[Bioc-devel] Updating a package due to reviewer comments and other questions

[Tim Nieuwenhuis]

Hello,

I am the creator of the HPAStainR package and have received reviewer comments from a journal I sent an accompanying paper to, which leads me to these 3 questions about responding to paper reviewer comments.


1.      Am I able to update my Release 3.12 version of the package based on the comments? I know that I should only push bug fixes, but I think that the changes suggested will greatly improve the current functionality of the package, making it much cleaner and reproducible.

2.      My package requires the downloading of data from an online source, however a reviewer suggested I could use their bioconductor package (hpar), the package lets you access the data (using data()) that my function downloads. I want to incorporate their data into my package (for reproducibility), but I'm not sure how. Should I add their package to Depends in the DESCRIPTION file, or is there a way to specifically import the necessary data() they have?

3.      I'm not sure if I should ask here or on stackoverflow, and redirect me if I should ask this on stackoverflow: I am trying to import functions from other packages into my current functions (primarily replacing read.table() with fread() from data.table), however this causes my package check to fail (specifically during the vignette building) as it cannot find "fread" function. I have added data.table to the imports in DESCRIPTION and added it to the @importFrom line in the function I'm adding it to, however neither of those methods worked. I'm wondering if I'm missing something or if I should in the function directly call data.table::fread()? Sorry if this is the wrong place to ask, I'm new to package development.

I am willing to supply whatever information you need, thank you for your time.

Best regards,
Tim Nieuwenhuis
4th Year Graduate Student
Human Genetics
Halushka Laboratory
Johns Hopkins University SOM


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