I tried to add the following line in my .Rprofile file:
options(device = quartz)
It produced an error:
Error in options(device = quartz) : object 'quartz' not found
Then I tried:
options(device = "quartz")
And it works.
However, both work in the regular R session. Can anyone tell me what is the reason for the difference in behavior?
The erro message says it all. There is no data-object named 'quartz' and the options function is not expecting (nor can it find) a function name as an argument value for the 'device'-node.
You are seeing the effect of the environment where .Rprofile is being evaluated because some of the usual packages (such as stats or graphics) are not yet loaded. Read more about this at ?Startup. You could avoid this by starting .Rprofile with require(grDevices)
Related
I got the error message:
Error: object 'x' not found
Or a more complex version like
Error in mean(x) :
error in evaluating the argument 'x' in selecting a method for function 'mean': Error: object 'x' not found
What does this mean?
The error means that R could not find the variable mentioned in the error message.
The easiest way to reproduce the error is to type the name of a variable that doesn't exist. (If you've defined x already, use a different variable name.)
x
## Error: object 'x' not found
The more complex version of the error has the same cause: calling a function when x does not exist.
mean(x)
## Error in mean(x) :
## error in evaluating the argument 'x' in selecting a method for function 'mean': Error: object 'x' not found
Once the variable has been defined, the error will not occur.
x <- 1:5
x
## [1] 1 2 3 4 5
mean(x)
## [1] 3
You can check to see if a variable exists using ls or exists.
ls() # lists all the variables that have been defined
exists("x") # returns TRUE or FALSE, depending upon whether x has been defined.
Errors like this can occur when you are using non-standard evaluation. For example, when using subset, the error will occur if a column name is not present in the data frame to subset.
d <- data.frame(a = rnorm(5))
subset(d, b > 0)
## Error in eval(expr, envir, enclos) : object 'b' not found
The error can also occur if you use custom evaluation.
get("var", "package:stats") #returns the var function
get("var", "package:utils")
## Error in get("var", "package:utils") : object 'var' not found
In the second case, the var function cannot be found when R looks in the utils package's environment because utils is further down the search list than stats.
In more advanced use cases, you may wish to read:
The Scope section of the CRAN manual Intro to R and demo(scoping)
The Non-standard evaluation chapter of Advanced R
While executing multiple lines of code in R, you need to first select all the lines of code and then click on "Run".
This error usually comes up when we don't select our statements and click on "Run".
Let's discuss why an "object not found" error can be thrown in R in addition to explaining what it means. What it means (to many) is obvious: the variable in question, at least according to the R interpreter, has not yet been defined, but if you see your object in your code there can be multiple reasons for why this is happening:
check syntax of your declarations. If you mis-typed even one letter or used upper case instead of lower case in a later calling statement, then it won't match your original declaration and this error will occur.
Are you getting this error in a notebook or markdown document? You may simply need to re-run an earlier cell that has your declarations before running the current cell where you are calling the variable.
Are you trying to knit your R document and the variable works find when you run the cells but not when you knit the cells? If so - then you want to examine the snippet I am providing below for a possible side effect that triggers this error:
{r sourceDataProb1, echo=F, eval=F}
# some code here
The above snippet is from the beginning of an R markdown cell. If eval and echo are both set to False this can trigger an error when you try to knit the document. To clarify. I had a use case where I had left these flags as False because I thought i did not want my code echoed or its results to show in the markdown HTML I was generating. But since the variable was then used in later cells, this caused an error during knitting. Simple trial and error with T/F TRUE/FALSE flags can establish if this is the source of your error when it occurs in knitting an R markdown document from RStudio.
Lastly: did you remove the variable or clear it from memory after declaring it?
rm() removes the variable
hitting the broom icon in the evironment window of RStudio clearls everything in the current working environment
ls() can help you see what is active right now to look for a missing declaration.
exists("x") - as mentioned by another poster, can help you test a specific value in an environment with a very lengthy list of active variables
I had a similar problem with R-studio. When I tried to do my plots, this message was showing up.
Eventually I realised that the reason behind this was that my "window" for the plots was too small, and I had to make it bigger to "fit" all the plots inside!
Hope to help
I'm going to add this on here even though it's not a new question as it comes quite highly in the search results for the error:
As mentioned above, re checking syntax, if you're using dplyr, make sure you have all the %>% pipes at the end of the lines above the error, otherwise the contents of anything like a select statement won't pass down into the next part of the code block.
I have a lot of unit tests using the testthat package that expect english error messages.
If other developer run the tests on a computer configured for a non-english locale the error message are emitted in a different language and my tests fail.
How can I initialize testthat to change the language settings only during the test run-time without manually or permanently changing the language or test environment from outside of R (like e. g. proposed here: in R how to get error messages in english)?
library(testthat)
# works only in english locales...
expect_error(log("a"), "non-numeric argument to mathematical function", fixed = TRUE)
Edit 1: Changing the locale during run-time does not change the language of the error messages (using Ubuntu and OSX High Sierra):
Sys.setlocale( locale = "en_US.UTF-8")
Sys.getlocale() # en_US is active now but messages are still in another language
Edit 2: It seems that Sys.setenv("LANGUAGE"="EN") seems to change the error message language immediately (tested using OSX). Where should I put this command for testthat? In the testthat.R file?
The R console is in German language, how can I set R to English?
Edit 3: As a first work-around I have put
Sys.setenv("LANGUAGE"="EN") # work-around to always create english R (error) messages
into my testthat.R file under the tests folder (it seems to work but I am not sure whether this is the right or best way...
Setting Sys.setenv("LANGUAGE" = "EN") works for me as well.
However, when testing with devtools::test() - as ctrl + shift + T in Rstudio will do - I had to call Sys.setenv() in the test scripts inside the tests/testthat/ directory. The reason being that devtools::test() will call testthat::test_dir() circumventing the tests/testthat.R file.
So far, this did not have undesirable side-effects. The environment variable will only be set for that particular R process as described in the help page:
Sys.setenv sets environment variables (for other processes called from within R or future calls to Sys.getenv from this R process).
For completeness, you can also unset the variable again on Windows (see comments).
Sys.setenv("LANGUAGE" = "DE")
expect_error(log("a"), "Nicht-numerisches Argument")
Sys.setenv("LANGUAGE" = "FR")
expect_error(log("a"), "argument non numérique ")
Sys.unsetenv("LANGUAGE")
RStudio might also give trouble (I was not able to change the language there interactively), but when executing with devtools::test() it works.
Finally, wrapping it in a helper function.
expect_error_lang <- function(..., lang = "EN") {
Sys.setenv("LANGUAGE" = lang)
expect_error(...)
Sys.unsetenv("LANGUAGE")
}
#...
expect_error_lang(log("a"), "non-numeric")
expect_error_lang(log("a"), "Nicht-numerisches", lang = "DE")
expect_error_lang(log("a"), "argument non", lang = "FR")
I am attempting to use the plot() function in the biomod2 package, following a vignette here (http://finzi.psych.upenn.edu/usr/share/doc/library/biomod2/doc/Simple_species_modelling.pdf). Below is the error I am getting:
getwd()
# [1] "/home/gjanzen/Documents/Hufford/Drought/Data/Layers"
plot(myBiomodData)
Error in getExportedValue(pkg, name) : cannot open file
'~/R/x86_64-pc-linux-gnu-library/3.3/viridisLite/data/Rdata.rdb': No
such file or directory In addition: Warning message: In
getExportedValue(pkg, name) : restarting interrupted promise
evaluation
I have confirmed that the Rdata.rdb exists, in the following directory:
f <- file.choose()
f
# [1] "/home/gjanzen/R/x86_64-pc-linux-gnu-library/3.3/viridisLite/data/Rdata.rdb"
So, to me, it looks like the plot() function is looking in the wrong place. How can I change where this function looks for Rdata.rdb? Can I alter the path somehow? Or would changing my working directory fix this?
PS - This is my first post on Stack Overflow, so please forgive any mistakes in etiquette, and/or feel free to point them out to me so that I do not repeat them.
I think that the first thing to try is to reinstall the package viridisLite that seems to be the one that is causing troubles.
install.packages('viridisLite', dep = TRUE)
If this not solves the issue you should try to open a new plotting device threw x11() to check if the issue is not coming from the R (resp. RStudio) plotting device itself.
this question has been asked before but non of the answers is working for me.
I am using the library rhdf5 from bioconductor.org to read HDF5 files: source("http://bioconductor.org/biocLite.R"); biocLite("rhdf5"); library(rhdf5);
When I use the h5read function to read particular variables that contain references the following warning message is printed:
"Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced by NA's"
(It is not shown in red like errors and warnings in RStudio. Just in black)
The warning is OK for me as I don't need those references. But I use this function to read hundreds of variables, so my screen gets polluted with these messages.
For example:
a <-h5read(f, "/#Link2#")
Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced by NA's
Warning: h5read for type 'REFERENCE' not yet implemented. Values replaced by NA's
I have tried all suggestions I found (capture.output, suppressMessage/Warning, sink, options(warn, max.print, show.error.messages):
capture.output(a <- h5read(f, "/#Link2#"), file='/dev/null')
I also tried invisible just in case: invisible(capture.output(a <- h5read(f, "/#Link2#"), file='/dev/null'))
suppressWarnings(suppressMessages(a <- h5read(f, "/#Link2#")))
I also tried suppressForeignCheck and suppressPackageStartupMessages just in case
{sink("/dev/null"); a <-h5read(f, "/#Link2#"); sink()}
{options(warn=-1, max.print=1,show.error.messages=FALSE); a <-h5read(f, "/#Link2#") }
They all keep producing the same warning messages.
Does anyone knows any other thing I might try, or why are these things not working?
How does the library manages to print the messages skipping all these? Sounds that I might be doing something wrong...
Any help is appreciated.
Just as reference these are the other posts I used:
r: do not show warnings
How to suppress warnings globally in an R Script
suppress messages displayed by "print" instead of "message" or "warning" in R
Suppress one command's output in R
You should ask maintainer("rhdf5") to provide a solution -- print message less frequently, and use standard R warnings -- the message is from C code and uses printf() rather than Rf_warning() or Rf_ShowMessage() or Rprintf() / REprintf().
Here's an illustration of the problem
> library(inline)
> fun = cfunction(character(), 'printf("hello world\\n"); return R_NilValue;')
> fun()
hello world
NULL
> sink("/dev/null"); fun(); sink()
hello world
>
and a solution -- use Rf_warning() to generate R warnings. The example also illustrates how writing to R's output stream via Rprintf() would then allow the output to be captured with sink.
> fun = cfunction(character(), 'Rf_warning("hello world"); return R_NilValue;')
> x = fun()
Warning message:
In fun() : hello world
> x = suppressWarnings(fun())
> fun = cfunction(character(), 'Rprintf("hello world\\n"); return R_NilValue;')
> sink("/dev/null"); fun(); sink()
>
None of this helps you directly, though!
UPDATE the maintainer updated the code in the 'devel' branch of the package, version 2.17.2.
I'd like to test that a function returns the expected data.frame. The data.frame is too large to define in the R file (eg, using something like structure()). I'm doing something wrong with the environments when I try a simple retrieval from disk, like:
test_that("SO example for data.frame retreival", {
path_expected <- "./inst/test_data/project_longitudinal/expected/default.rds"
actual <- data.frame(a=1:5, b=6:10) #saveRDS(actual, file=path_expected)
expected <- readRDS(path_expected)
expect_equal(actual, expected, label="The returned data.frame should be correct")
})
The lines execute correctly when run in the console. But when I run devtools::test(), the following error occurs when the rds/data.frame is read from a file.
1. Error: All Records -Default ----------------------------------------------------------------
cannot open the connection
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls, message = function(c) invokeRestart("muffleMessage"),
warning = function(c) invokeRestart("muffleWarning"))
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: readRDS(path_expected) at test-read_batch_longitudinal.R:59
5: gzfile(file, "rb")
To make this work, what adjustments are necessary to the environment? If there's not an easy way, what's a good way to test large data.frames?
I suggest you check out the excellent ensurer package. You can include these functions inside the function itself (rather than as part of the testthat test set).
It will throw an error if the dataframe (or whatever object you'd like to check) doesn't fulfill your requirements, and will just return the object if it passes your tests.
The difference with testthat is that ensurer is built to check your objects at runtime, which probably circumvents the entire environment problem you are facing, as the object is tested inside the function at runtime.
See the end of this vignette, to see how to test the dataframe against a template that you can make as detailed as you like. You'll also find many other tests you can run inside the function. It looks like this approach may be preferable over testthat in this case.
Based on the comment by #Gavin Simpson, the problem didn't involve environments, but instead the file path. Changing the snippet's second line worked.
path_qualified <- base::file.path(
devtools::inst(name="REDCapR"),
test_data/project_longitudinal/expected/dummy.rds"
)
The file's location is found whether I'm debugging interactively, or testthat is running (and thus whether inst is in the path or not).