[Bioc-devel] BiocCheck warnings and errors

[Robert M. Flight]

Hi Christian,

In my tests directory, there is a file "testthat.R" that contains:


library(testthat)
library(mypackage)
test_check("mypackage")


did you use the "usethis::use_testthat()" to setup your testing
infrastructure?

-Robert

------------------------------------------
Dr. Robert M Flight, PhD
Bioinformatics Analyst Senior
Puller of Rabbits from Hats
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Moseley Bioinformatics Lab
Resource Center for Stable Isotope Resolved Metabolomics
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Markey Cancer Center
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University of Kentucky
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Twitter: @rmflight
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PH 502-509-1827 <(502)%20509-1827>

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computational sciences, https://arxiv.org/pdf/2009.14258.pdf

On Tue, Sep 13, 2022 at 11:03 AM Christian Arnold <chrarnold using web.de> wrote:

> I have a few questions regarding BiocCheck errors and warnings that I
> receive for a new package version that I feel are not warranted:
>
>
> 1. I want to use the testthat framework in combination with
> devtools::test, and from my understanding, a subdirectory /testthat/
> within tests has to be used for this and is created when using
> devtools::test(). I still get an ERROR when using BiocCheck because I
> have no .R files in tests/ but within tests/testthat:
>
> * Checking unit tests... * ERROR: Add a .R or .Rin file in tests/
> directory or unit tests will not be run by R CMD check. See
> http://bioconductor.org/developers/how-to/unitTesting-guidelines/
>
> 2. My package has many packages listed in Suggests, with a lot of effort
> I tried to move as many packages there as possible to reduce the
> installation burden. From my understanding, BiocManager does NOT install
> the packages listed under /Suggests/. Thus, since I have 10+ packages in
> /Suggests/ that actually enhance user functionality and may be needed, I
> wrote a helper function that automatically installs these if the user
> wants, as a convenience so users dont have to install them manually on
> their own. However, no I get this error:
>
> ERROR: Remove install() calls (found 2 times)
>
> 3. Minor but still: Can I use Biochceck also for the devel branch? I get
> the following warning because I am checking the devel version and not
> the release version:
>
> WARNING: y of x.y.z version should be even in release
>
> ***Thanks for your input and thoughts!****Christian*
>
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