change import function in R

[sbenateau]

Use data.table::fread, a more versatile function to import data. Allows the use of space, comma, semicolon as separator. Instead of only space and comma

Same as the one I cancelled but probably cleaner...

[sbenateau]

Ok the Lint R script is quite impressive but it would require a lot of changes...

[yvanlebras]

Thank you Simon! Don't hesitate to ask if we can help somewhere! Here we updated the CI workflow from Travis system to Github actions, that's why tests are different, notably considering the lint R part who allows to aply best practices to code. I don't know why the "Combine chunked test results" is failing regarding tool testing....

[sbenateau]

Do you have access to this file? 'All tool test results' artifact for details.
I won't be able to make all the changes to pass the lint R test:

• Variable and function name style should be snake_case -> this can be tricky as column names are sometimes names thank to this and therefore it require a lot of time to make sure it's ok
• functions should have cyclomatic complexity of less than 15, this has 28. -> this require to rewrite a function I don't fully understand and I don't think I have the skills and / or enough time to do that.

[bgruening]

@sbenateau please have a look at https://rdrr.io/cran/lintr/man/exclude.html

[sbenateau]

Thank you @bgruening this is what we need. @yvanlebras where can I edit the lint config file ?

[sbenateau]

I now have some tests failing... I must have done something wrong with all this reformatting.

[bgruening]

Oh you can add # nolint to your code line. And then it will be skipped.

[sbenateau]

all tests passed again in planemo :-). I will try your trick @bgruening, thank you.

[sbenateau]

Any ideas? The reformatting of the R script seems to be ok planemo gives me no error. But I don't get the last error.

[bgruening]

:)

[sbenateau]

It looks like an encoding problem... It works on my computer.

[yvanlebras]

Yes, encoding problem apparently looking at the "..residuals.." sentences