Lately I'm having a strange problem with RStudio (v1.3.1056 on Ubuntu 18.04): When I try to open some text files, RStudio refuses with the message file is binary rather than text:
Yet, the file I'm trying to open is definitely a text file. As an example, take this bibtex file:
#misc{test,
author = {test},
year = {2018},
title = {test},
}
When I try to open it with the file name "test.bib", I get the error above. When renaming it to "test.txt" RStudio opens it without complaining. Here the steps as R code:
rstudioapi::navigateToFile("test.bib") # won't work
file.copy("test.bib", "test.txt", overwrite = TRUE)
rstudioapi::navigateToFile("test.txt") # works perfectly
I'm pretty sure that RStudio wouldn't mind the file ending and just try to open files as text no matter what in the past. But now I either have to rename the file or get a different text editor to edit my bib and other files.
As far as I can tell, this is not a problem of Ubuntu marking the file as binary. Otherwise one of these commands would complain, I think:
readLines("test.bib")
system("grep 'misc' test.bib")
The solution to this problem is rather stupid. Apparently it is possible in Linux to include newline characters in your folder name, yet either RStudio or file doesn't like that. I had no idea that my test.bib file was sitting in a folder with a newline character. So the problem can be reproduced with:
bib <- "#misc{test,
author = {test},
year = {2018},
title = {test},
}"
dir.create("test\nfolder")
writeLines(bib, "./test\nfolder/test.bib")
rstudioapi::navigateToFile("./test\nfolder/test.bib") # throws error
While it works when the folder is just called "test folder"! Sorry for wasting people's time, I should have just tested it elsewhere...
You can see the current test of whether a file is text or not here: https://github.com/rstudio/rstudio/blob/d1289249b11e0d12d2be12b3ceb701c41f110cec/src/cpp/session/SessionModuleContext.cpp#L1216. It looks for a recorded MIME type according to the filename extension (and .bib isn't in the list currently, so that will fail).
It then tries to run
file --dereference --mime --brief test.bib
and looks at the result. Maybe your system doesn't recognize test.bib as text/plain? A few other types would also be recognized as text; see the end of that function on github.
Related
Whenever I knit to a PDF in RStudio, the error "The system cannot find the file specified."
Here is the code that I'm using:
##importing data
library(readr)
Quiz1data_2 <- read_csv("C:/Users/erinp/Downloads/Quiz1data-2.csv")
I have restarted RStudio multiple times and I have copied and pasted the exact link that my file is saved to and it's still not working.
What am I not seeing or what am I not thinking?
Some suggestions/questions:
Without knitting, when you run the line reading in the csv, does it work?
Also, are you sure that the error is referring to the data csv? Could it be referring to the (I'm assuming) markdown file you are writing your code in? Have you moved that file since you started working in it?
Are you able to knit other documents to pdf? You need MiKTeX on a windows machine. Does knitting to html work?
I've found R to be a little tricky reading in files. I usually use the base function like this:go to the environment tab>import dataset>from text(base)> (select the file you want, hit open)>(select settings so that the dataframe preview looks right>import. Code that does this will run in the console, and I copy it into my markdown file so that every time it knits, it replicates that successful process.
I figured it out. It's because I forgot to assign a value to an object so it wouldn't knit into a PDF. I made a comment earlier, but it's small so I thought I would add this to the answer section.
I have an excel file that I want to open in R. I tried both of these commands after saving the excel file as a csv file or a text file.
read.table() or read.csv()
I think part of the problem is where the file is located. I have it saved on the desk top. What am I missing here?
Here is the R output
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> help.search("read.csv")
> read.csv("Rtrial.csv")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> read.table("tab")
To throw out another option, why not set the working directory (preferably via a script) to the desktop using setwd('C:\John\Desktop') and then read the files just using file names
Try
f <- file.choose()
to choose the file interactively and save the name in f.
Then run read.csv on the saved filename
d <- read.csv(f)
Sound like you just have an issue with the path. Include the full path, if you use backslashes they need to be escaped: "C:\\folder\\folder\\Desktop\\file.csv" or "C:/folder/folder/Desktop/file.csv".
myfile = read.csv("C:/folder/folder/Desktop/file.csv") # or read.table()
It may also be wise to avoid spaces and symbols in your file names, though I'm fairly certain spaces are OK.
I had to combine Maiasaura and Svun answers to get it to work: using setwd and escaping all the slashes and spaces.
setwd('C:\\Users\\firstname\ lastname\\Desktop\\folder1\\folder2\\folder3')
data = read.csv("file.csv")
data
This solved the issue for me.
Here is one way to do it. It uses the ability of R to construct file paths based on the platform and hence will work on both Mac OS and Windows. Moreover, you don't need to convert your xls file to csv, as there are many R packages that will help you read xls directly (e.g. gdata package).
# get user's home directory
home = setwd(Sys.getenv("HOME"));
# construct path to file
fpath = file.path(home, "Desktop", "RTrial.xls");
# load gdata library to read xls files
library(gdata);
# read xls file
Rtrial = read.xls(fpath);
Let me know if this works.
Save as in excel will keep the file open and lock it so you can't open it. Close the excel file or you won't be able to use it in R.
Give the full path and escape backslashes read.csv("c:\\users\\JoeUser\\Desktop\\JoesData.csv")
I have experienced that this error occurs when you either move the excel file to the destination other than where your r file is located or when you move your r file to the destination other than where your excel file is located.
Good Practice:
Keep your .r and .csv files in the same directory.
open your .r file from getting into its directory instead of opening the r file from rstuio's open file option.
You also have import Dataset option at Environment Block, just click there and get your required packages installed & from next time use this option to read datasets. You will not get this error again.
I also appreciate the above provided answers.
Another way of reading Excel including the new format xlsx could be the package speedR (https://r-forge.r-project.org/projects/speedr/). It is an interactive and visual data importer. Besides importing you can filter(subset) the existing objects from the R workspace.
My issue was very simple, the working directory was not the "Source" directory that was printed when the file ran. To fix this, you can use getwd() and setwd() to get your relative links working, or just use a full path when opening the csv.
print(getwd()) # Where does the code think it is?
setwd("~/Documents") # Where do I want my code to be?
dat = read.csv("~/Documents/Data Visualization/expDataAnalysis/one/ac1_survey.csv") #just make it work!
MAC OS It happened to me as well. I simply chose from the R toolbar MISC and then chose Change Working Directory. I was able to choose the directory that the .csv file was saved in. When I went back to the command line and typed getwd() the full directory was updated and correct and the read.csv function finally worked.
I had the same problem and when I checked the properties of the file on file explorer, it shows me the next message:
"Security: This file came from another computer and might be blocked to help protect this computer"
You click on the "Unblock" button and... you can access to the file from R without any problem, just using read.csv() function and from the directory specified as your working directory, even if is not the same as the file’s directory you are accessing to.
I just had this problem and I first switched to another directory and then switched back and the problem was fixed.
this work for me, accesing data from root. use double slash to access address.
dataset = read.csv('C:\\Users\\Desktop\\Machine Learning\\Data.csv')
Kindly check whether the file name has an extension for example:
abc.csv
if so remove the .csv extension.
set wd to the folder containing the file (~)
data<-read.csv("abc.csv")
Your data has been read the data object
In my case this very problem was raised by wrong spelling, lower case 'c:' instead of upper case 'C:' in the path. I corrected spelling and problem vanished.
You can add absolute path to the file
heisenberg <- read.csv(file="C:/Users/tiago/Desktop/sample_100000.csv")
If really want to run something like
heisenberg <- read.csv(file="sample_100000.csv")
then you'll have to change the working directory to match the place the .CSV file is at. More about it here.
I'm on RStudio, just wanting to read a csv file:
newdata <- read_csv("Nameofdata.csv",
col_names = TRUE)
But it keeps telling me that the file doesn't exist. It does exist. I'm staring DIRECTLY at it, underneath the file path that RStudio insists is wrong. I can open it in another tab, I can open in in excel, it's EXACTLY where RStudio says it's not existing. Please help.
Looking very closely at your screen shot, commenters are suggesting that you have an extra space at the beginning of your file name.
Also, I see that the working directory appears to be correct (the error message lists it as C:/users/mdavi/Desktop/School/Research/Sc, which appears to match what is listed in the Files pane
A couple of strategies for trouble-shooting file-locating problems:
use getwd() and list.files() to confirm your working directory and what files R can see from there (you can read this introduction to get more background on working directories):
use file.choose() to select a file interactively; it's generally a bad idea to use this in production code, as it will add an interactive step when you usually want to be able to run all of your code start to finish without needing manual steps, but it's quite useful for debugging.
If you wanted R to list files that approximately matched your specified filename, you could use
L <- list.files(pattern="*.csv")
agrep("myfile.csv", L, value=TRUE)
You need to set your working directly correctly, either via setwd("~/Desktop/School/Research/SC") in the R Console (that's what I think I see in your screenshot: ~ stands for your home directory, i.e "Users/Whoever") or via Session > Set Working Directory > To File Pane in the RStudio menus.
You can read a variety of Stack Overflow questions about setting the working directory for more complete context ... web searching on "R 'working directory'" might help too.
I have an excel file that I want to open in R. I tried both of these commands after saving the excel file as a csv file or a text file.
read.table() or read.csv()
I think part of the problem is where the file is located. I have it saved on the desk top. What am I missing here?
Here is the R output
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> help.search("read.csv")
> read.csv("Rtrial.csv")
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file 'Rtrial.csv': No such file or directory
> read.table("tab")
To throw out another option, why not set the working directory (preferably via a script) to the desktop using setwd('C:\John\Desktop') and then read the files just using file names
Try
f <- file.choose()
to choose the file interactively and save the name in f.
Then run read.csv on the saved filename
d <- read.csv(f)
Sound like you just have an issue with the path. Include the full path, if you use backslashes they need to be escaped: "C:\\folder\\folder\\Desktop\\file.csv" or "C:/folder/folder/Desktop/file.csv".
myfile = read.csv("C:/folder/folder/Desktop/file.csv") # or read.table()
It may also be wise to avoid spaces and symbols in your file names, though I'm fairly certain spaces are OK.
I had to combine Maiasaura and Svun answers to get it to work: using setwd and escaping all the slashes and spaces.
setwd('C:\\Users\\firstname\ lastname\\Desktop\\folder1\\folder2\\folder3')
data = read.csv("file.csv")
data
This solved the issue for me.
Here is one way to do it. It uses the ability of R to construct file paths based on the platform and hence will work on both Mac OS and Windows. Moreover, you don't need to convert your xls file to csv, as there are many R packages that will help you read xls directly (e.g. gdata package).
# get user's home directory
home = setwd(Sys.getenv("HOME"));
# construct path to file
fpath = file.path(home, "Desktop", "RTrial.xls");
# load gdata library to read xls files
library(gdata);
# read xls file
Rtrial = read.xls(fpath);
Let me know if this works.
Save as in excel will keep the file open and lock it so you can't open it. Close the excel file or you won't be able to use it in R.
Give the full path and escape backslashes read.csv("c:\\users\\JoeUser\\Desktop\\JoesData.csv")
I have experienced that this error occurs when you either move the excel file to the destination other than where your r file is located or when you move your r file to the destination other than where your excel file is located.
Good Practice:
Keep your .r and .csv files in the same directory.
open your .r file from getting into its directory instead of opening the r file from rstuio's open file option.
You also have import Dataset option at Environment Block, just click there and get your required packages installed & from next time use this option to read datasets. You will not get this error again.
I also appreciate the above provided answers.
Another way of reading Excel including the new format xlsx could be the package speedR (https://r-forge.r-project.org/projects/speedr/). It is an interactive and visual data importer. Besides importing you can filter(subset) the existing objects from the R workspace.
My issue was very simple, the working directory was not the "Source" directory that was printed when the file ran. To fix this, you can use getwd() and setwd() to get your relative links working, or just use a full path when opening the csv.
print(getwd()) # Where does the code think it is?
setwd("~/Documents") # Where do I want my code to be?
dat = read.csv("~/Documents/Data Visualization/expDataAnalysis/one/ac1_survey.csv") #just make it work!
MAC OS It happened to me as well. I simply chose from the R toolbar MISC and then chose Change Working Directory. I was able to choose the directory that the .csv file was saved in. When I went back to the command line and typed getwd() the full directory was updated and correct and the read.csv function finally worked.
I had the same problem and when I checked the properties of the file on file explorer, it shows me the next message:
"Security: This file came from another computer and might be blocked to help protect this computer"
You click on the "Unblock" button and... you can access to the file from R without any problem, just using read.csv() function and from the directory specified as your working directory, even if is not the same as the file’s directory you are accessing to.
I just had this problem and I first switched to another directory and then switched back and the problem was fixed.
this work for me, accesing data from root. use double slash to access address.
dataset = read.csv('C:\\Users\\Desktop\\Machine Learning\\Data.csv')
Kindly check whether the file name has an extension for example:
abc.csv
if so remove the .csv extension.
set wd to the folder containing the file (~)
data<-read.csv("abc.csv")
Your data has been read the data object
In my case this very problem was raised by wrong spelling, lower case 'c:' instead of upper case 'C:' in the path. I corrected spelling and problem vanished.
You can add absolute path to the file
heisenberg <- read.csv(file="C:/Users/tiago/Desktop/sample_100000.csv")
If really want to run something like
heisenberg <- read.csv(file="sample_100000.csv")
then you'll have to change the working directory to match the place the .CSV file is at. More about it here.
When opening .rmd files in RStudio 3.3.2, they show up as completely empty. There is text if I open using Notepad or if I open on another machine. What is going on?
RMD file in question
I had a similar issue with older R files that opened as empty. It turned out that RStudio didn't use the correct encoding as default and therefore wasn't able to read the file (presented the file as empty).
You can make sure that you are using the correct encoding by:
Opening the file in RStudio as you normally would (the file will be empty)
Navigate to File -> Reopen with Encoding...
Select UTF-8 and click OK
UTF-8 will most likely be the encoding you need. You can also choose to set this as the default for all source files.
This issue was also addressed on RStudio Support
In RStudio go to:
Tools
Global Setting
Left hand side "Code"
a. under "Saving" - Default text econding: change to UTF-8
save #Richard N mentioned, save the files with "UTF-8" encoding. Will solve the issue.
Incase you saved the files without encoding, use the open with encoding option under "Files" tab.