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.
Related
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.
I have written the Boggler package which includes a Play.Boggle() function that calls, on line 87, a progress bar script using shell:
shell(cmd = sprintf('Rscript.exe R/progress_bar.R "%i"', time.limit + 1), wait=FALSE)
Everything works fine when sourcing the files individually and then calling the main Play.Boggle() function, but when I try to check/build the package (under Win7-64 using RStudio), I get a failure message -- here's what the 00install.out reports:
** preparing package for lazy loading
Warning in eval(expr, envir, enclos) : NAs introduced by coercion
Error in time.limit:0 : NA/NaN argument
To make sure the argument "%i" (time.limit + 1) was correctly passed to the progress_bar.R, I added a cat(time.limit) to the script (commenting the rest out to make sure the package would build without any errors) and directed its output to a log file like this:
'Rscript.exe R/progress_bar.R "%i" > out.log'
Conclusion: the time limit is indeed passed along as expected. So I can't figure out why I get this "NA/NaN argument" error message. It must have something to do with lazy loading, concept that I haven't fully got my head around yet.
So my question is: what can I do to successfully check/build this package with full functionality (including progress_bar.R)?
Note: On github, the progress_bar.R script is there but all its content is commented out so that the package can successfully be installed. The shell(...) function call is still active, doing nothing but executing an empty script.
So the problem arises when trying to build or check, in which case all R scripts are executed, as pointed out by Roland. A simple workaround allows the package to check/build without any problems. The fix is just to add to the progress_bar.R the following lines after it tries to recuperate the commandargs (lines 10-11):
if(time.limit %in% c(NA, NaN))
time.limit <- 10 # or any minimal number
There's surely other ways to go about this. But this being a game programmed for fun, I'll happily go with that patch. Hopefully this can be of help to someone down the road and I won't have wasted 50 precious rep points in vain for that bounty! :D
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)
I'm learning R programming, using the book, "The Art of R Programming".
In chapter 3.2.3 Extended Example: Image Manipulation. The author Matloff tries to use a Mount Rushmore gray-scale image to illustrate that the image is stored in matrix. He used a library called pixmap. And I downloaded the package, installed it.
> library(pixmap)
> mtrush1 <- read.pnm("mtrush1.pgm")
> mtrush1
Pixmap image
Type : pixmapGrey
Size : 194x259
Resolution : 1x1
Bounding box : 0 0 259 194
> plot(mtrush1)
This is what the book has written, and I tried to run this, but got the error message,
> library(pixmap)
> mtrush1 <- read.pnm("mtrush1.pgm")
Error in file(file, open = "rb") : cannot open the connection
In addition: Warning message:
In file(file, open = "rb") :
cannot open file 'mtrush1.pgm': No such file or directory
starting httpd help server ... done
What does this mean? cannot open the connection? And also the mtrush1.pgm does not exist? How should I fix it here? Any help? Much appreciated.
Summary:
Add the argument cellres=1 to your function call and you should be fine.
Answer:
The second error you saw--Warning message: In rep(cellres, length = 2) : 'x' is NULL so the result will be NULL--is because you haven't set the cellres argument and, as a result, "cellres" assumes its default value (i.e. 'NULL'--hence the warning). For what you're working on, setting the cellres argument to 1 will do the trick (though you can pass in a two-element vector with unequal values and see just how it affects your figure by plotting the resulting object).
Note: Though it's a little late to be answering, I figure that since I had the same problem earlier today (and since Google was no help) a response was probably warranted.
This means that the file mtrush1.pgm is not in current directory. You should either setwd to the directory that contains this file, or specify the complete path in read.pnm.
For the file mtrush1.pgm, you can download it from http://heather.cs.ucdavis.edu/~matloff/
The file mtrush1.pgm and the R scripts from the book "The Art Of R Programming" can be found at this GitHub site.
I want to make colored dendrograms and have yet to find a sufficient library: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=79
This graphic/library looks promising but cannot install the A2E library?
Trying to install on windows, downloaded the tar.gz file and cannot install package from the R console.
In addition:
Warning messages:
1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
2: In gzfile(file, "r") :
cannot open compressed file 'A2R_0.0-4.tar.gz/DESCRIPTION', probable reason 'No such file or directory'
Can anyone see if they can get this A2R library working, confirm error, or suggest a good colored dendrogram library?
(It might help if you spelled it correctly.) A2R is a source package. So you might need to have the system toolchain for compilation. Those are typically in your system if you are on Linux, but not if you are on a Mac (as I am) or on Windows. The package does compile from source on a Mac. And the compilation process may not have needed the toolchain. So try this:
install.packages("<fullpath> A2R_0.0-4.tar.gz", type ="source")
There are a few other dependencies: 'trimcluster', 'prabclus' , 'MASS' , 'cluster', 'mclust', 'flexmix', 'modeltools', 'stats4', 'multcomp', 'mvtnorm'. I am able to get most of that graphic but the left side curve does not appear as shown and I did get an error:
Error in hubertgamma[i] <- cluster.stats(d.usa, cutree(h.usa, k = i + :
replacement has length zero:
If you do not want the heights of the dendrogram scaled to their depth you can add this modification to the hclust object:
h.usa$height <- log(h.usa$height)
You could use the dendrapply() function in R's built-in dendrogram code to apply custom leaf and node coloring. See the following mailing list thread for hints.