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-boun...@r-project.org> on behalf of Martin Morgan
<mtmorgan.b...@gmail.com>
Sent: Wednesday, February 3, 2021 1:00 PM
To: Tim Nieuwenhuis <tnieu...@jhmi.edu>; bioc-devel@r-project.org
<bioc-devel@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-boun...@r-project.org on behalf of tnieu...@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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