warning from {lintr} workflow in [namespace_lintr]

[avallecam]

In #104 from workflow in https://github.com/epiverse-trace/tutorials/actions/runs/7699737505/job/20982024773?pr=104 to line:

tutorials/episodes/read-delays.Rmd

Lines 187 to 190 in a253dac

	```{r}
	epiparameter::epidist_db(
	disease = "covid"
	)

I'm getting this {lintr} warning

Warning: file=read-delays.Rmd,line=188,col=1,[namespace_linter] Package 'epiparameter' is not installed.

Some thoughts:

• epiparameter is called and installed from the renv.lock. Where does lintr expect to find dependencies or if a package is installed?
• This is a feature we agreed on in Use explicit namespacing in reports episoap#91, and suggested to keep using it in writing as in add {package} and function() notation #25. should we adapt to lintr? or adapt lintr to some of our features?

tagging @Bisaloo since this is related with #96

[Bisaloo]

It looks like epiparameter and epidemics and not properly installed during the lintr check. I'll look into it.

2024-02-01T11:11:48.6709022Z Skipping 2 packages not available: epiparameter, epidemics

[avallecam]

thank you @Bisaloo this is the only lintr pending to pass for #104 as in this last run https://github.com/epiverse-trace/tutorials/actions/runs/7754598773/job/21148236369?pr=104

the list of packages highlighted as sources of warning are:

• {epiparameter}
• {here} (recently added in favour of using portable paths)
• {outbreaks}

[avallecam]

also only lintr pending to pass in #58 as in last run https://github.com/epiverse-trace/tutorials/actions/runs/7755166483/job/21149968993?pr=58

package highlighted is {here}

[avallecam]

@Bisaloo, in order to give it more time to investigate the source of the issue, we can temporarily replace namespace::function() with library(package) followed by function() to achieve the goal of ready to merge this week. Happy to read your thoughts.

[Bisaloo]

The simplest option at this time is probably to disable this linter altogether by editing the .lintr file with the following content:

linters: all_linters(
    packages = "lintr",
    object_name_linter = NULL,
    implicit_integer_linter = NULL,
    brace_linter = NULL,
    extraction_operator_linter = NULL,
    missing_package_linter = NULL,
    library_call_linter = NULL,
    namespace_linter = NULL,
    undesirable_function_linter(
      modify_defaults(
        default_undesirable_functions,
        library = NULL # this is fine in Rmd files
      )
    )
  )

[avallecam]

got it, just found the .lintr file! I can proceed by:

• edit this in a new PR
• request your approval to merge
• rebase PR add episodes on introduction and read delays #104 and Middle task tutorials  #58
• request your approval for them to merge

but keeping this issue open for further investigation or decision.

happy to read your suggestions about this