I'm trying to download a zip file from a source, unzip it and after move to another directory.
First the download:
if (!file.exists("inst/extdata/sp_resultados_universo")) {
tmp <- tempfile(fileext = ".zip")
download.file("ftp://ftp.ibge.gov.br/Censos/Censo_Demografico_2010/Resultados_do_Universo/Agregados_por_Setores_Censitarios/SP_Capital_20180416.zip", tmp, quiet = TRUE)
unzip(tmp, exdir = "inst/extdata/sp_resultados_universo", junkpaths=T)
unlink(tmp)
}
The file i want is on this directory inst/extdata/sp_resultados_universo/SP Capital/Base informa�oes setores2010 universo SP_Capital (codificação inválida)/CSV/, so when i try copy to inst/extdata/sp_resultados_universo/ i get an error
file.rename("inst/extdata/sp_resultados_universo/SP%20Capital/Base%20informa%87oes%20setores2010%20universo%20SP_Capital(condificação inválida)/CSV/Domicilio02_SP1.csv",
"inst/extdata/sp_resultados_universo/Domicilio02_SP1.csv")
Warning message:
In file.rename("inst/extdata/sp_resultados_universo/SP%20Capital/Base%20informa%87oes%20setores2010%20universo%20SP_Capital(condificação inválida)/CSV/Domicilio02_SP1.csv", :
it was not possible to rename file 'inst/extdata/sp_resultados_universo/SP%20Capital/Base%20informa%87oes%20setores2010%20universo%20SP_Capital(condificação inválida)/CSV/Domicilio02_SP1.csv'
for 'inst/extdata/sp_resultados_universo/Domicilio02_SP1.csv',
reason 'File or directory not found'
I'm translating the error message, so it could be inconsistent with english message.
I can change the directory name or move the file manually, but breaks the flow and it's not nice for reproducibility. How can i handle it inside R?
My system info:
Sys.info()
sysname
"Linux"
release
"4.9.0-6-amd64"
version
"#1 SMP Debian 4.9.88-1+deb9u1 (2018-05-07)"
machine
"x86_64"
Many thanks in advance for any help.
when using R you can interact with the linux shell (or the windows cmd line) through a call to system() where you put the quoted command just as you would use in the shell,
for instance:
system("pwd") # prints current working directory
system("date") # prints
system("ls | grep .R") # prints a list of r scripts in the current working directory
system("mv file.txt /home/new_directory/file.txt") # moves your file to another directory
Related
I installed R and RStudio this week on a new Windows 10 machine. I want to use this R code to launch Excel and open a CSV file that is in a subdirectory of the current working directory:
file <- "example.csv"
sub_dir <- "subdirectory"
shell.exec(file.path(sub_dir, file))
But I get this error:
Error in shell.exec(file.path(sub_dir, file)) :
'subdirectory/example.csv' not found
However, if I provide shell.exec with the full file path, this code works as expected:
shell.exec(file.path(getwd(), sub_dir, file))
The documentation for shell.exec states:
The path in file is interpreted relative to the current working
directory.
R versions 2.13.0 and earlier interpreted file relative to the R home
directory, so a complete path was usually needed.
Why doesn't my original code (without getwd) not work? Thanks.
It looks to be related to the path separator in some wacky way. Below, I specify the the file path separator as \ and the command executes as expected. You could keep your call to file.path() and simply wrap in normalizePath() as another option.
file <- "example.csv"
sub_dir <- "subdirectory"
dir.create(sub_dir)
writeLines("myfile",file.path(sub_dir, file))
# Works
shell.exec(file.path(sub_dir, file, fsep = "\\"))
shell.exec(file.path(sub_dir, file))
#> Error in shell.exec(file.path(sub_dir, file)): 'subdirectory/example.csv' not found
I am trying to extract a file from a LZMA archive downloaded from an API containing JSON files, using R. On my computer I can extract the file manually in Windows Explorer with no problems.
Here's my code currently (API details removed):
tempFile <- tempfile()
destDir <- "extracted-files"
if (!dir.exists(destDir)) dir.create(destDir)
download.file("api_url.tar.xz", destfile = tempFile)
untar(tempFile, exdir = destDir)
When I attempt to extract the file, I receive the following error messages:
/usr/bin/tar: This does not look like a tar archive
/usr/bin/tar: Skipping to next header
/usr/bin/tar: Exiting with failure status due to previous errors
Warning messages:
1: running command 'tar.exe -xf "C:\Users\XXX\AppData\Local\Temp\RtmpMncPWp\file2eec75e23a15" -C "extracted-files"' had status 2
2: In untar(tempFile, exdir = destDir) :
‘tar.exe -xf "C:\Users\XXX\AppData\Local\Temp\RtmpMncPWp\file2eec75e23a15" -C "extracted-files"’ returned error code 2
I am using Windows 10 with R version 3.3.1 (2016-06-21).
Using library(archive) one can also read in a particular csv file within an archive without having to UNZIP it first :
library(archive)
library(readr)
read_csv(archive_read("api_url.tar.xz", file = 1), col_types = cols()) # adjust file=XX as appropriate
This is quite a bit faster.
To unzip everything one can use
archive_extract("api_url.tar.xz", dir=XXX)
That worked very well for me & is faster than the unbuilt untar(). It also works on all platforms. It supports 'tar', 'ZIP', '7-zip', 'RAR', 'CAB', 'gzip', 'bzip2', 'compress', 'lzma' and 'xz' formats.
SOLVED:
While it seemed to work perfectly on Mac, for it to work on Windows you need to open the compressed .xz file connection for reading in binary mode, before passing it to untar():
download.file(url, tmp)
zz <- xzfile(tmp, open = "rb")
untar(zz, exdir = destDir)
An alternative, and even simpler solution is to specify the 'mode' parameter for download.file() as follows:
download.fileurl, destfile = tmp, mode = "wb")
After upgrading Ubuntu from 14.04 to 16.04, whenever I use
knit2pdf(input="ABC.Rnw", quiet = TRUE)
in RStudio Version 0.99.1197, I get the following error:
processing file: ./202Analysis.Rnw Error in texi2dvi(file = file, pdf
= TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'ABC.tex' failed. Messages: mkdir: cannot create directory
‘Yaseen/XYZ’: No such file or directory /usr/bin/texi2dvi: cannot
create directory: Yaseen/XYZ
Edited
My directory ‘Yaseen/XYZ STU’ is containing spaces. Everything works fine after removing these spaces. However the same code was working fine with Ubuntu 14.04. How can I make this (directory names containing spaces) workable with Ubuntu 16.04?
Edited 2
This link says:
To build the PDF documentation, you will need a version of TeX Live or texinfo that includes texi2dvi (BEWARE: recent TeX Live, and some texinfo RPMs, do NOT include texi2dvi).
I agree with the previous comments in that the space in the directory seems to be the culprit.
Have you tried escaping the whitespace in your output directory?
knit2pdf(input="ABC.Rnw", quiet = TRUE, output = "Yaseen/XYZ\ STU")
I'm trying to download and extract a zip file using R. Whenever I do so I get the error message
Error in unzip(temp, list = TRUE) : 'exdir' does not exist
I'm using code based on the Stack Overflow question Using R to download zipped data file, extract, and import data
To give a simplified example:
# Create a temporary file
temp <- tempfile()
# Download ZIP archive into temporary file
download.file("http://cran.r-project.org/bin/windows/contrib/r-release/ggmap_2.2.zip",temp)
# ZIP is downloaded successfully:
# trying URL 'http://cran.r-project.org/bin/windows/contrib/r-release/ggmap_2.2.zip'
# Content type 'application/zip' length 4533970 bytes (4.3 Mb)
# opened URL
# downloaded 4.3 Mb
# Try to do something with the downloaded file
unzip(temp,list=TRUE)
# Error in unzip(temp, list = TRUE) : 'exdir' does not exist
What I've tried so far:
Accessing the temp file manually and unzipping it with 7zip: Can do this no problem, file is there and accessible.
Changing the temp directory to c:\temp. Again, the file is downloaded successfully, I can access it and unzip it with 7zip but R throws the exdir error message when it tries to access it.
R version 2.15.2
R-Studio version 0.97.306
Edit: The code works if I use unz instead of unzip but I haven't been able to figure out why one works and the other doesn't. From CRAN guidance:
unz reads (only) single files within zip files...
unzip extracts files from or list a zip archive
On a windows setup:
I had this error when I had exdir specified as a path. For me the solution was removing the trailing / or \\ in the path name.
Here's an example and it did create the new folder if it didn't already exist
locFile <- pathOfMyZipFile
outPath <- "Y:/Folders/MyFolder"
# OR
outPath <- "Y:\\Folders\\MyFolder"
unzip(locFile, exdir=outPath)
This can manifest another way, and the documentation doesn't make clear the cause. Your exdir cannot end in a "/", it must be just the name of the target folder.
For example, this was failing with 'exdir' does not exist:
unzip(temp, overwrite = F, exdir = "data_raw/system-data/")
And this worked fine:
unzip(temp, overwrite = F, exdir = "data_raw/system-data")
Presumably when unzip sees the "/" at the end of the exdir path it keeps looking; whereas omitting the "/" tells unzip "you've found it, unzip here".
A couple of years late but I still get this error when trying to use unzip(). It appears to be a bug because the man pages for unzip state if exdir is specified it will be created:
exdir The directory to extract files to (the equivalent of unzip -d).
It will be created if necessary.
A workaround I've been using is to manually create the necessary directory:
dir.create("directory")
unzip("file-to-unzip.zip", exdir = "directory/")
A pain, but it seems to work, at least for me.
I am using R3.2.1 on a Windows 7 machine.
The way I found to address this issue takes a few steps, but it works for me:
Create a vector that contains the name of the url from where you are downloading the file, e.g.
file_url <- "http://your.file.com/file_name.zip"
Use download.file to specify the url where you are downloading the file from (using your newly created vector), followed by the file name of the zipped file (that should be the last part of the url name). It will be saved as such in your working directory*, e.g.
download.file(file_url, "file_name.zip")
*If you are not sure of your working directory, you can use getwd() to check it. If you want to change your working directory, you can use setwd("C:users/username/...") to set it to what you want.
Use "unzip" to unzip the file into your working directory, with the name you will set using exdir, e.g.
unzip("file_name.zip", exdir = "file_name")
To check your work, you can use list.files, e.g.
list.files("file_name")
Hope this helps!
I would like to download a file directly into my working directory
I can do this to a temp directory:
download.file("http://www.abc.com/abc.zip",temp)
but what do I have to replace temp with to get it to download to the working directory?
If your url is in a variable, you can use basename to get the "filename" part out of it:
u <- "http://www.abc.com/abc.zip"
basename(u) # "abc.zip"
# downloads to current directory:
download.file(u, basename(u))
# downloads to subdirectory "foo":
download.file(u, file.path("foo", basename(u)))
The second argument of download.file() is destfile and it must be specified. I don't have a Windows machine to test this on, but both of these work on my linux box and I can't see why at least the second won't work on Windows too:
download.file("http://www.abc.com/abc.zip", "./abc.zip")
download.file("http://www.abc.com/abc.zip", "abc.zip")
The second of those indicates that if you just give a filename, the file will be download to the current working directory and saved under the stated name.