I have a rmd file and would like to run that on a university remote cluster. But have not been able. I appreciate help.
let's say I named the rmd file as "mycode.rmd" and below is its sample example.
title: "title"
output:
html_document:
toc: true
toc_depth: 3
number_sections: true
theme: united
highlight: tango
header-includes:
- \usepackage{amsthm}
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
rm(list = ls())
library(readr)
data = read_csv("df.csv")
.
.
.
Here is an step by step procedure I did
- got connected to the cluster I loaded the R module on the cluster
- installed the packages in the code and set the R library environment variable (R_LIBS) to include my R package directory
export R_LIBS=~/Rlibs
a) After copying the file in the cluster's given storage space I tried to create a binary file to run. Here is the code in the cmd
R mycode.Rmd -o run.exe
I got the following error:
ARGUMENT 'mycode.Rmd' __ ignored __ WARNING: unknown option '-o' ARGUMENT 'run.exe' __ ignored __
b) I also tried this code
R rmarkdown::render"('mycode.Rmd',output_file='result.html')" -o run.exe
The error was the same.
is the above a way to do it but commands are wrong? If not how can I run a rmd file on a cluster.
Finally, The cluster is using Slurm so once the binary is created I will need to write a sbatch file and run the binary.