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

[Kern, Lori]

Additionally on the fread not being found:  if you are using roxygen and devtools to develop you may need to run document() again for the changes to be made to the NAMESPACE.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Martin Morgan <mtmorgan.bioc using gmail.com>
Sent: Wednesday, February 3, 2021 1:00 PM
To: Tim Nieuwenhuis <tnieuwe1 using jhmi.edu>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] Updating a package due to reviewer comments and other questions

1. New features -- even those that improve the package ;) -- should be added to devel; your users will have access to them soon enough, and it provides a chance for the bugs and errors that new code inevitably introduces to be worked out.

2. If the data is used in the package per se, e.g., in a function defined in your package, then you should Import: hpar. If the data is used in examples or in the vignette, then use Suggests:

3. If fread is used in one of your functions, then having Imports: data.table importFrom(data.table, fread) should be sufficient. If you use fread() in your vignette, e.g., 'hey reader, read the data using fread like so...' then the data.table package needs to be loaded (e.g., via library(data.table) in the vignette itself. If you've made changes to a public github or other repository then providing that link might help...

Martin

On 2/3/21, 10:45 AM, "Bioc-devel on behalf of Tim Nieuwenhuis" <bioc-devel-bounces using r-project.org on behalf of tnieuwe1 using jhmi.edu> wrote:

    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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