Roary suddenly stopped working (see message below). I receive the same message no matter what roary command I input. I used roary last week and everything went smoothly. I have updated brew, but I get the following message when I try to reinstall roary. I would be very grateful if you can assist me with this.
In a closed feed I noticed another user got the same error message back in June last year but I don’t have conda or miniconda installed so different solution.
Can’t locate Bio/Roary/CommandLine/Roary.pm in @INC (you may need to install the Bio::Roary::CommandLine::Roary module) (@INC contains: /home/ubuntu/ajb_store/test_Lactobacillus/roary/L_buchneri/lib /home/linuxbrew/.linuxbrew/Cellar/perl/5.28.0/lib/perl5/site_perl/5.28.0/x86_64-linux-thread-multi /home/linuxbrew/.linuxbrew/Cellar/perl/5.28.0/lib/perl5/site_perl/5.28.0 /home/linuxbrew/.linuxbrew/Cellar/perl/5.28.0/lib/perl5/5.28.0/x86_64-linux-thread-multi /home/linuxbrew/.linuxbrew/Cellar/perl/5.28.0/lib/perl5/5.28.0 /home/linuxbrew/.linuxbrew/lib/perl5/site_perl/5.28.0/x86_64-linux-thread-multi /home/linuxbrew/.linuxbrew/lib/perl5/site_perl/5.28.0) at /usr/local/bin/roary line 12.
BEGIN failed–compilation aborted at /usr/local/bin/roary line 12.
thank you so much for looking into this. To update you, I’ve just run ‘cpanm Bio::Roary::CommandLine::Roary’ but the outcome was ‘FAIL’ (after installing 90 dependencies). It suggested I run it again with ‘–force’, this resulted in ‘FAIL’ again but installed anyway. This module is related to protein files, which I’m not actually working with right now.
I’ve just run roary and it didn’t fail however, it did give the following error messages:
Use of uninitialized value in require at /home/linuxbrew/.linuxbrew/Cellar/perl/5.28.0/lib/perl5/5.28.0/x86_64-linux-thread-multi/Encode.pm line 69.
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
Use of uninitialized value in require at /home/linuxbrew/.linuxbrew/Cellar/perl/5.28.0/lib/perl5/5.28.0/x86_64-linux-thread-multi/Encode.pm line 69.
Use of uninitialized value in require at (eval 5044) line 1.