I am trying to get R and NetLogo to talk to each other using the r extension. I am passing graph objects rather than simply variables. This means I need to export a file from NetLogo and import a file in R, which means they need to point to the same directory. The code runs perfectly. However, once it is run, NetLogo loses the connection to the extensions folder.
It appears to be related to setting the working directory in R because the following MWE also creates the problem.
extensions [r]
to testSETWD
r:eval "setwd(\"C:\")"
end
After running this successfully, then trying to do any edits to the NetLogo, I get the error Can't find extension ....
As long as I don't try to edit after running the R code, NetLogo continues to work and I can use the extensions without problems. The problem only arises when I edit the code and run the syntax parser (green tick).
I have done a bug report, but it is apparently not reproducible. I am running Windows 8.1 64bit. Is this a problem for anyone else?
I found something similar when using the r extension in NetLogo.
I simply reset to the original working directory.
For example:
;retain old working directory
r:eval "oldWD <- getwd()"
;The code you are running. ie.
r:eval "setwd(\"C:\")"
r:put "something" NetLogoSomething
r:eval "ReturnedThing <- SomethingElse(something)"
;And then reset the working directory:
r:eval "setwd(oldWD)"
Related
I'm using visual studio code to program in R and I have recently had trouble using the ?func and ??func command.
When typing something like ?rnorm, the message Couldn't show help for path: /library/stats/html/Normal.html shows up. The path is there and I'm sure R is in the path environment. This is really boggling me.
When I first installed R it was working absolutely fine in VSC but now it does not work. However the function works in the R shell. When I try to navigate to the R extension and click on "Help Topics by Package" it says help provider not available.
The packages/html files are there, but VSC doesn't want to access them.
Please advise what I can do to solve this.
I solved the same issue by checking my environmental variables. The steps I followed:
I added the bin installation file (C:\R\R-4.1.3\bin in my case, or C:\Program Files\R\R-4.1.3\bin) to the path in my user environmental variables. If you have an admin account, then you have to add the bin folder to the system environmental variables.
Check if you can start a R console from any terminal.
If that is positive, then in the Rpath settings for the R extension in vscode write r, or in the settings.json: "r.rpath.windows":"r"
Restart vscode. Check if the help pages are working.
Hope this helps ! Cheers.
This happened to me as well. I googled and tried different things and this works for me:
You need to provide the Rpath for the system you are using in the settings for the vscode R package. For example, for a windows machine, you need C:\Program Files\R\R-4.1.3\bin\x64\R.exe there if you installed the latest R using the default settings, and similarly for other systems.
Hope it helps!
Attempting to use the mread function to open a cpp file through R. However, when I run the script I get the following:
setwd("C:/Users/Gustavo/Documents/R/page-2018-mrgsolve-master/model")
getwd()
#> [1] "C:/Users/Gustavo/Documents/R/page-2018-mrgsolve-master/model"
library(mrgsolve)
mod <- mread("simple", "model")
#> Error: project directory 'model' must exist and be readable.
Obviously I am setting the directory to "model" itself. So why isn't R able to read it? Any help would be appreciated as I am still learning R and want to learn the mrgsolve package as well.
Additional info: R version 3.4.4. Rtools version 3.4.0. Rstudio version 1.1.463.
An adaptation to the email I sent my colleagues that were assisting me with a similar issue:
To review, I was unable to open any files through RStudio because RStudio returned error messages indicating either that the file itself or the work directory did not exist. I've done multiple installations of different versions of R, RStudio, and Rtools in an attempt to resolve the issue. I also moved the locations of files and programs of interest and changed the work directory to see if that made a difference. Unfortunately, when RStudio is first initiated on a computer, it establishes a "hidden directory" folder that retains the settings of the program when it was first initiated. However, by deleting this folder, RStudio was wiped and I was able to regain control of where files would be stored and read as desired (more on this in the following link: https://support.rstudio.com/hc/en-us/articles/200534577-Resetting-RStudio-Desktop-s-State). A combination of this and forcing Rtools to the front of the 'path' also allowed me to resolve 'status 127' errors that I was receiving as well.
Unfortunately, this is the result of a more personal issue between the initial settings that RStudio took to my computer and my attempt to manipulate where RStudio should read files which I guess were discordant of one another? Regardless, it seems that I would need to be more cognizant of how RStudio establishes a folder which retains its initial settings.
I cannot run a R session from the command line by typing 'R', despite having
C:/Program Files/R
and
C:/Program Files/R/R-3.3.2/bin
in both 'Path' (System) and 'PATH' (User) environment variables (the latter directory is where the actual application is located, I was just trying everything by adding the former).
If I manually change the working directory to C:/Program Files/R/R-3.3.2/bin and type R, a session runs.
Any insight as to why this might be the case? Other programs such as Python 3 run fine, provided the the environment variable is set, why not with R?
This question is part of a larger problem where I am trying to get rpy2 working, but though successfully installed, none of it's basic functions are working, and I thought this maybe to do with a version of R being installed at C:/Users/Anaconda2/R (Because this dir was in Path). The R application installed here would not work when opened, but was the directory returned when I typed R RHOME into cmd - despite the fact this installation is not even functioning, and has apparently only existed since I installed rpy2 a couple of hours ago. I reasoned that rpy2 is trying to use the instance of R installed here rather than my normal one, thus causing the error when I call robjects.r. But this still doesn't explain why I can't run R from cmd. When using R.home(component = "home") from inside a an R session (in RStudio or out of it), it returns my normal, working R directory, at C:/PROGRA~1/R/R-33~1.2. By moving the R file tree installed in Anaconda's directory to a somewhere not in Path, I hoped Windows would find the correct installation via Path - but instead I just get Failed to create process.
My last guess was that Windows didn't like the space in "Program Files", but loads of variables in Path go through the same folder. Any ideas?
I am using:
Windows 10,
R 3.3.2,
Python 2.17.13
UPDATE, PERHAPS SOLVED:
On Josh O'Brien's recommendation (thanks!), I typed where R into cmd, returning:
C:\Users\charl\Anaconda2\Scripts\R.exe
C:\Program Files\R\R-3.3.2\bin\R.exe
The first path is marginally different from the C:\Users\charl\Anaconda2\R listed in my first post (both are in Path), and leads to a third R.exe. It's outside the R file tree located in Anaconda, unlike my standard R installation, but seems to be dependent on it nonetheless. If I remove this R.exe to another location (not in Path), Typing R in cmd will run R from the desired directory, thus fixing the problem. R.home() from inside that session confirms this.
My only remaining concern then; is whether this installation of R in Anaconda necessary for rpy2 or can I just delete it, fixing the original problem? It may just be my ignorance, but I was not conscious that installing rpy2 (I used the standard Windows installer rather than compiling manually) would install another instance of R - is it necessary for the package or just a default/option I failed to omit?
When I run a Julia Script that prints "Hello World" on HTCondor, I get the following error
fatal: error thrown and no exception handler available.
Base.InitError(mod=:Pkg, error=Base.KeyError(key="HOME"))
The code runs without a problem on my local Ubuntu machine. I can run
eval julia --version
in a bash script on condor and the output is
julia version 0.5.0
This problem has been discussed in two places on github: one, two.
ENV["HOME"] is used in a single file and the common recommendation is to modify that. However, I cannot change the julia installation on condor.
Is there a way to fix this on the fly before running a script without sudo?
As #sujeet suggested, it is possible to set environmental parameters in condor. The issue is resolved by adding the following line in the condor submit script
Environment = "HOME=""/tmp"""
, which sets the home directory to the tmp. Julia code runs fine then (as long one is careful not to write to home before resetting it in the script itself).
I've just had RStudio crash on me unexpectedly, and on re-starting, contrary to what I've come to expect, the R script I had been tinkering around with was nowhere to be found.
I've managed to track down the Rhistory file so I'll be able to piece together all the commands, which is reassuring.
However, I am curious if there's somewhere I might try looking to find the temporary unsaved file on the off chance that might be cached somewhere (after all, it is usually cached somewhere that RStudio apparently knows to look). Is there a particular file extension/format I should be searching for?
Currently running R 3.3.1 through RStudio 0.99.903 on Linux Mint 17.3 (over Ubuntu 14.04.3 LTS).
I've tried running grep on the command line to find some of the more recently updated lines of code; I may be out of luck. I found two files:
~/.rstudio-desktop/history_database
Which appears to basically be a more centralized .Rhistory for RStudio
and
~/.rstudio-desktop/sdb/s-9CD2C698/D7986B2A
This looks JSON-like and also appears to basically be an Rhistory. Please correct me if I'm wrong.
As indicated by #KevinUshey from RStudio:
RStudio stores autosave data as part of the JSON 'blobs' within the sdb folder. You should see the document serialized as a long 'string', with newlines embedded.
Use packages such as jsonlite to parse this and best of luck.
if you used Rstudio on linux, the temporary R script files were stored in .rstudio/sources folder, and you can open all of the script files directly.
Good luck
In Rstudio if you saved or not a script but you ran this code, you can check the history off the app, this is the "telemetric data" that Rstudio has about you.
In windows, this is the path,
C:\Users\ANALISTA\AppData\Local\RStudio\history_database
you should use "visual studio code" or something similar to see it.