runnning in 2026!

[Lil-Psilocybe]

Hello!

Thank you for creating an accessible GO tool for non (emerging) model species.

I am trying this tool in a conda environment with python 3.8. I have downloaded the 1.0.2 release and am testing on the example data. I get the following error when I run the python3 src/main.py command from the main directory:

Performing Background Filtering from data/annotation/functional_annotation_proteinas.emapper.annotations...
Performing enrichment analysis for aa with candidates data/candidates/aa.candidates.txt and universe data/universe
Loading required package: optparse
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: install.packages -> contrib.url
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘optparse’
Execution halted
Starting processing for file: /Users/jb_programs/NonModelGOToolkit-1.0.2/examples/output/aa/aa.candidates
Processing file /Users/jb_programs/NonModelGOToolkit-1.0.2/examples/output/aa/aa.candidates/aa.candida
Processing file /Users/jb_programs/NonModelGOToolkit-1.0.2/examples/output/aa/aa.candidates/aa.candida
Processing file /Users/jb_programs/NonModelGOToolkit-1.0.2/examples/output/aa/aa.candidates/aa.candida
Job submitted with ID 446503218 for namespace CC
Job submitted with ID 446503219 for namespace MF
Job submitted with ID 446503220 for namespace BP
Error occurred while fetching results for namespace CC
Error occurred while fetching results for namespace MF
Error occurred while fetching results for namespace BP
Traceback (most recent call last):
  File "src/main.py", line 10, in <module>
    main()
  File "src/main.py", line 7, in main
    revigo_main()
  File "/Users/jb_programs/NonModelGOToolkit-1.0.2/src/revigo_plotting.py", line 191, in main
    process_and_plot(tables_paths['BP'], tables_paths['MF'], tables_paths['CC'], os.path.join(file_dir, 'results_r
KeyError: 'BP'

Any tips? Might try to run on commandline thru Rstudio? I'm on a mac if that helps!

[Lil-Psilocybe]

update! after opening my RStudio locally the command kept running from the CLI (terminal in my case). I ended up getting some other errors related to packages within 3D_treemap.R. It seems i had to download additional conda packages like so, conda install conda-forge::r-treemap which fixed the initial error but then I got the following after the treemaps are created (I have truncated output for simplicity):

...
null device 
          1 
Treemap created and saved.
null device 
          1 
Treemap created and saved.
null device 
          1 
Treemap created and saved.
...
All files processed.
Loading required package: treemap
Loading required package: d3treeR
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Calls: check_and_install_packages -> install.packages -> startsWith -> contrib.url
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘d3treeR’
Execution halted

I went to anaconda to get d3tree like I did for treemap like so from here. But i think the discrepancy lies in the 3D_treemap.R where the software is called library(d3treeR) but in the conda install the suffix R is missing. I tried manual editing of 3D_treemap.R to library(d3tree), but no avail.