jhcuarta
commented
1 year ago 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)
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)