Failed rendering report

[buchanri]

Hello, I've been unable to get the main report to render on the CQLS. I'm using the up to date dev branch. It errors when trying to create the enviroment, at first I got the error:

processing file: index.qmd
1/77                        
2/77 [knitr_settings]       
3/77                        
4/77 [load_libraries]       
Error:
! package or namespace load failed for 'adegenet' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'igraph'
Backtrace:
  1. global .main()
  2. execute(...)
  3. rmarkdown::render(...)
  4. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  5. knitr:::process_file(text, output)
     ...
 16. base::withRestarts(...)
 17. base (local) withRestartList(expr, restarts)
 18. base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 19. base (local) docall(restart$handler, restartArgs)
 21. evaluate (local) fun(base::quote(`<smplErrr>`))

Quitting from lines 26-60 [load_libraries] (index.qmd)
Execution halted

I then changed the adegenet package to be installed with bioconda and not conda-forge, and did mamba clean -all. But I get this error:

Oct-23 13:46:26.720 [Actor Thread 48888] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=PATHOGENSURVEILLANCE:MAIN_REPORT (2); work-dir=null
  error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to create Conda environment
  command: mamba create --mkdir --yes --quiet --prefix /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/ps_pipeline_riley/pathogensurveillance/work/conda/env-5c2610f1853ead61f6c6e3e1f537b62c conda-forge::r-devtools conda-forge::r-leaflet conda-forge::r-biocmanager conda-forge::quar>
  status : 143
  message:

I'm able to render in my local computer on R just fine just not on CQLS.

[zachary-foster]

I checked that the docker container is working recently, but I have not checked the conda environment recently. However, it does say that igraph should be installed. Perhaps that conda environment did not get built correctly? That happens sometimes. Can you delete that environment and try again? You can find the path to the environment in the .command.sh file and it should be in the work directory.

[buchanri]

I tried that and it gave the same Failed to create Conda environment error as before, unfortunately.