[Bioc-devel] BiocCheck warnings and errors
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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Resource Center for Stable Isotope Resolved Metabolomics
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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 at 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* [[alternative HTML version deleted]]
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