I am new to the R programming language and am having basic issues with it. I want to untar a file, but it has not been able to work for me.
Here is the code that I enter:
untar("CD_data.tar", exdir="data")
It then returns the following error message:
/bin/sh: /usr/bin/gnutar: No such file or directory
Warning message:
In untar("CD_data.tar", exdir = "data") :
‘/usr/bin/gnutar -xf 'CD_data.tar' -C 'data'’ returned error code 127
Please help! Thanks!
R on OS X 10.9 (Mavericks) seems to set a wrong TAR environment variable.
You can fix this by adding the following to your .Rprofile (or executing it manually):
Sys.setenv(TAR = '/usr/bin/tar')
Alternatively, you can provide the tar path as an argument when calling untar.
My 2 cents is that you are using a mac and have not installed tar. You are getting value 127 because the command is not found within your $PATH and it's not a built-in command (which is usually the case if you were in unix...
In other words you need to install tar.
Or run it in linux.
Related
I have a '.js' script that I usually activate from the terminal using the command node script.js. As this is part of a process where I first do some data analysis in R, I want to avoid the manual step of opening the terminal and typing the command by simply having R do it for me. My goal would be something like this:
...R analysis
write.csv(df, "data.csv")
system('node script.js')
However, when I use that specific code, I get the error:
sh: 1: node: not found
Warning message:
In system("node script.js") : error in running command
Of course, the same command runs without problem if I type it directly on the terminal.
About my Software
I am using:
Linux computer with the PopOS!
RStudio 2021.09.1+372 "Ghost Orchid"
R version 4.0.4.
The error message node: not found indicates that it couldn't find the program node. It's likely in PATH in your terminal's shell, but not in system()'s shell (sh).
In your terminal, locate node by executing which node. This will show the full path to the executable. Use that full path in system() instead.
Alternatively, run echo $PATH in your terminal, and run system('echo $PATH') or Sys.getenv('PATH') in R. Add any missing directories to R's path with Sys.setenv(PATH = <your new path string>)
Note that system2() is recommended over system() nowadays - but for reasons unimportant for your case. See ?system and ?system2 for a comparison.
Examples
Terminal
$ which node
/usr/bin/node
R
system('/usr/bin/node script.js')
# alternatively:
system2('/usr/bin/node', c('script.js'))
or adapt your PATH permanently:
Terminal
% echo $PATH
/usr/local/bin:/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin
R
> Sys.getenv('PATH')
[1] "/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback"
> Sys.setenv(PATH = "/home/caspar/programs:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/RStudio.app/Contents/MacOS/postback")
Sorry for a basic question. I'm trying run a R script called cuffdiff_gtf_attributes (please find it at enter link description here in R 3.3.1 installed on the Windows 7. The script is started with the below line:
#!/usr/bin/env Rscript
When I type cuffdiff_gtf_attributes in R, it says Error: object 'cuffdiff_gtf_attributes' not found. Also, I tried Rscript cuffdiff_gtf_attributes that returned me: Error: unexpected symbol in "Rscript cuffdiff_gtf_attributes".
Moreover, I tried source('cuffdiff_gtf_attributes.R')that seems to work and returned the usage of the script as bellow
Error:
usage: cuffdiff_gtf_attributes --input=<inputGTF> [--output=outputGTF] | --help
But, when I add the arguments as source('cuffdiff_gtf_attributes.R') --input=file.gtf, it says that: Error: object 'file.gtf' not found. I also tried this command as source('cuffdiff_gtf_attributes.R') --input file.gtf, it says that Error: unexpected symbol in "source('cuffdiff_gtf_attributes.R') --input file.gtf"
Sorry, I couldn't post a sample GTF file, you can find a short sample of it at enter link description here
Everything is the current path. Could you please help me out to execute the script?
Thanks in advance
This is a script file. You should run using Rscript instead for Rgui.exe. From a command prompt, navigate to the directory where file.gtf is and run:
"%Programfiles%\R\R-3.3.3\bin\Rscript" cuffdiff_gtf_attributes.R --input=file.gtf
When building a package, I received the following warning:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
I have no idea how to even begin diagnosing this. Is there a tool that tells me what .Rd file the problem is in?
I get no warnings about any of my Rd files in the checking documentation step....
Try R CMD Rd2pdf mypackage to create the manual, and possibly also set the --no-clean option to keep the temporary files. This should allow you to debug the LaTeX code triggering the error.
Though #Dirk's answer also helped me to fix the problem I would like to add a bit which might especially help recent updaters. That is, people who haven't encountered other LaTeX / R troubles after the update to 3.1.3 yet. The problem is little bit more general than just building. For me, on OS X the problem was that R CMD Rd2pdf as well as the R CMD CHECK expected texi2dvi to be in /usr/local/bin while it was in /usr/bin.
A symlink helped to fix the problem. On terminal type:
# to check whether the same issue exists for you
which texi2dvi
# if so
cd /usr/local/bin
ln -s /usr/bin/texi2dvi
Of course if the first line returns something else, you need to adapt the symlink here.
Concluding from the comments and from my own experience the problem often seems to be that some TeX fonts are missing, most often
inconsolata.sty and
upquote.sty
First you have to find the right directory where TeX fonts are stored - in my case this is:
C:\Program Files\R\R-3.3.0\share\texmf\tex\latex
Then you can download them here:
https://www.ctan.org/tex-archive/fonts/inconsolata/?lang=en
https://www.ctan.org/tex-archive/macros/latex/contrib/upquote?lang=en
Just copy them to the respective folder and in many cases the problem will be solved (in my case too). This should work for all operating systems.
...and another reason is that you haven't installed MikTex yet.
Download MikTex from here and follow the dialog prompts to install. I found the defaults to be reasonable and worked well for me.
Try to build your R package again. It should be OK now.
In my case, I had no error when running devtools::check() nor devtools::document() but when running R CMD check mypackage_version.tar.gz I got an error:
* checking PDF version of manual ... WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
* checking PDF version of manual without hyperrefs or index ... ERROR
In this question in RStudio Community they point to a problem with LATEX installation.
I have the LATEX installation suggested in R markdown cookbook: TinyTex.
I fixed the issue by running in the R console
tinytex::latexmk(file = "../mypackage.Rcheck/mypackage-manual.tex")
This command automatically updated my LATEX installation so the output file mypackage-manual.pdf was created. After this, I did not get any other error related to PDF when running R CMD check:
* checking PDF version of manual ... OK
* DONE
If you are on Ubuntu just install Tex Live by this command:
apt-get install texlive and restart Rstudo if you use it.
First, #dirk-eddelbuettel's approach in the current question identified the missing tex package (which was "makeindex" in my case).
system("R CMD Rd2pdf --no-preview --output=./documentation-peek.pdf ." )
# ... <omitted pages of output> ...
# Warning in sys2(makeindex, shQuote(idxfile)) : '"makeindex"' not found
# Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
# unable to run 'makeindex' on 'Rd2.idx'
# Error in running tools::texi2pdf()
Then #pedro-lima's answer in https://stackoverflow.com/a/69968791/1082435 worked for my specific case.
tinytex::tlmgr_install("makeindex")
Oftentimes this error occur because of Unicode characters in the package. In this cases, the error message might look like this.
See the inputenc package documentation for explanation.
Type H <return> for immediate help.
! Package inputenc Error: Unicode character (U+009D)
(inputenc) not set up for use with LaTeX.
You can find any Unicode characters in your package using tools::showNonASCIIfile(). Here's a simple way to check for these characters in your functions and documentation:
# functions
functions <- list.files(path = './R', all.files = T, recursive = T, full.names = T)
lapply(X=functions, FUN = tools::showNonASCIIfile)
# documentation
docs <- list.files(path = './man', all.files = T, recursive = T, full.names = T)
lapply(X=docs, FUN = tools::showNonASCIIfile)
OS- Windows 7
R version 3.0.3
What I typed on R console :
if(!file.exists("data")){dir.create("data")}
fileUrl <- "https://data.baltimorecity.gov/api/views/dz54-2aru/rows.xlsx?accessType=DOWNLOAD"
download.file(fileUrl,destfile="./data/cameras.xlsx",method="curl")
dateDownloaded <- date()
What I got on R console
Warning messages:
1: running command 'curl "https://data.baltimorecity.gov/api/views/dz54-2aru/rows.xlsx?accessType=DOWNLOAD" -o "./data/cameras.xlsx"' had status 127
2: In download.file(fileUrl, destfile = "./data/cameras.xlsx", method = "curl") :
download had nonzero exit status
How do I make it right ?
Your code works for me. You probably don't have cURL installed on your system. See ?download.file:
For methods "wget", "curl" and "lynx" a system call is made to the tool given by method, and the respective program must be installed on your system and be in the search path for executables.
Install cURL and make sure it is in your path.
After removing the method="curl" parameter, it works well on Windows.
I wanted to run this example script: http://mazamascience.com/WorkingWithData/?p=912 from Windows command line. So I opened the command line and typed Rscript tryCatch.R 1. However, I keep getting the error message Error: R not found. I did set the PATH environment variable as C:\Programme\R\R-3.0.1\bin. If I just type R.exe, it does start R, but it cannot find the packages that are to be loaded at start (e.g. package 'utils' in options<"defaultPackages"> was not found). I guess I have to set another path to the libraries somewhere, but I haven't got any idea where to do this.
UPDATE: After explicitly typing PATH C:\Programme\R\R-3.0.1\bin (rather than just adding this to the value of the environment variable PATH) it seems that R is found. However, a new problem occurs: In normalizePath<path.expand(path), winslash, mustWork>: path[2] = "C:/Programme/R/R-3.0.1/library": Access denied, the same than for the methods library. Then: Calls: .First ... library -> .getRequiredPackages2 -> library -> normalizePath Execution stopped. I'm using Windows 7 and I do have administrator rights.
Rscript is very handy (R CMD BATCH is the old way to ) specially under windows, But generally under I create a batch file to avoid all path's headache.
For example say launcher.bat:
#echo off
C:
PATH C:\Programme\R\R-3.0.1\bin;%path%
cd PATH_TO_YOUR_RSCRIPT
Rscript tryCatch.R 1
pause
And open a console(using cmd) , go where you have stored your launcher.bat and launch it. Or from the R cosnole using shell:
shell('path_to_launcher\launcher.bat')
I've found out that it was a language-specific problem on Windows 7, similar to what is described here: https://stat.ethz.ch/pipermail/r-help/2011-May/276932.html
After changing PATH to C:\Program Files\R\R-3.0.1\bin the script is properly executed from the command prompt.
Thanks to everyone who tried to help!
I ran into this problem under windows 7, apparently, when setting environment variables>user variables the path is not added into the PATH, so the user must add this path in system variables > PATH
at the end just add the path to your .EXE files and voila.