I am working on an R markdown notebook in an active renv in my R project directory. Before I had activated the environment, I could use the load function from base R without a problem. But since activating the environment, I get errors when I use load(file=abc.RData).
I have a code chunk as follows:
rm(list=ls())
library(haven)
library(dplyr)
library(data.table)
# Load complete (individual+network) data ---------------------------
load(file="/Volumes/caas/CADRE CLC Data Project5/Clean Data/AK-SU-NETWORKS-ROUT/eda.RData")
If I try to run the chunk, I get the following error:
Error in load(file = "/Volumes/caas/CADRE CLC Data Project5/Clean Data/AK-SU-NETWORKS-ROUT/eda.RData") :
unused argument (file = "/Volumes/caas/CADRE CLC Data Project5/Clean Data/AK-SU-NETWORKS-ROUT/eda.RData")
But if I knit the document, it compiles without a problem.
What might I be doing wrong?
It looks like all I had to do was specify that I wanted to use load from base, as:
base::load(file="/Volumes/caas/CADRE CLC Data Project5/Clean Data/AK-SU-NETWORKS-ROUT/eda.RData")
That seems to have fixed it.
Related
When I run "send2cy" function in R studio, I got error.
# Basic setup
library(igraph)
library(RJSONIO)
library(httr)
dir <- "/currentdir/"
setwd(dir)
port.number = 1234
base.url = paste("http://localhost:", toString(port.number), "/v1", sep="")
print(base.url)
# Load list of edges as Data Frame
network.df <- read.table("./data/eco_EM+TCA.txt")
# Convert it into igraph object
network <- graph.data.frame(network.df,directed=T)
# Remove duplicate edges & loops
g.tca <- simplify(network, remove.multiple=T, remove.loops=T)
# Name it
g.tca$name = "Ecoli TCA Cycle"
# This function will be published as a part of utility package, but not ready yet.
source('./utility/cytoscape_util.R')
# Convert it into Cytosccape.js JSON
cygraph <- toCytoscape(g.tca)
send2cy(cygraph, 'default%20black', 'circular')
Error in file(con, "r") : cannot open the connection
Called from: file(con, "r")
But I didn't find error when I use "send2cy" function from terminal R (Run R from terminal just calling by "R").
Any advice is welcome.
I tested your script with local copies of the network data and utility script, and with updated file paths. The script ran fine for me in R Studio.
Given the error message you are seeing "Error in file..." I suspect the issue is with your local files and file paths... somehow in an R Studio-specific way?
FYI: an updated, consolidated and update set of R scripts for Cytoscape are available here: https://github.com/cytoscape/cytoscape-automation/tree/master/for-scripters/R. I don't think anything has significantly changed, but perhaps trying in a new context will resolve the issue you are facing.
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.
I am trying to run code chunks in my markdown document. I have an R script that runs all the code that I need without any issues. Then, when I copy and paste the code into the markdown document, the code will run within the chunk, but will fail when trying to knit into an output document (html/pdf).
I had to create a safe.ifelse function to prevent r from converting my dates to a numeric format as discussed here.
The error appears to be with the code:
safe.ifelse = function(cond, yes, no){structure(ifelse(cond, yes, no), class = class(yes))
}
The error message I get is:
Line 121 Error in structure(ifelse(cond,yes,no), class = class(yes)) : could not find function "days" Calls: ... transform.data.frame ->eval->eval-> safe.ifelse-> structure Execution halted
The line of code following my safe.ifelse function is
seminoma1 = transform(seminoma1, recur.date = safe.ifelse(salvage.tx=="Yes",
date.diagnosis + days(pmax(time.rad, time.chemo, na.rm=TRUE)), NA))
Any help would be appreciated. Thanks.
I'm still too new to comment, but the only time I get an error like that is when I forget to define a function/variable or forget to source a package.
Since days() isn't part of R's base package, I think you need to add:
```{r echo = FALSE}
library("lubridate")
```
I have two data sets full and raw that I placed in the data/ directory of my package. However, when I load my package, they are not available. I tried looking for them using the data function, but did not see them.
data(raw, package = "pkg")
Warning message:
In data(raw, package = "pkg") : data set 'raw' not found
Do I have to export them somehow?
I noticed when I tried to open the file using load from another computer, it read in as a string. Maybe I'm not writing the data frame properly? I used:
save(df.full, file = "full.RData")
save(df.raw, file = "raw.RData")
I am trying to run an R script from the Windows command prompt (the reason is that later on I would like to run the script by using VBA).
After having set up the R environment variable (see the end of the post), the following lines of code saved in R_code.R work perfectly:
library('xlsx')
x <- cbind(rnorm(10),rnorm(10))
write.xlsx(x, 'C:/Temp/output.xlsx')
(in order to run the script and get the resulting xlsx output, I simply type the following command in the Windows command prompt: Rscript C:\Temp\R_code.R).
Now, given that this "toy example" is working as expected, I tried to move to my main goal, which is indeed very similar (to run a simple R script from the command line), but for some reason I cannot succeed.
Again I have to use a specific R package (-copula-, used to sample some correlated random variables) and export the R output into a csv file.
The following script (R_code2.R) works perfectly in R:
library('copula')
par_1 <- list(mean=0, sd=1)
par_2 <- list(mean=0, sd=1)
myCop.norm <- ellipCopula(family='normal', dim=2, dispstr='un', param=c(0.2))
myMvd <- mvdc(myCop.norm,margins=c('norm','norm'),paramMargins=list(par_1,par_2))
x <- rMvdc(10, myMvd)
write.table(x, 'C:/Temp/R_output.csv', row.names=FALSE, col.names=FALSE, sep=',')
Unfortunately, when I try to run the same script from the command prompt as before (Rscript C:\Temp\R_code2.R) I get the following error:
Error in FUN(c("norm", "norm"))[[1L]], ...) :
cannot find the function "existsFunction"
Calls: mvdc -> mvdcCheckM -> mvd.has.marF -> vapply -> FUN
Do you have any idea idea on how to proceed to fix the problem?
Any help is highly appreciated, S.
Setting up the R environment variable (Windows)
For those of you that want to replicate the code, in order to set up the environment variable you have to:
Right click on Computer -> Properties -> Advanced System Settings -> Environment variables
Double click on 'PATH' and add ; followed by the path to your Rscript.exe folder. In my case it is ;C:\Program Files\R\R-3.1.1\bin\x64.
This is a tricky one that has bitten me before. According to the documentation (?Rscript),
Rscript omits the methods package as it takes about 60% of the startup time.
So your better solution IMHO is to add library(methods) near the top of your script.
For those interested, I solved the problem by simply typing the following in the command prompt:
R CMD BATCH C:\Temp\R_code2.R
It is still not clear to me why the previous command does not work. Anyway, once again searching into the R documentation (see here) proves to be an excellent choice!