genome.fasta -d -v” , And without plots generating.

How can I test the software installation successfully and is this problem caused by the software installation?

[Juke34]

R command do not seems to work. I will have a look. You should not use the plot then (avoid -d or -p parameter)

[Hans-zhao831]

Indeed, I used conda to install twice, the first time is when it also showed that “R could not be found”, I uninstalled and reinstalled, I thought it was OK. Then I guess it's still a problem with R by conda.

[Juke34]

It is fixed in version 0.6.1. It it is not yet available in conda. You can install it following this procedure:
https://github.com/NBISweden/AGAT#use-a-version-of-agat-from-a-specific-branch

[Hans-zhao831]

Nice. It works.