Can't locate Bio/Roary/CommandLine/Roary.pm in @INC v2


#1

Hello,

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.

Amy

ubuntu@gbaprototype-volac1:~/ajb_store/test_Lactobacillus/roary/L_buchneri$ brew reinstall roary

Error: No available formula with the name “Bio::Perl” (dependency of tseemann/bioinformatics-linux/roary)

ubuntu@gbaprototype-volac1:~/ajb_store/test_Lactobacillus/roary/L_buchneri$ roary -h

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.


#2

Hi Amy,

I am looking into this now. I should have some feedback for you later this afternoon.

All the best,
Sion


#3

Hi Sion,

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.


With best wishes,
Amy


#4

Hi Amy,

Can you try installing the perl dependencies using?

cpan Bio::Roary

All the best,
Sion


#5

Done, I’ll run roary again to see what happens :slight_smile:


#6

Hi Amy,

Roary on a new GVL instance runs and produces the Encode.pm error you describe above. However, it completes and produces the appropriate output files.

It maybe a blast versioning issue (https://github.com/sanger-pathogens/Roary/issues/323)

If you cannot get it to work on your current instance I would recommend that you start a fresh instance and transfer your data.

All the best,
Sion


#7

Hi Sion,

thanks for your help yesterday. I’ve used roary a few times today and all looks good.

have a good weekend,
Amy


#8

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