Question: code format for Bioconductor submission
gravatar for jlfmssm
2.1 years ago by
jlfmssm0 wrote:

I tried to use  "R CMD BiocCheck" to check a package I am working on.

I got the following notes from checking:

I just want to know  if there is an easy way to format my codes. 

Or I have to format all codes line by line. 

* CONSIDER: Shortening lines; 214 lines (11%) are > 80 characters


* CONSIDER: Replacing tabs with 4 spaces; 3 lines (0%) contain


* CONSIDER: Indenting lines with a multiple of 4 spaces; 507 lines

      (26%) are not.

ADD COMMENTlink modified 2.0 years ago by Marcel Ramos ♦♦ 310 • written 2.1 years ago by jlfmssm0
gravatar for Marcel Ramos
2.0 years ago by
Marcel Ramos ♦♦ 310
United States
Marcel Ramos ♦♦ 310 wrote:


There are several ways you can check and format your code as suggested in BiocCheck.

These include:

goodpractice::gp (checker function - MangoTheCat/goodpractice github repository)

lintr (checker package)

formatR (text formatting package)

RStudio settings (best used when writing)


You can also ask this question about package development in the bioc-devel mailing list for more input. 



Best regards,


ADD COMMENTlink written 2.0 years ago by Marcel Ramos ♦♦ 310
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