I am getting an error when I am trying to run the code below in R-Studio 3.3.2 on a Mac (OS Sierra)
devtools::install_github('ramnathv/rCharts')
install.packages("knitr")
require(rCharts)
require(knitr)
haireye <- as.data.frame(HairEyeColor)
n1 <- nPlot(Freq ~ Hair, group = 'Eye', type = 'multiBarChart',
data = subset(haireye, Sex == 'Male')
)
n1$save('fig/n1.html', cdn = TRUE)
cat('<iframe src="fig/n1.html" width= 100%, height=600</iframe>')
Pls see output below:
Error in file(con, "w") : cannot open the connection
In addition: Warning message: In file(con, "w") : cannot open file 'fig/n1.html': No such file or directory
But I am able to generate the reqd bar graph in the viewer when I use:
n1$show(cdn = TRUE)
in lieu of n1$save('fig/n1.html', cdn = TRUE)
To take care of write permission issues (if any), I also tried including the line below, altering the WD path wherever necessary.
knitr::knit2html('Users/documents/n1.html')
But it did not help. I see the n1.html file created but it only opens an empty browser.
Any help to resolve this is appreciated.
Best,
S
A lot of times we face this error due to caching in RStudio and in that case, actual code errors don't show up. Restart RStudio and this error will be gone and actual code errors would show.
You have two separate problems.
The connection error appears because the fig/ folder does not exist. Create the folder and the save command will work. R has functions to check the existance of directories and create new ones if you would like to do it in your code.
The second problem comes from the way you save, you should use n1$save('fig/n1.html', standalone = TRUE). Here you have a similar situation.
As a side-note, I would say rCharts is not currently developed or mantained at all, so I would recommend you to use another library for your charts. In my opinion Plotly is quite nice. rCharts brought the NVD3 project to R and the chart style is in my opinion really nice. However, as far as I know both projects are stopped so I would look for a library that is still alive.
I have fixed this problem with good old rm(list=ls()) . I know I have
fallen into sequences where the error stops execution of my script. I fix the error, and then it won't run. This is likely due to lazy evaluation but it is a near impossible problem to diagnose, so the solution at the top works almost all the time.
Related
I have graph output in the R/Radian console and in Jupyter, Jupyterlab, and VS Code notebooks. I also get the Rplots.pdf sent to the working directory as expected. However, I don't get embedded "pop-up" graph output when running R scripts in the VS Code editor e.g. filename.R. I always get this error message from CodeStream.
WebviewPanel: FAILED posting webview/editors/didChangeVisible to the webview; Webview is invisible and can't receive messages.
I've read a few SO questions on the Webviews, but they seem to be related to web/JSON loading issues and not R plots.
Seems I am missing a setting or package that pushes the Webview out.
Example code block if needed.
data("mtcars")
cars <- mtcars
print(nrow(cars))
print(head(cars, 10))
x <- c(0:10)
plot(x, sin(x))
I'm trying to do a confirmatory factor analysis on R for the first time.
I've researched this error and nothing helped so far (changing the working directory and so on).
Creating my model worked. But when I try to run the "fit" I get the error with
"Error in file(file, "r"): cannot open connection".
My first data frame is saved in "downloads" folder of my Mac. But I'm working with data Frame "data4" which is saved in a different folder. data4 is in the same folder as the whole project. It seems like the error has something to do with the path.
I also tried:
fit <- cfa(model, data = "~/Documents/BACHELORARBEIT/Daten/data4.RData, missing = "ML")
instead of:
fit <- cfa(model, data = data4, missing = "ML")
but I still get the same error message.
thank you in advance!!!
It seems you have set up the wrong working direction.
The easiest Solution would be to put all your files and the script in the same folder and just use on the toolbar:
Session -> Set working direction ->to source file.
Or check this post and see it can
help.
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.
When I want to create the map using the gvisGeoMap() from googleVis, I get error:
## Using the google visualization API with R
library(googleVis)
input<- read.csv("data.csv")
select<- input[which(input$Subgroup=="Total 5-14"),]
select<- input[which(input$Subgroup=="Total 5-14 yr"),]
Map<- data.frame(select$Country.or.Area, select$Value)
names(Map)<- c("Country", "Percentage")
Geo=gvisGeoMap(Map, locationvar="Country", numvar="Percentage",
options=list(height=350, dataMode='regions'))
plot(Geo)
#starting httpd help server ... done
#Error in ifelse(interactive(), getOption("browser"), "false") :
#replacement has length zero
The above is the error in the "RGui". The error message in "RStudio" is differet:
#object of type 'closure' is not subsettable
and the browser does not fire at all. The HTTP server works fine since I can simply call help pages.( for example ?googleVis will fire up the browser and give the help page). The "Geo" object in the code above is fine and contains the html code only that the plot() does not do what it is supposed to do (I can manually run the html file in the temp folder and see the results). The example above is available here.
I would appreciate your clues.
Thank you
This is the result of correspondance with the the Authors of the packages. It seems that there was a bug that prevented the plot to work properly. The released a new version. You can find the link below.
TQ
.....
Yesterday evening I realised that with version 0.3.0 of googleVis I unfortunately introduced a bug in RStudio and R on Windows.
The bug has been fixed already and a new version (0.3.1) is available from our project site (here is the link), but not on CRAN yet.
I have put a note on my blog (here is the link) to inform others as well.
I hope this helps.
Best regards
Markus
I have a R Job that is submitted to the condor, The R file(one.R) which is submitted to the condor is reading another R file(two.R), when I submit the job to the condor its is failed and the reason for that is the submitted R(one.R) file is not reading the called R file(two.R)
Error in text file is :
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'C:/Users/pcname/Desktop/test_case/two.R': Permission denied
Execution halted
and my submit file is
#test_input.condor
#
executable = C:\R\R-2.10.1\bin\Rscript.exe
arguments = one.R
universe = vanilla
getenv = true
#requirements = ARCH == "INTEL" && OPSYS == "WINNT60"
input = one.R
should_transfer_files = yes
transfer_executable = false
when_to_transfer_output = ON_EXIT
transfer_input_files = C:/Users/OmegaAdmin/Desktop/test_case/two.R
log = test_input.log
output = test_input.out
error = test_input.err
queue
Appreciate any ideas on this.
Thanks,
This is not an R-related problem, but a problem of accessibility. The error message seems rather clear to me: the server has no reading rights for that file. Make sure you share the file or folder you want to read in. I don't know what the setup is of the network and clusters wherever you're located, but you better contact the admins to ask how you get your files to the right places.
Also make sure that if you transfer files to the servers/cluster, you adapt your R script so it points to the right directories. Which is probably not your own harddrive...
When you say
transfer_input_files = C:/Users/OmegaAdmin/Desktop/test_case/two.R
That tells Condor to copy two.R into the current working directory when the job starts. The current working directory is a specially created workspace, not (usually) a home directory. Thus I would expect the full path to look something like
C:/condor/execute/dir_28412/two.R
However, R is actually looking in
C:/Users/pcname/Desktop/test_case/two.R
Why is R looking there? Does one.R potentially say "Find two.R in $HOME/Desktop/test_case"? Does it perhaps say, "Look in Desktop/testcase/two.R" and R has configuration that wants to look relative to the user's home directory?
The solution is almost certainly to modify one.R or your R configuration to look for two.R in the current working directory. If for some reason R changes its current working directory, the environment variable _CONDOR_SCRATCH_DIR should contain it.
On a related note, you said:
arguments = one.R
input = one.R
The first is an argument passed to Rscript.exe, which I'm guessing tells R to load and run a file called one.R. Except that script isn't present! If you want that to work, you'll need to add it to transfer_input_files. But it obviously appears to work; why? Because "input=one.R" means "take the contents of one.R and pipe it in as standard input to Rscript.exe; the same as if you'd typed those contents in." I'm guessing you can remove the arguments, or remove the input and add one.R to your transfer_input_files, removing the ambiguity.