I was using R installed on a Linux server using SSH. Everything was fine, but now I have been denied access to temp folder and if I am loading R it is giving error cannot create 'R_TempDir', as it can't create the temp folder.
Can you please tell me how to create own local temp folder so that R can create temporary directory there ?
You can try to set one of these environment variable :
TMPDIR, TMP, TEMP:
Consulted (in that order) when setting the temporary directory for the session: see tempdir. TMPDIR is also used by some of the utilities see the help for build
by doing for instance :
export TMPDIR=/tmp
source
Hope this answers.
From what I understand,
I just thought that you could use .bashrc files in your /home/username/ directory
~# nano /home/username/.bashrc
You can put the command to create the folder inside this .bashrc file by just adding this line mkdir /your/dir/path/yourDir
This file is just like an autorun file which run everytime you upstart your linux server
But this is just working per user setting
Related
I am trying to add my R script into a dockerfile. The beginning of the file (loading base image, installing necessary packages) works fine when I run it in my terminal, but I keep getting this error when it gets to the line that contains the R script I want to run:
Step 15/17 : COPY /Users/emma/Documents/folder1/examples/question-1/model-1.r .
COPY failed: stat /var/lib/docker/tmp/docker-builder376572603/Users/emma/Documents/folder1/examples/question-1/model-1.r: no such file or directory
I am already running the terminal out of the "question-1" directory (my shell command looks like this) :
Emmas-MacBook-Air-2:question-1 emma$
and the R script file "model-1.r" is in that folder. What am I doing wrong in detailing the path to the R script? Do I have to somehow transform the script before adding it to the dockerfile?
Thank you
I believe, that you have to specify relative (to your build folder) path to copy from. Source:
Multiple resources may be specified but the paths of files and directories will be interpreted as relative to the source of the context of the build.
And file to copy should be inside context of the build. So if your Dockerfile is located in folder A, then the objects you would like to copy should be placed in the folder A or it's subfolders.
Hi I'm using pyspark interactively. I think I'm failing loading a LOCAL file correctly.
how do I check current directory, so that I can go to browser to take a look at that actual file?
Or is the default directory where pyspark is? Thanks
You can't load local file unless you have same file in all workers under same path. For example if you want to read data.csv file in spark, copy this file to all workers under same path(say /tmp/data.csv). Now you can use sc.textFile("file:///tmp/data.csv") to create RDD.
Current working directory is the folder from where you have started pyspark. You can start pyspark using ipython and run pwd command to check working directory.
[Set PYSPARK_DRIVER_PYTHON=/path/to/ipython in spark-env.sh to use ipython]
import os
cwd = os.getcwd()
print(cwd)
I want to change the prompt in R from > to R> and I know I should use the options command options(prompt="...") and it works, but then when I restart R the prompt is back to >.
Is there anyway to save the change so that it sticks?
Use .Rprofile file:
You can customize the R environment through a site initialization file or a directory initialization file. R will always source the Rprofile.site file first. On Windows, the file is in the C:\Program Files\R\R-n.n.n\etc directory. You can also place a .Rprofile file in any directory that you are going to run R from or in the user home directory.
At startup, R will source the Rprofile.site file. It will then look for a .Rprofile file to source in the current working directory. If it doesn't find it, it will look for one in the user's home directory. There are two special functions you can place in these files. .First( ) will be run at the start of the R session and .Last( ) will be run at the end of the session.
More details are here
I am currently trying out on the docker link between my app and db containers. I've checked on my app container and environment variables are automatically set when I link the containers together.
What I want to do is for my config file, which is packaged into a jar file, to receive the environment variables and set the required values to it. Any advice or help?
And this is how I create a config file in my jar file to connect to MySQL
database { url="jdbc:mysql://${MYSQL_PORT_3306_TCP_ADDR}:${MYSQL_PORT_3306_TCP_PORT}/mydb" driver="com.mysql.jdbc.Driver"}
Updating the config file inside the jar could be quite overkill.
It think you have several choices
read the config environment variable directly in you program
use variable either directly or generate the config file there
create launch script (details of this depends of you guest os in docker how to do it; sh/bash for linux etc..)
that script can generate new config file from environment and put it on classpath before jar so you program sees it.
EDIT: added example
You can save this kind of launcher script on docker image which dynamically creates configuration before launching actual program.
#!/bin/bash
# some default values for testing even without links to other container
MYSQL_PORT_3306_TCP_ADDR=${MYSQL_PORT_3306_TCP_ADDR:-127.0.0.1}
MYSQL_PORT_3306_TCP_PORT=${MYSQL_PORT_3306_TCP_PORT:-3306}
cat << EOF > /opt/yourprogram/dbconfig.conf
database { url="jdbc:mysql://${MYSQL_PORT_3306_TCP_ADDR}:${MYSQL_PORT_3306_TCP_PORT}/mydb" driver="com.mysql.jdbc.Driver"
}
EOF
scala -classpath /opt/yourprogram YourProgram
What I did is that I wrote the sh file in my directory /tmp/restcore-1.0-SNAPSHOT/bin like this:
#!/bin/bash echo "database{url="jdbc:mysql://"${MYSQL_PORT_3306_TCP_ADDR}":"${MYSQL_PORT_3306_TCP_PORT}"/mydb" driver="com.mysql.jdbc.Driver" }" > myconf.conf
jar uf /tmp/restcore-SNAPSHOT/lib/com.organization.restcore-1.0-SNAPSHOT.jar /tmp/restcore-1.0-SNAPSHOT/bin/myconf.conf
After building the Dockerfile and running the sh file in CMD, I use cat myconf.conf to check the config file and I'll be able to see the environment set.
I am working with a "factory fresh" version of RStudio on Windows 7. R is installed under C:/Program Files which means the default libraries are stored here, and the two locations contained in .libPaths() on startup are both within this folder.
I want to work with another R library (igraph). Since the C:\Program Files folder is write-protected, I have set up another area to work in: C:\Users\nick\R and installed the igraph library in C:\Users\nick\R\library. I can manually add this location to the .libPaths() variable and use the library with no problems.
However, my problem is getting RStudio to automatically add this location to the .libPaths() variable on startup. I read that I could add the relevant command to my .Rprofile file - but I couldn't find any such file (presumably they are not automatically created when RStudio is installed). I then created a file called .Rprofile containing only this command. This only seemed to work when the .Rprofile file was saved in C:\Users\nick\Documents (which is the path stored in both the R_USER and HOME environmental variables). What I would like is to have the .Rprofile file stored in C:\Users\nick\R.
I have read all the information in ?Startup and it talks about where to store commands that run on startup. But I just can't make this work. For example there seems to be no way to change the location of the home directory without reading a file stored in the home directory. I don't seem to have any .Renviron files and creating these myself doesn't seem to work either.
I would really appreciate an answer in simple terms that explains how I could go about changing where the .Rprofile file is read from.
In Windows, you set the R_USER profile by opening up a command line and running:
SETX R_PROFILE_USER "C:/.../.Rprofile"
Where (obviously) the path is the path to your desired .Rpofile. In R, you can check that it worked:
Sys.getenv("R_PROFILE_USER")
Should return the path you specified. Note that you likely need to have all R sessions closed before setting the R_USER variable.