I'm trying to test a function of mine with the testthat package. The function is supposed to create an excel file, and I want to test if that excel file exists and contains the things it's supposed to contain. I tried running the function to create a simple mockup excel file and then reading in the output again, but that seems to not do anything, I'm guessing because of the localized testing environment. I also feel like writing code outside of the tests is not a good idea since it gave me a warning message about it.
Is there a way to test an external output with testthat that I don't know about? I'm new to unit testing and this package so any help would be appreciated.
I actually solved this myself by accident: code run in test_that DOES produce output, just in the test folder. I could read it from there and then test.
I'm trying to setup the testthat unit test framework and having some trouble to get the source file location right.
My package folder structure is like below:
.\R\abc.R
.\R\def.R
.\tests\testthat\test_01.R
In my test case file test_01.R, I need to import abc.R. I managed to get this working by specifying a relative path like below:
'../../R/abc.R'
Now the abc.R file can be sourced successfully from my test cases. However, it failed at the step where abc.R tries to source def.R. I think this is because the working directory is set to ./tests/testthat by testthat.
The fix I can think of is to add a relative path '../../R/' to def.R, but this looks to me like a terrible solution as it will break when I run abc.R directly. And also there are a lot more files like abc.R and def.R in my package.
Is there a more graceful way to handle this?
Sorry if this is a straightforward question as I'm still new to R.
Inside ./tests/ there should be a file named testthat.R
Within this file you can add 3 lines:
library(testthat)
library(yourLibraryName)
test_check("yourLibraryName")
Of course replace "yourLibraryName" with the name of your package.
Then all the functions exported by your package will be loaded and tests will be able to use them.
So I'm rather new to R, and I'm learning how to mine text from this handy website: https://eight2late.wordpress.com/2015/05/27/a-gentle-introduction-to-text-mining-using-r/
I do have my own text set of .doc, .docx, and .xlsx files and I'm trying to mine them. They're located in a folder in my working directory called 'files', but I have already encountered an error after simply writing a few lines of code.
The code I have so far is:
library(tm)
library(readtext)
data = readtext('files')
At this point, after waiting for 25 seconds or so, I get the error:
Error: System call to 'antiword' failed (1): The Big Block Depot is damaged
and the code stops running there.
I have tried searching online for solutions but it seems like a fairly rare error and so I only found 1 possible solution at https://github.com/ropensci/antiword/issues/1 but that did not work for me.
This solution suggested that one of my files were corrupt, and suggested using the code
fixInNamespace(antiword, pos="package:antiword")
to change the error to a warning to not interrupt the reading of the files. I tried that, and at first it raised the error of
Error in as.environment(pos):
no item called "package:antiword" on the search list
After which, I loaded the antiword library with a library(antiword) and changed the stop( to a warning(. However, when I ran the data = readtext('files') line again, it immediately raised the error
Error in is_windows() : could not find function "is_windows"
I'm at a loss here! Any help would be appreciated. Should I be using another package in this case?
I had the same problem with my code, where I tried to get a doc. file in R. I also used the readtext library. What helped me was converting the Word documents I was trying to get into R from doc. to docx. When I ran the same code after it worked.
I am just starting to explore the rmarkdown package. I don't use Rstudio. I use the default R environment. What I did was as follows.
I created a new R document.
Started typing few lines in rmarkdown format.
Saved the file with Rmd extension.
I saved the file in the working directory.
I installed the pandoc using the pkg file.
I installed 'rmarkdown' package. Loaded the package.
Used the following command to render the Rmd file.
rmarkdown::render("Untitled.Rmd")
I get the following error.
Error in tools::file_path_as_absolute(input) : file 'Untitled.Rmd'
does not exist
I tried all the possible ways such as giving the exact path instead of filename etc. But nothing worked out. I googled the error message and found that none had similar error. Can someone help me with this. What I am missing. What the error message mean?
Most of the time the error file not found is either a type error or a real missing file (as in your case, the real one is named in another way).
In order to discard those possibilities:
Copy the fullpath from your filebrowser.
Make sure the file exists, inside R you could type:
file.exists("/fullpath/to/file")
If that return TRUE and the error persists, then you suspect another thing is going on.
I want to find the location of the script .R files which are used for computation in R.
I know that by typing the object function, I will get the code which is running and then I can copy and edit and save it as a new script file and use that.
The reason for asking to find the foo.R file is
Curiosity
Know what is the algorithm used in the numerical computations
More immedietly, the function from stats package I am using, is running results for two of the arguments and not the others and have to figure out how to make it work.
Error shown by R implies that there might be some modification required in the script file.
I am looking for a more general answer, if its possible.
Edit: As per the comments so far, here is the code to compute spectrum of a time series using autoregressive methods. The data input is a univariate series.
x = ts(data)
spec.ar(x, method = "yule-walker") 1
spec.ar(x, method = "burg") 2
command 1 is running ok.
command 2 gives the following error.
Error in ar.burg.default(x, aic = aic, order.max = order.max, na.action = na.action, :
Burg's algorithm only implemented for univariate series
I did try specify all the arguments correctly like na.action=na.fail, order.max = NULL etc but the message is the same.
Kindly suggest possible solutions.
P.S. (This question is posted after searching the library folder where R is installed and zip files which come with packages, manuals, and opening .rdb, .rdx files)
See FAQ 7.40 How do I access the source code for a function?
In most cases, typing the name of the function will print its source
code. However, code is sometimes hidden in a namespace, or compiled.
For a complete overview on how to access source code, see Uwe Ligges
(2006), “Help Desk: Accessing the sources”, R News, 6/4, 43–45
(http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf).
When R installs a package, it evaluates all the ".R" source files and re-saves them into a binary format for faster loading. Therefore you typically cannot easily find the source file.
As has been suggested elsewhere, you can simply type the function name and see the source code, or download the source package and find the source there.
library(plyr)
ddply # prints the source for ddply
# See the content of the R directory for plyr,
# but it's only binary files:
dir(file.path(find.package("plyr"), "R"))
# [1] "plyr" "plyr.rdb" "plyr.rdx"
# Get the source for the package:
download.packages("plyr", "~", type="source")
# ...then unpack and inspect the R directory...
.libPaths() should tell you all of your current library locations. It's possible to have more than one installation of a package if there are two libraries but only the one that is in the first library will be used. Unless you offer the code and the exact error message, it's not likely that anyone will be able to offer better advice.
I think you are asking to see what I call the source code for a function in a package. If so, the way I do it is as follows, which has worked successfully for me on the three times I have tried. I keep these instructions handy in a few places and just copied and pasted them here:
To see the source code for a function in Program R download the package containing the function. Specifically, download the file that ends in "tar.gz". This is a compressed file. Expand the compressed file using, for example, "WinZip". Now you need to open the uncompressed file that ends in ".tar". Download the free software "7-Zip". Click on the file "7zFM.exe" and navigate to the directory containing the ".tar" file. You can extract the contents of that ".tar" file into a new folder. The contents consist of R files showing the source code for the functions in the R package.
EDIT:
Today (July 8, 2012) I was able to open the 'tar.gz' file using the latest version of 'WinZIP' and could copy the contents (the source code) from there without having to use '7-Zip'.
EDIT:
Today (January 19, 2013) I viewed the source code for functions in base R by downloading the file
'R-2.15.2.tar.gz'
To download that file go to the http://cran.at.r-project.org/ webpage and click on that file in this line:
"The latest release (2012-10-26, Trick or Treat): R-2.15.2.tar.gz, read what's new in the latest version."
Unzip the file. WinZip will work, or it did for me. Then search your computer for readtable.r or another base R function.
agstudy noted here https://stackoverflow.com/questions/14417214/source-file-for-r-function that source code for read.csv is located in the file readtable.r, so do not expect every base R function to have its own file.