I want to connect R with Jupyter Notebook, and I have installed IRkernel. However, when I run the code IRkernel::installspec(), an error occurs:
Error: lexical error: invalid char in json text.
C:\Users\xin_chen\AppData\Local
(right here) ------^
I had the same problem on one of my machines. I ended up manually copying the kernelspec files from another PC. The path is:
C:\Users\_username_\AppData\Roaming\jupyter\kernels\ir
If you don't have a working installation, you can copy the files from
https://github.com/IRkernel/IRkernel/tree/master/inst/kernelspec.
You might need to edit the kernel.json file to set the path of your R executable. For example:
{
"argv": ["C:/Program Files/Microsoft/R Client/R_SERVER/bin/x64/R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"],
"display_name": "R",
"language": "R"
}
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")
I am trying to merge some .csv files with the
hdfs dfs -getmerge /path/folderfile filename.csv command.
If I run this command from a terminal or from rstudio's internal terminal, it works fine. If I execute the same command using system("hdfs dfs -getmerge /path/folderfile /destinationpath/filename.csv") it returns the following error:
sh: hdfs: command not found
Warning message:
In system("hdfs dfs -getmerge /path/folderfile /destinationpath/filename.csv") :
error in running command
Thanks for suggestions
I am using a Dockerized image and Jupyter notebook along with SparkR kernel. When I create a SparkR notebook, it uses an install of Microsoft R (3.3.2) instead of vanilla CRAN R install (3.2.3).
The Docker image I'm using installs some custom R libraries and Python pacakages but I don't explicitly install Microsoft R. Regardless of whether or not I can remove Microsoft R or have it side-by-side, how I can get my SparkR kernel to use a custom installation of R?
Thanks in advance
Docker-related issues aside, the settings for Jupyter kernels are configured in files named kernel.json, residing in specific directories (one per kernel) which can be seen using the command jupyter kernelspec list; for example, here is the case in my (Linux) machine:
$ jupyter kernelspec list
Available kernels:
python2 /usr/lib/python2.7/site-packages/ipykernel/resources
caffe /usr/local/share/jupyter/kernels/caffe
ir /usr/local/share/jupyter/kernels/ir
pyspark /usr/local/share/jupyter/kernels/pyspark
pyspark2 /usr/local/share/jupyter/kernels/pyspark2
tensorflow /usr/local/share/jupyter/kernels/tensorflow
Again, as an example, here are the contents of the kernel.json for my R kernel (ir)
{
"argv": ["/usr/lib64/R/bin/R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"],
"display_name": "R 3.3.2",
"language": "R"
}
And here is the respective file for my pyspark2 kernel:
{
"display_name": "PySpark (Spark 2.0)",
"language": "python",
"argv": [
"/opt/intel/intelpython27/bin/python2",
"-m",
"ipykernel",
"-f",
"{connection_file}"
],
"env": {
"SPARK_HOME": "/home/ctsats/spark-2.0.0-bin-hadoop2.6",
"PYTHONPATH": "/home/ctsats/spark-2.0.0-bin-hadoop2.6/python:/home/ctsats/spark-2.0.0-bin-hadoop2.6/python/lib/py4j-0.10.1-src.zip",
"PYTHONSTARTUP": "/home/ctsats/spark-2.0.0-bin-hadoop2.6/python/pyspark/shell.py",
"PYSPARK_PYTHON": "/opt/intel/intelpython27/bin/python2"
}
}
As you can see, in both cases the first element of argv is the executable for the respective language - in my case, GNU R for my ir kernel and Intel Python 2.7 for my pyspark2 kernel. Changing this, so that it points to your GNU R executable, should resolve your issue.
To use a custom R environment I believe you need to set the following application properties when you start Spark:
"spark.r.command": "/custom/path/bin/R",
"spark.r.driver.command": "/custom/path/bin/Rscript",
"spark.r.shell.command" : "/custom/path/bin/R"
This is more completely documented here: https://spark.apache.org/docs/latest/configuration.html#sparkr
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
I think I have managed to mess my zsh shell. I am getting the following message when I use the up or down arrow keys:
"_history-substring-search-end:13: _zsh_highlight: function definition file not found"
Just to give you some background:
I installed antigen using
curl https://cdn.rawgit.com/zsh-users/antigen/v1.4.0/bin/antigen.zsh > antigen.zsh
source antigen.zs
This worked fine.
Someone mentioned to install it via brew, so I installed it via brew. This is when antigen stopped working and the highlighter.
I tried installing antigen again via
curl https://cdn.rawgit.com/zsh-users/antigen/v1.4.0/bin/antigen.zsh > antigen.zsh
source antigen.zs
Antigen works while I am in the shell, but the highlighter is not working.
But when I re-launch a new shell and type the antigen command, I receive the following message:
"zsh: command not found: anitgen"
And also the following message when I use the up and down arrow keys:
"_history-substring-search-end:13: _zsh_highlight: function definition file not found"
How can I fix this?