"Error in file(file, "r") : cannot open the connection" - r

I'm trying to conduct CFA but suddenly this error appear and now I cannot use r anymore since no metter what data I use it always give me the "Error in file(file, "r") : cannot open the connection".
This is the code that I'm using right now:
data
data <- read.delim("C:/Users/Nyname/Desktop/data.txt")
View(data)
model
overall_data <- '
f1 =~ item_3 + item_4 + item_12 + item_16
f2 =~ item_1 + item_5 + item_9 + item_14 + item_18
fit
overall_datafit <- cfa(overall_data, data=data, meanstructure = TRUE)
Error in file(file, "r") : cannot open the connection
I'v tried to change the directory, using setwd() and to unistall and install but nothing seems to work. I really hope somebody can help me because I've no idea what to do next and I really need to finish my work.
Thank you

I also came across similar kind of error when I worked on windows, and was not able to resolve what was the problem with my code.
If you are windows below will help, as I finally found out what the problem actually was:
When you name your file "blabla.txt" then windows name it "blabla.txt.txt"... That's the same with .CSV files so windows create a file named "bla.csv.csv" if you called it "bla.csv"
So, when you create your .txt file, just rename it "data" and open it in R using data <- read.delim("C:/Users/Nyname/Desktop/data.txt")
It worked for me.

It is a bit late for answering this question, but others may also face it.
It is possible that you have loaded another package that masks the function cfa() from lavaan (e.g., package "sem" or other packages that require it such as "faoutlier"). If so, you will face this error.
If this is the case, using lavaan::cfa() instead of cfa() should resolve the problem.

Related

R/ RStudio: Error in file(file, "r") : cannot open connection // German // Macbook Air

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.

Error in file(con, "w") : cannot open the connection [Using R-Studio to plot interactive bar graphs using rCharts, knitr]

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.

R {ape} clustal cannot find clustalw2

I am a beginner in R.
I would like to use R clustal function in package ape to process my DNA sequence, so I can us {pegas} to perform further analysis.
However, when I first try the example provided in the manual:
clustal(woodmouse, pw.gapopen = 1, pw.gapext = 1, exec = "clustalw2")
But I got an error message:
/bin/sh: clustalw2: command not found
Error in file(file, "r") : cannot open the connection. In addition: Warning massage: In file(file, "r") : cannot open file '/var/folders/vm/fzyykk3x21g55fdvpctj7s900000gn/T//Rtmp0RjsMr/input_clustal.aln' :No such file or directory
I would like to know how to fix this problem? By the way, the OS I use is Mac OS 10.9. Thank you.
Make sure that you have clustalw2 installed. Download *.msi from here:
http://www.clustal.org/download/current/
Then run
require(ape)
fix(clustal)
Make sure that the following part of the clustal function:
shortPathName("C:/Program Files/ClustalW2/clustalw2.exe")
...matches the placement of clustalw2.exe in your system perfectly. Also exhange all the "/" with "\".
Hope that works - worked for me...

Error in ls(envir = envir, all.names = private)?

The below error keeps coming up inconsistently when I try to read excel files into R using the 'XLConnect' package.
Error in ls(envir = envir, all.names = private) :
invalid 'envir' argument
I have actually run into this error while even using other packages that read excel files like package 'xlsx' and 'xlsReadWrite'. Many times restarting the R session solves this problem, which leads me to think that something else I am doing in my R session is changing the environment and not allowing me to load excel files anymore. Below is the latest example of code that is causing this error. In this case I know that the following coding sequence is causing the error to appear - but why is that happening? And how can I get past this error if I need the chron package.
library("XLConnect")
wb2 <- loadWorkbook("excel_file", create = FALSE)
library(chron)
wb2 <- loadWorkbook("excel_file", create = FALSE)
Anyone else run into this issue before? Any help on this issue is greatly appreciated!
Before reopening the workbook try removing the reference to previously opened one, so:
rm(wb2)
wb2 <- loadWorkbook("excel_file", create = FALSE)
Also, make sure that "excel_file" is not open by excel or any other program while you run the R test.
I've seen the same error come up when using XLConnect and the above seemed to help.
Had this problem a couple of times and the call stack looks like this message is generated when a "OutOfMemory" Exception is thrown.
To solve this problem I used:
options( java.parameters = "-Xmx4g" )
to increase the heap size rJava is able to use.
Debugging with options(error=utils::recover) helped a lot, because the R error messages are not very specific.

Using R package BerkeleyEarth

I'm working for the first time with the R package BerkeleyEarth, and attempting to use its convenience functions to access the BEST data. I think maybe it's just a problem with their servers (a matter I've separately addressed to the package's maintainer) but I wanted to know if it's instead something silly I'm doing.
To reproduce my fault
library(BerkeleyEarth)
downloadBerkeley()
which provides the following error message
trying URL 'http://download.berkeleyearth.org/downloads/TAVG/LATEST%20-%20Non-seasonal%20_%20Quality%20Controlled.zip'
Error in download.file(urls$Url[thisUrl], destfile = file.path(destDir, :
cannot open URL 'http://download.berkeleyearth.org/downloads/TAVG/LATEST%20-%20Non-seasonal%20_%20Quality%20Controlled.zip'
In addition: Warning message:
In download.file(urls$Url[thisUrl], destfile = file.path(destDir, :
InternetOpenUrl failed: 'A connection with the server could not be established'
Has anyone had a better experience using this package?
The error message is pointing to a different URL than one should get judging what URLs are listed at http://berkeleyearth.org/data/ that point to the zip formatted files. There are another set of .nc files that appear to be more recent. I would replace the entries in the BerkeleyUrls dataframe with the ones that match your analysis strategy:
This is the current URL that should be in position 1,1:
http://berkeleyearth.lbl.gov/downloads/TAVG/LATEST%20-%20Non-seasonal%20_%20Quality%20Controlled.zip
And this is the one that is in the package dataframe:
> BerkeleyUrls[1,1]
[1] "http://download.berkeleyearth.org/downloads/TAVG/LATEST%20-%20Non-seasonal%20_%20Quality%20Controlled.zip"
I suppose you could try:
BerkeleyUrls[, 1] <- sub( "download\\.berkeleyearth\\.org", "berkeleyearth.lbl.gov", BerkeleyUrls[, 1])

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