How to set up a Nemo (file manager) Actions to execute an R script in BATCH mode. Knitr spin based versions included.

about_nemo_actions.md

This files and scripts are used to set up some actions for the Nemo file manager. Those actions will let you execute an R script in BATCH mode but using the Nemo graphical interface.

The first action uses the Linux shell command R CMD BATCH and will produce an .Rout file (besides the script results).

The two last action use knitr::spin and Pandoc to create HTML or PDF log/report files.

nemo_action_r_cmd_batch.nemo_action

##nemo_action_r_cmd_batch.nemo_action
##2013-12-09 [email protected]
##Nautilus action file to execute R CMD BATCH

## Custom action files (.nemo_action) may be located at: 
## - /usr/share/nemo/actions/
## - $HOME/.local/share/nemo/actions/

## Icon-Name: must be the name of the file containing the image without extension.
##            Must be located some of the icon folders of the system.
##            In my Xfce this means: /usr/share/icons

## Selection: What type selection: [S]ingle, [M]ultiple, Any, NotNone, None (background click), 
##            or a number representing how many files must be selected to display.
##            Defaults to Single if this field is missing.

## Extensions: What extensions to display on - this is an array, end with a semicolon
##             Use "dir" for directory selection and "none" for no extension
##             Use "any" by itself, semi-colon-terminated, for any file type
##             Extensions are NOT case sensitive. jpg will match JPG, jPg, jpg, etc...


[Nemo Action]
Active=true
Name=R CMD BATCH
Comment=Runs an R script in batch mode

Exec=/home/dmontaner/bin/000_david/nemo_action_r_cmd_batch.sh %F

Icon-Name=Rlogo
Selection=Single
Extensions=r;

nemo_action_r_cmd_batch.sh

#!/bin/sh
#nemo_action_r_cmd_batch-sh
#2013-12-09 [email protected]
#execute an R scripts in R CMD BATCH from Nemo

## Argument $1 should catch %F, the full path to the file to be executed.

mydir=`dirname $1`
cd $mydir

R CMD BATCH --no-save --no-restore $1

nemo_action_spin_html.nemo_action

##nemo_action_spin_html.nemo_action
##2014-04-29 [email protected]
##Nautilus action file to run knitr::spin

## Custom action files (.nemo_action) may be located at: 
## - /usr/share/nemo/actions/
## - $HOME/.local/share/nemo/actions/

## Icon-Name: must be the name of the file containing the image without extension.
##            Must be located some of the icon folders of the system.
##            In my Xfce this means: /usr/share/icons

## Selection: What type selection: [S]ingle, [M]ultiple, Any, NotNone, None (background click), 
##            or a number representing how many files must be selected to display.
##            Defaults to Single if this field is missing.

## Extensions: What extensions to display on - this is an array, end with a semicolon
##             Use "dir" for directory selection and "none" for no extension
##             Use "any" by itself, semi-colon-terminated, for any file type
##             Extensions are NOT case sensitive. jpg will match JPG, jPg, jpg, etc...


[Nemo Action]
Active=true
Name=knitr spin HTML
Comment=Runs knitr spin to crate an html file.

Exec=/home/dmontaner/bin/000_david/nemo_action_spin_html.r %F

Icon-Name=Rlogo
Selection=Single
Extensions=r;

nemo_action_spin_html.r

#! /usr/local/bin/Rscript --vanilla

##nemo_action_spin_html.r
##2014-04-29 [email protected]
##This script uses knitr::spin to process an R file.
##Pandoc is may be used to obtain a PDF file.

## I use hidden variables in this script (names start with dot)
## so that rm in the compiled script does not clear them.
 
## In spin
## format = "Rmd" -> always creates the file .Rmd
## knit   = TRUE  -> creates the file .md
## report = TRUE  -> creates the file .html

## R.version.string ##"R version 3.0.2 (2013-09-25)"
## packageDescription ("knitr", fields = "Version") #"1.5"

library (tools)
library (knitr)
opts_chunk$set (echo = FALSE, comment = "", results = "hide") ## results = "markup" results = "hide" results = "asis"

## input file
.inFile = commandArgs (trailingOnly = TRUE)[1]
.baFile <- file_path_sans_ext (.inFile)

 .mdFile  <- paste0 (.baFile, ".md")
.rmdFile  <- paste0 (.baFile, ".Rmd")

## wd for knitr; otherwhise it works at home
setwd (dirname (.inFile))


## spin HTML
.htmlFile <- paste0 (.baFile, ".html")
unlink (.htmlFile)
spin (.inFile, knit = TRUE, report = TRUE, format = "Rmd") ##html
unlink (c (.rmdFile, .mdFile))

## ## spin PDF
## .pdfFile  <- paste0 (.baFile, ".pdf")
## unlink (.pdfFile)
## spin (.inFile, knit = TRUE, report = FALSE, format = "Rmd") ##just md
## system (paste ("pandoc -V geometry:margin=25mm -o", .pdfFile, .mdFile))
## unlink (c (.rmdFile, .mdFile))

## exit
q ("no")

nemo_action_spin_pdf.nemo_action

##nemo_action_spin_html.nemo_action
##2014-04-29 [email protected]
##Nautilus action file to run knitr::spin

## Custom action files (.nemo_action) may be located at: 
## - /usr/share/nemo/actions/
## - $HOME/.local/share/nemo/actions/

## Icon-Name: must be the name of the file containing the image without extension.
##            Must be located some of the icon folders of the system.
##            In my Xfce this means: /usr/share/icons

## Selection: What type selection: [S]ingle, [M]ultiple, Any, NotNone, None (background click), 
##            or a number representing how many files must be selected to display.
##            Defaults to Single if this field is missing.

## Extensions: What extensions to display on - this is an array, end with a semicolon
##             Use "dir" for directory selection and "none" for no extension
##             Use "any" by itself, semi-colon-terminated, for any file type
##             Extensions are NOT case sensitive. jpg will match JPG, jPg, jpg, etc...


[Nemo Action]
Active=true
Name=knitr spin PDF
Comment=Runs knitr spin to crate an html file.

Exec=/home/dmontaner/bin/000_david/nemo_action_spin_pdf.r %F

Icon-Name=Rlogo
Selection=Single
Extensions=r;

nemo_action_spin_pdf.r

#! /usr/local/bin/Rscript --vanilla

##nemo_action_spin_html.r
##2014-04-29 [email protected]
##This script uses knitr::spin to process an R file.
##Pandoc is may be used to obtain a PDF file.

## I use hidden variables in this script (names start with dot)
## so that rm in the compiled script does not clear them.
 
## In spin
## format = "Rmd" -> always creates the file .Rmd
## knit   = TRUE  -> creates the file .md
## report = TRUE  -> creates the file .html

## R.version.string ##"R version 3.0.2 (2013-09-25)"
## packageDescription ("knitr", fields = "Version") #"1.5"

library (tools)
library (knitr)
opts_chunk$set (echo = FALSE, comment = "", results = "hide") ## results = "markup" results = "hide" results = "asis"

## input file
.inFile = commandArgs (trailingOnly = TRUE)[1]
.baFile <- file_path_sans_ext (.inFile)

 .mdFile  <- paste0 (.baFile, ".md")
.rmdFile  <- paste0 (.baFile, ".Rmd")

## wd for knitr; otherwhise it works at home
setwd (dirname (.inFile))


## ## spin HTML
## .htmlFile <- paste0 (.baFile, ".html")
## unlink (.htmlFile)
## spin (.inFile, knit = TRUE, report = TRUE, format = "Rmd") ##html
## unlink (c (.rmdFile, .mdFile))

## spin PDF
.pdfFile  <- paste0 (.baFile, ".pdf")
unlink (.pdfFile)
spin (.inFile, knit = TRUE, report = FALSE, format = "Rmd") ##just md
system (paste ("pandoc -V geometry:margin=25mm -o", .pdfFile, .mdFile))
unlink (c (.rmdFile, .mdFile))

## exit
q ("no")