I googled, found this; accordingly, ran test_dir() (it errors), tried test_dir(getwd()) from the package root (it also errors). I also tried test_package(), but it also errors if the argument is left NULL or returns nothing if the package name is provided as a string.
Question
How do you quickly run all tests in a package from the R console (assuming getwd() is at the package root)?
Note
I know you can R CMD check but I don't need the other checks, just the tests
You simply run
devtools::test()
Note there are also some other methods here
Related
R CMD check automatically runs tests located in tests/ directory. However running the tests this way requires building the package first. After that R CMD check goes through various different sanity checks before finally reaching the tests at the end.
Question: Is there a way to run those tests without having to build or install the package first?
NOTE: without using testthat or other non-standard packages.
To summarise our discussion.
To my knowledge there is no standard alternative to R CMD check for unit testing provided by base R
Typically for unit testing, I source everything under R/ (and dyn.load everything under source/) and then source everything under tests/ (actually, I also use the Example sections of the help pages in the man/ directory as test cases and compare their outcome to those from previous package versions)
I assume that these are the basic testing functionalities provided by devtools and testthat. If you expect to develop multiple packages and want to stay independent from non-base-R, I'd recommed to automate the above processes with custom scripts/packages.
I'd recomment looking into http://r-pkgs.had.co.nz/tests.html.
I'm writing a package containing several functions to make running and evaluating models more streamlined.
I have a function that I'm going to make the first function within my package detailed with roxygen2 comments, which I can include into this write-up as an edit if necessary, but my issue is more with Package Creation.
I've created a separate .R file for the function and it lives within the R folder in within my package folder. I've run R CMD build pkgname and R CMD INSTALL pkgname successfully.
At the document() stage I run it (from console or whether in my terminal using R -e 'library(devtools);document()', deleting the existing NAMESPACE file first) and I get the following error: Try removing ‘/Library/Frameworks/R.framework/Versions/ 3.5/Resources/library/00LOCK-pkgname.
I've already seen the [issue posted here][1] and haven't had success after deleting the 00LOCK-pkgname folder, for two reasons: when I run document(), even when it throws the above error, it doesn't stop running, it just keeps looping (that happens whether I run this in R or use the Terminal). Additionally, no matter how many times I delete the folder, it keeps re-appearing even though I've stopped running the function.
Any insight into why that error is being thrown and the document() function continually runs in a loop?
Best answer I've found is in this blog post: Hilary Parker R-Package Blog Post
The steps I follow to document and install are as follows:
Within the project that contains my package, open a new R Script and run setwd('..')
Run devtools::document()
Run devtools::install()
This works for me when initially installing my package and also updating it.
I'm new to R and I'm having some trouble to get the testthat unit test package work via devtools::test().
I've setup a package and created a test case under the .\tests\testthat folder. My R source code files are located at .\R.
When I run:
testthat::test_dir("./tests/testthat/")
The test ran successfully.
However when I tried to run the test via
devtools::test()
Instead of running the test cases, it tried to run my source code files located under .\R.
How can I get devtools::test() to just run my test cases?
Thank you for your help.
BTW, there is little documentation about how to setup and use testthat which is very frustrating as a new R user.
test() (re)loads your package before running your tests. That's why you see your package source code being executed.
I'd like to profile functions in an installed R package (data.table) using Rprof() with line.profiling=TRUE. Normally, installed package are byte compiled, and line numbers are not available for byte compiled packages. The usual instructions for line profiling with Rprof() require using source() or eval(parse()) so that srcref attributes are present.
How can I load data.table so that line numbers are active? My naive attempts to first load the package with library(data.table) and then source('data.table.R') fails because some of the compiled C functions are not found when I attempt to use the package, presumably because library() is using a different namespace. Maybe there is some way to source() into the correct namespace?
Alternatively, perhaps I can build a modified version of data.table that is not byte compiled, and then load that in a way that keeps line numbers? What alterations would I have to make, and how would I then load it? I started by setting ByteCompile: FALSE and then trying R CMD INSTALL -l ~/R/lib --build data.table, but this still seems to be byte compiled.
I'm eager to make this work and will pursue any suggestions. I'm running R 3.2.1 on Linux, have full control over the machine, and can install anything else that is required.
Edit:
A more complete description of the problem I was trying to solve (and the solution for it) is here: https://github.com/Rdatatable/data.table/issues/1249
I ended up doing essentially what Joshua suggested: recompile the package with "KeepSource: TRUE" in the DESCRIPTION. For my purposes, I also found "ByteCompile: FALSE" to be helpful, although this might not apply generally. I also changed the version number so I could see that I was using my modified version.
Then I installed to a different location with "R CMD INSTALL data.table -l ~/R/lib", and loaded with "library(data.table, lib='~/R/lib')". When used with the patches given in the link, I got the line numbers of the allocations as I desired. But if anyone knows a solution that doesn't require recompilation, I'm sure that others would appreciate if you shared.
You should be able to get line numbers even if the package is byte-compiled. But, as it says in ?Rprof (emphasis added):
Individual statements will be recorded in the profile log if
line.profiling is TRUE, and if the code being executed was
parsed with source references. See parse for a discussion of
source references. By default the statement locations are not
shown in summaryRprof, but see that help page for options to
enable the display.
That means you need to set KeepSource: TRUE either in the DESCRIPTION file or via the --with-keep.source argument to R CMD INSTALL.
I'm working on my first package (GitHub). Pretty basic. Two functions.
R CMD INSTALL --no-multiarch --with-keep.source qualtricsR
library(qualtricsR)
Works fine as far as I can tell. Running check in RStudio results in a final message of R CMD check succeeded.
However, when I try to run my functions (e.g., template <- importTemplate("inst/doc/template.xlsx")), I get an error that R cannot find my function. ?importTemplate shows my help page.
#jablacalle and #mdsumner put me on the right track.
Adding export(importTemplate) and export(writeQtxt) to NAMESPACE did the trick. running devtools::document() automated this process once I added #' #export before the function in my .R file.