I'm having issues on windows with R failing when changing the working directory to a mapped network drive (e.g. \Share\Folder mapped to Z:) in batch mode. If I run the same script in an interactive console I don't have any issues. I am accomplishing this by running R.exe with the script specified inside of a windows batch (.bat) file. The .bat file contains the following.
"C:\RRO\R-3.2.1\bin\R.exe" CMD BATCH "C:/Scripts/Rscript.R"
The error is simply...
> setwd( 'Z:/' )
Error in setwd("Z:/") : cannot change working directory
I'd be open to a different approach entirely for scheduling these scripts via the windows task scheduler if that helps avoid the issue. The reason for mapping the drive is that I need to supply some credentials in order to access it, which is done automatically when it is mapped, but can test to see if that's not the case in R if anyone knows how.
I hope this can help with your question.
I duplicated the problem with no errors by using Rscript command instead of a CMD BATCH
my R code which I saved as a script (test1.R)
library(openxlsx)
setwd("P:/Records/Indexing Operations/Indexing Data Analysis/Daily Reports")
my.data = read.xlsx("FSI Daily Project Status Report - 18 Mar 2016.xlsx", sheet = 1)
setwd("C:/Users/golieth/Documents/")
png(filename = "test.png", width = 500, height = 350 )
plot(my.data$Total.Images, my.data$Completed.Images.A,
main = Sys.time())
dev.off()
Note I change the directory 2 times in this file. Once to access data on a mapped network drive and a 2nd to save the image to the computer. I put a timestamp of the current time as the main plot title so you can run the batch file repeatedly and verify it works
my batch file
cd C:\Program Files\R\R-3.2.3\bin\i386
Rscript C:\Users\golieth\Documents\test1.R
Note: On the batch file if your code relies on 32 bit you need to change the directory of your R program (cd) to the R 32bit program. Same with R64. Next the Rscript should reference where you have saved your .R file
Finally, and this might be stating the obvious but make sure you are connected to your VPN before running the batch file.
Imagine a batch file with
cd Z:\<Destination>
Z:
RScript "C:/Scripts/Rscript.R"
This will enable Windows to change to the directory with all credentials and then start R within that directory. So the working dir. is the location from where R is started. Doing so requires that "C:\RRO\R-3.2.1\bin\" is part of your PATH variable.
Good luck!
When writing a .bat file, remember that cd is not used to change drive letters. To change drive letters you simply enter the name of the drive letter, which should be done prior to issuing the final cd to the working directory.
Like this:
sample.bat
z:
cd z:\your\working\directory\
C:\RRO\R-3.2.1\bin\Rscript.exe C:/Scripts/Rscript.R
You can save the files locally in your code, and use file.copy in your code to copy the files over to your network drive. Also try replacing the path in file.copy the network drive letter by the full network address name eg. \\....\.....\
Related
I have successfully run a simple cronR tutorial using the cronR add in within R Studio. Here is the following code that I have saved in a R script file:
library(glue)
current_time <- Sys.time()
print(current_time)
msg <- glue::glue("This is a test I am running at {current_time}.")
cat(msg, file = "test.txt")
The R script file is saved within a specific project directory. The log file when the job runs is also saved there. However, the output of the script file, test.txt, is saved in my home directory. I am on a Mac. In the tutorial, it was stated that this would happen, that cron would save any output in the home directory and that if I want to change the location that I have to "specify otherwise". However, the tutorial gives no instructions for how to do this and I am not sure if I am supposed to do this through the terminal in mac and if so how? Changing the file path in the script file (e.g. Documents/test.txt) changes nothing, as the test.txt file is still saved in the home drive. I suspect I have to make this change somewhere else but I am not sure where. Any help would be appreciated.
For anyone who runs into the same issue, I was able to solve my problem by using launchD. I followed this tutorial https://babichmorrowc.github.io/post/launchd-jobs/. It worked as anticipated and now my .txt file is saved to the correct place. There is also a tutorial there for cron jobs, though if you are on a mac, launchD is apparently the preferred method.
I would like to write a csv file to a remote folder in a computer identified by user#ip-address, running a different OS (e.g. my current OS is iOS and remote OS is Ubuntu-19).
Below, the straightforward code saves a file in local folder
write.csv(1:10, 'Save.csv')
But I want to have something like
write.csv(1:10, "root#xx.xxx.x.x:/folder/Save.csv")
Any pointer will be highly appreciated.
This seems to be possible with the cp.remote function of the ssh-utils package
https://cran.r-project.org/web/packages/ssh.utils/ssh.utils.pdf
A wrapper around the scp shell command that handles local/remote files and allows copying between remote hosts via the local machine.
cp.remote(remote.src, path.src, remote.dest, path.dest, verbose = FALSE,
via.local = FALSE, local.temp.dir = tempdir())
Could you separate it into two steps?
Save it locally with write.csv()
Call iOS's equivalent of scp (wrapped in R's system()) to copy the file to the remote machine.
It would look like
write.csv(1:10, 'Save.csv')
system("scp Save.csv root#xx.xxx.x.x:/folder/Save.csv")
I usually switch between Windows and Mac while accessing my R codes from Google Drive. One of the repetitive tasks I need to do whenever I switch between my desktop and laptop is to (un-)comment the file path to the respective directories where my google drive is located. Can anyone share an automation code on how to do this? I am already doing this in Stata.
Usually, for each project or analysis that I start I use a "config-like" R file which looks more or less like this:
.job <- list ()
## rootDir in my laptop
.job$base_data_dir <- file.path ("", "home", "dmontaner", "datos")
## rootDir in my server
##.job$base_data_dir <- file.path ("", "scratch", "datos")
In this "config" file I set the root directory where I am keeping the data in each machine. I keep a different "config" file in each machine and do not synchronize them via dropbox.
Then I start my R scripts with this line:
try (source (".job.r"))
and when I have to address any file or folder I do:
setwd (file.path (.job$base_data_dir, "raw_data"))
...
setwd (file.path (.job$base_data_dir, "results"))
Like this, if you keep the internal structure of the data directory in both machines, you are able to set the base or root dir where it is allocated and reach the data in both machines.
Also the file.path function takes care of the changes in operative system.
In the R session I call the config variable starting with a dot for it to be a hidden variable so I do not see it when I do a ls () or similar things.
That's my solution:
setwd(ifelse(.Platform$OS.type=="unix", "/Users/.../Google Drive", "C:/Users/.../Google Drive/"))
I've been digging into several places for 2 simple needs but couldn't find a final answer.
I'm running an R script in batch mode. Not sure whether my solution is the best one but I'm using R CMD BATCH as per http://stat.ethz.ch/R-manual/R-patched/library/utils/html/BATCH.html included in a bat file.
First I'd like to have the directory where the R script is saved set up as the working directory rather than where the bat file is saved.
Secondly I'd like to divert all the output from the R script (csv files and charts) to a specific directory other than the working directory. I cannot find any options for such basic requirement.
The final idea is to be able to run the bat file across different computers no matter where the R script is saved.
Thanks
You don't give code so my answer will be just an advise or what I would do for such job.
Use Rscript.exe it is the way to go for batch script. R CMD is a sort of legacy tool.
You don't need to set or change the working directory. It is a source of problems
You can launch you bat file where you want and within it you go to R script location using cd for example you bat file can be like:
cd R_SCRIPT_PATH
Rscript youscript.R arg1 arg2
You can use one of the script argument as an output directory for your result files. For example inside your script you do somehing like this:
args <- commandArgs(trailingOnly = TRUE)
resultpath <- as.character(args[1])
.....
write.table(res1, file=paste(resultpath,'res1.csv',sep='/')
I am trying to convert a PDF document into a PNG file using ImageMagick command line tools from a ASP.NET website. I create a new shell process and ahve it execute the following command:
convert -density 96x96 "[FileNameAndPath].pdf" "[FileNameAndPath].png"
This runs well when testing the website on my local machine with the ASP.NET Develeopment Server of VS and the command also works well when manually entered into the shell. When running from the programatically created shell in ASP.NET there is the following error message:
Invalid Parameter - 96x96
Does anybody know why that happens and what to do?
I have tested the command while being logged in on the server via RDP with a different user account than the ASP.NET process. I have used exactly the same ImageMagick and Ghostscript installation files as on my local machine and have activated adding the ImageMagick installation path to the enironment variables during installing. The server has not been rebooted since than.
convert is also the name of a windows executable which converts FAT filesystem to NTFS. When you do not specify the full path of an executable, quote:
...the system first searches the current working directory and then
searches the path environment variable, examining each
directory from left to right, looking for an executable filename that
matches the command name given.
"C:\Windows\System32" is generally present in the beginning of %PATH% variable, causing the Windows convert utility to launch, which fails with "Invalid Parameter" error as expected.
Try specifying the full path of the ImageMagick's convert.exe like so:
"C:\Program Files\ImageMagick\convert.exe" -density 96x96 "path_and_filename.pdf" "path_and_filename.png"
As others have stated convert points to a different program in your PATH. Instead preface your command with magick. So your command would instead be:
magick convert -density 96x96 "[FileNameAndPath].pdf" "[FileNameAndPath].png"
In Window actually exists a "convert.exe" in system32 - make sure your script doesn't start that one (maybe the environment paths on your development machine are set differently).
I am only answering this late because imagemagick was updated. Now, if you wish to use the "convert" command, you do it like this:
magick convert "image.png" "document.pdf"
or
magick convert "image_00*.png" "document.pdf"
for multiple images.
Same syntax for command, just add magick before it
A couple more options for fixing this:
Edit your Path system variable to contain the path to imagemagick
as it's first content and then add the rest after it. This will make
windows always find the imagemagic convert first before it finds
the other convert program. So something like this: C:\Program Files\ImageMagick-6.9.2-Q16;C:\Program Files\Haskell Platform\2014.2.0.0\lib\extralibs\bin;...
Another option is to create a dedicated folder somewhere on your machine where you will place shortcuts for some of these name clashes. Then what you do is that you rename those shortcuts to meaningful names, for example convert_image_magick, then add the path to this folder to your system path. So now as you hit tab more, you will finally find the right program you want to run
yes! if you launch an Administrator command window it defaults to C:\windows\sytem32\ ... as long as you're not in that directory the command will pickup the ImageMagick convert.exe
My issue was I was using the "FORFILES" command which is tricky because it requires using
"cmd /c" and passing the convert command with #path and #file parameters and it does some escaping of slashes... needless to say it's caused me hours and hours of headache. It even parses hex characters, like if your filepath has the combination 0x00 in it, it will think that's a hex value and mangle your path. I had a filepath named C:\ImageRes3000x3000
and FORFILES interprets that literally and it caused a strange path issue. Sorry if this is a long useless post but it's meant to be FYI, if someone runs across this, maybe it will help them. That being said, FORFILES and "convert.exe" are a powerful and simple image renaming line script combo.
here's my full 3 line image renaming script
robocopy D:\SRC_DIR\ D:\DEST_DIR\_staging *.jpg /e /MAXAGE:2
FORFILES /P D:\DEST_DIR\_staging\ /S /M *.jpg /C "cmd /c convert.exe #path -quality 65 -resize 1500 D:\RESIZED_DIR\\#file"
DEL D:\DEST_DIR\_staging\*.* /S /Q