goseq: update to 1.44.0

[mblue9]

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[mblue9]

Have fixed the linting issues here except 2,
no visible binding for global variable ‘go_map’
no visible global function definition for ‘goseq’

Other R tools here have similiar issue e.g deseq2

I wonder if the lintr here is too strict as this issue was reported here
r-lib/lintr#27

Seems because (as says here r-lib/lintr#382)

lintr is currently mostly geared towards package development rather than scripts unfortunately

Workaround in first issue

You can disable the object_usage_linter to avoid it.

e.g.
linters=subset(lintr::default_linters,!lintr::default_linters %in% lintr::default_linters["object_usage_linter"])

Is that what needs to be done or something else?

[bgruening]

@mblue9 can you use #nolint? https://rdrr.io/cran/lintr/man/exclude.html

If you think this is more problematic than useful we need to discuss the linting step of R code again.

[mblue9]

I'll have a look, will be good to use the linting if possible.

By the way these R jobs are also failing here due to timeouts during the planemo testing, taking > 6hrs
The job running on runner GitHub Actions 9 has exceeded the maximum execution time of 360 minutes.
They don't take very long to test locally so is something wrong here?

[bgruening]

@mblue9 please try to add r-base as dependency. r-base=4.0 should hopefully work.

[bgruening]

@mblue9 fixed!

The failing tests now are real:

We also included linting of R code, do you have time to fix that?

We also included xref and EDAM tags. It would be nice if those could be added too:

https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-xrefs-xref
https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-edam-topics

You can find that information here: https://bio.tools/goseq

Thanks!

[bgruening]

Gracias! :)