Maaslin2 error reporting in RStudio

Downstream analysis and statistics MaAsLin
1

I was running this in RStudio and it gave me this error. I saw that the errors were not being handled in github anymore, so I am posting it here.
Warning message:

The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.

:information_source: Please use the `linewidth` argument instead.

:information_source: The deprecated feature was likely used in the Maaslin2 package.

Please report the issue at https://github.com/biobakery/maaslin2/issues.

This warning is displayed once per session.

Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.

> lifecycle::last_lifecycle_warnings()

[[1]]

Error in loadNamespace(x) : there is no package called ‘crayon’

Thanks!

2

I’ll bump the relevant people internally, but would you be able to use MaAsLin 3 instead? The ggplot warning you’re getting is from a ggplot update a few months ago (fixed in MaAsLin 3), though I’m not sure what they crayon issue is off the top of my head.

3

Thanks! I’m trying to install Maaslin3 now, but I am getting this issue:
there is no package called ‘knitr’

from this installation command:
for (lib in c(‘maaslin3’, ‘dplyr’, ‘ggplot2’, ‘knitr’)) {
suppressPackageStartupMessages(require(lib, character.only = TRUE))
}

4

Does install.packages(‘knitr’) work?

1 Like
5

Yes, this worked! Thanks