I am running a project that requires reading .tif files as rasters. However, when I try to load the files in now, I get th error:
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer", :
Cannot create a RasterLayer object from this file.
In addition: Warning message: 'file location/name.tif' not recognized as a supported file format. (GDAL error 4)
I'm using the function raster("file location/name.tif") and it has been working until recently.
I am currently working with the raster package along with sp and rgdal. I've updated each of the packages and still get this error. I've also tried installing and using the terra package but get the same error with that as well.
I'm not sure what to do at this point since I'm pretty sure it isn't an issue with the code I'm running because I haven't changed anything since the last time it worked.
I receive weekly emails from a database as zip files. In the zip file is a single xls file. When I use unzip() and place the xls file into a designated shared network directory, I cannot use any xls read functions to actually access and manipulate the data (I haven't tried read.xls because of the Perl dependencies, but I'm willing to if there are no other options).
I've tried every Excel reader I can find.
read_xls(unzip(zipfile = zfile, files = "Data Extract.xls", exdir = "~\\Excel Files"))
Errors include the following where I would simply expect a dataframe output:
"libxls error: Unable to open file"
"Error in open.connection(file, "rt") : cannot open the connection
In addition: Warning message:
In open.connection(file, "rt") :
cannot open zip file 'Data.zip:F'
EDIT: It turns out that despite the DB interface calling this file within the zip an .xls file, it's an HTML file and readHTMLTable() from library(XML) did the trick just fine. Thank you for the questions which lead me to looking at ths issue from a different angle.
I just downloaded R onto my computer, but when I try to read a .csv file I get the following error:
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
cannot open file '[filename].csv': No such file or directory
This happens both when I command the program to read the .csv or when I try to import it manually (although that error code is slightly different).
Could this be because I don't have Microsoft Office (and subsequently, Excel) on my computer? The .csv file exists and is not corrupt because I have no problem uploading the file to Google sheets and displaying the data there. Either that, or I didn't install R correctly. Any suggestions?
No, you don't need any special packages to read plain text CSV files in R.
Looking at your error message:
Warning message: In file(file, "rt") : cannot open file '[filename].csv': No such file or directory
I would guess that the problem is your path to the file in question. As a quick fix, you can try using the fully qualified path to your file. For example, on Windows you might try this:
data <- read.csv(file="c:/path/to/filename.csv", header=TRUE, sep=",")
If this works, then the issue was the location of your CSV file. Then, if you want to continue using a relative path, you'll have to figure out what that would be given your current R setup.
I am working with R package raster for sometime now. Recently I updated my system to Windows 10 where I used the a backup R package file to install-back all my packages.
Now while using raster packages especially when I use:
getData('SRTM', lon= Longitiude, lat =Latitude)
I get the follwoing error:
trying URL 'ftp://xftp.jrc.it/pub/srtmV4/tiff/srtm_50_08.zip'
downloaded 263 bytes
Error in .SRTM(..., download = download, path = path) : file not found
In addition: Warning message:
In utils::unzip(zipfilename, exdir = dirname(zipfilename)) :
error 1 in extracting from zip file
I read through a few post that says that the url is no longer accessible, this true and can be checked just by visiting the link.
However getData function should move-on to the next link which is accessable automatically but it is not doing that. Is there a way I can tell it to look for the other links.
For some reason I am suddenly not able to install packages in R (I have subsequently updated to the latest version of R and am running Windows 7). For example, if I type:
install.packages('beeswarm')
Installing package into ‘D:/Rlibs’ (as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session --- trying URL 'http://www.stats.bris.ac.uk/R/bin/windows/contrib/3.0/beeswarm_0.1.5.zip'
Content type 'text/html' length unknown opened URL downloaded 1859
bytes
Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package",
"Type")) : cannot open the connection In addition: Warning
messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting
from zip file 2: In read.dcf(file.path(pkgname, "DESCRIPTION"),
c("Package", "Type")) : cannot open compressed file
'beeswarm/DESCRIPTION', probable reason 'No such file or directory'
I have read that in Windows 7 there can be important restrictions on rights to writing to certain folders etc. so I've gone to some lengths to install R and library folders in non-default areas of my computer, and to allow myself rights to certain folders, but to no avail. Possibly also of importance is when I type:
.libPaths()
# [1] "D:/Rlibs"
# [2] "C:/Users/L.Halsey/Documents/R/win-library/3.0"
# [3] "C:/Users/L.Halsey/Documents/Documents/R-3.0.1/library"
I have created several folders in an attempt to create one that I could successfully install libraries into and set them up to be recognised by R using 'environment variables' from the start button. I don't know how to delete any of them though - not sure if this is relevant to my overall problem of not now being able to install/update packages for some reason.
The error being reported is inability to open a connection. In Windows that is often a firewall problem and is in the Windows R FAQ. The usual first attempt should be to run internet2.dll. From a console session you can use:
setInternet2(TRUE)
(You are correct in thinking this is not due to your library setup. The error says nothing about permissions.) I don't think just typing .libPaths should return that character vector since on my machine I would need to type .libPaths() to see something like that. If you wanted to reduce the number of places for libraries you can use the .libPaths function for setting the values. This would pick the second and third of the existing paths
.libPaths( .libPaths()[2:3] )
The inner call retrieves the path vector and the outer call sets it to a reduced vector.
Running RStudio as administrator fixed it for me!
I will probably duplicate a lot of other answers on the stackoverflow, but I got exactly the same error as OP, namely:
Warning messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 2: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : cannot open compressed file 'zoo/DESCRIPTION', probable reason 'No such file or directory'
Turned out, while I as a user had permissions to write in a certain directory, R did not. In order to be sure you don't have something similar, do following:
get a usb drive, let's name it E
download package source as a .zip file and store it onto usb-drive in some directory, let's name it E:/source
Create directory for libraries on the usb drive, let's name it E:/libs
Install packages calling R command install.package from the R console and setting all relevant directories to point to your usb drive:
(here I use package zoo as an example)
install.packages("E:/source/zoo_1.7-12.zip",
destdir = 'E:/source', # no "/" after the path
lib = 'E:/libs',
repos = NULL)
Load the package from the directory, where you installed it:
library('zoo', lib.loc = 'E:/libs')
After you are sure, it works this way on your usb drive, you can start resolving directories permissions, and try out by changing the paths in the code above.
update:
In some windows environments even your usb-stick might be protected from read-write by the R. Make sure you check the permissions using the machine you are working from.
The following worked for me (based on the answer above)
install.packages("clustvarsel", lib = "C:/Users/dnentchev/My Programs/R-3.2.2/library")
I had the same problem. I turned the windows firewall off, and Run RStudio as administrator. so, that error fixed.