Roary needs Rscript 3 or higher Please upgrade and try again

[jhcuarta]

Hi
I'm getting the following error [rscript execution error: No such file or directory] using conda installation or aptitude
this is what it shows when I run roary -a
(roary) jason@jason:/home/jason/Documents/roary/Vibrio_complete$ roary -a
Use of uninitialized value in require at /home/jason/mambaforge/envs/roary/lib/site_perl/5.26.2/x86_64-linux-thread-multi/Encode.pm line 61.

Please cite Roary if you use any of the results it produces:
Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
"Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693
doi: http://doi.org/10.1093/bioinformatics/btv421
Pubmed: 26198102

2023/02/10 15:32:09 Looking for 'Rscript' - found /gpsr/local/bin/Rscript
2023/02/10 15:32:10 Determined Rscript version is 2.14
2023/02/10 15:32:10 Roary needs Rscript 3 or higher. Please upgrade and try again.
2023/02/10 15:32:10 Looking for 'awk' - found /usr/bin/awk
2023/02/10 15:32:10 Looking for 'bedtools' - found /home/jason/mambaforge/envs/roary/bin/bedtools
2023/02/10 15:32:10 Determined bedtools version is 2.30
2023/02/10 15:32:10 Looking for 'blastp' - found /home/jason/mambaforge/envs/roary/bin/blastp
2023/02/10 15:32:10 Determined blastp version is 2.13.0
2023/02/10 15:32:10 Looking for 'grep' - found /usr/bin/grep
2023/02/10 15:32:10 Optional tool 'kraken' not found in your $PATH
2023/02/10 15:32:10 Optional tool 'kraken-report' not found in your $PATH
2023/02/10 15:32:10 Looking for 'mafft' - found /home/jason/mambaforge/envs/roary/bin/mafft
2023/02/10 15:32:10 Determined mafft version is 7.515
2023/02/10 15:32:10 Looking for 'makeblastdb' - found /home/jason/mambaforge/envs/roary/bin/makeblastdb
2023/02/10 15:32:10 Determined makeblastdb version is 2.13.0
2023/02/10 15:32:10 Looking for 'mcl' - found /home/jason/mambaforge/envs/roary/bin/mcl
2023/02/10 15:32:10 Determined mcl version is 14-137
2023/02/10 15:32:10 Looking for 'parallel' - found /home/jason/mambaforge/envs/roary/bin/parallel
2023/02/10 15:32:10 Determined parallel version is 20230122
2023/02/10 15:32:10 Looking for 'prank' - found /home/jason/mambaforge/envs/roary/bin/prank
2023/02/10 15:32:10 Determined prank version is 170427
2023/02/10 15:32:10 Looking for 'sed' - found /usr/bin/sed
2023/02/10 15:32:10 Looking for 'cd-hit' - found /home/jason/mambaforge/envs/roary/bin/cd-hit
Use of uninitialized value in concatenation (.) or string at /home/jason/mambaforge/envs/roary/lib/site_perl/5.26.2/Bio/Roary/External/CheckTools.pm line 131.
2023/02/10 15:32:10 Determined cd-hit version is
Use of uninitialized value in numeric lt (<) at /home/jason/mambaforge/envs/roary/lib/site_perl/5.26.2/Bio/Roary/External/CheckTools.pm line 132.
2023/02/10 15:32:10 Roary needs cd-hit 4.6 or higher. Please upgrade and try again.
2023/02/10 15:32:10 Looking for 'FastTree' - found /home/jason/mambaforge/envs/roary/bin/FastTree
2023/02/10 15:32:11 Determined FastTree version is 2.1
2023/02/10 15:32:11 Roary version 3.13.0

Honestly dont know why it throws that error since I have a current R version
(roary) jason@jason:/home/jason/Documents/roary/Vibrio_complete$ R --version
R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

but Rscript is still halted

(roary) jason@jason:/home/jason/Documents/roary/Vibrio_complete$ Rscript --version
R scripting front-end version 2.14.2 (2012-02-29)

[jhcuarta]

Hi
I found a compatible Rscript version
/usr/bin/Rscript --version
Rscript (R) version 4.2.2 Patched (2022-11-10 r83330)

But I dont know how to override the one encountered by roary
(roary) jason@jason:/home/jason/Documents/roary/Vibrio_complete$ Rscript --version
R scripting front-end version 2.14.2 (2012-02-29)