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 | |
| ##2013-12-09 dmontaner@cipf.es | |
| ##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; |
| #!/bin/sh | |
| #nemo_action_r_cmd_batch-sh | |
| #2013-12-09 dmontaner@cipf.es | |
| #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 | |
| ##2014-04-29 dmontaner@cipf.es | |
| ##Nautilus action file to run knitr::spin | |
| ## Custom action files (.nemo_action) may be located at: | |
| ## - /usr/share/nemo/actions/ | |
| ## - $HOME/.local/share/nemo/actions/ | |
| ## Icon-Name: must be the name of the file containing the image without extension. | |
| ## Must be located some of the icon folders of the system. | |
| ## In my Xfce this means: /usr/share/icons | |
| ## Selection: What type selection: [S]ingle, [M]ultiple, Any, NotNone, None (background click), | |
| ## or a number representing how many files must be selected to display. | |
| ## Defaults to Single if this field is missing. | |
| ## Extensions: What extensions to display on - this is an array, end with a semicolon | |
| ## Use "dir" for directory selection and "none" for no extension | |
| ## Use "any" by itself, semi-colon-terminated, for any file type | |
| ## Extensions are NOT case sensitive. jpg will match JPG, jPg, jpg, etc... | |
| [Nemo Action] | |
| Active=true | |
| Name=knitr spin HTML | |
| Comment=Runs knitr spin to crate an html file. | |
| Exec=/home/dmontaner/bin/000_david/nemo_action_spin_html.r %F | |
| Icon-Name=Rlogo | |
| Selection=Single | |
| Extensions=r; |
| #! /usr/local/bin/Rscript --vanilla | |
| ##nemo_action_spin_html.r | |
| ##2014-04-29 dmontaner@cipf.es | |
| ##This script uses knitr::spin to process an R file. | |
| ##Pandoc is may be used to obtain a PDF file. | |
| ## I use hidden variables in this script (names start with dot) | |
| ## so that rm in the compiled script does not clear them. | |
| ## In spin | |
| ## format = "Rmd" -> always creates the file .Rmd | |
| ## knit = TRUE -> creates the file .md | |
| ## report = TRUE -> creates the file .html | |
| ## R.version.string ##"R version 3.0.2 (2013-09-25)" | |
| ## packageDescription ("knitr", fields = "Version") #"1.5" | |
| library (tools) | |
| library (knitr) | |
| opts_chunk$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_html.nemo_action | |
| ##2014-04-29 dmontaner@cipf.es | |
| ##Nautilus action file to run knitr::spin | |
| ## Custom action files (.nemo_action) may be located at: | |
| ## - /usr/share/nemo/actions/ | |
| ## - $HOME/.local/share/nemo/actions/ | |
| ## Icon-Name: must be the name of the file containing the image without extension. | |
| ## Must be located some of the icon folders of the system. | |
| ## In my Xfce this means: /usr/share/icons | |
| ## Selection: What type selection: [S]ingle, [M]ultiple, Any, NotNone, None (background click), | |
| ## or a number representing how many files must be selected to display. | |
| ## Defaults to Single if this field is missing. | |
| ## Extensions: What extensions to display on - this is an array, end with a semicolon | |
| ## Use "dir" for directory selection and "none" for no extension | |
| ## Use "any" by itself, semi-colon-terminated, for any file type | |
| ## Extensions are NOT case sensitive. jpg will match JPG, jPg, jpg, etc... | |
| [Nemo Action] | |
| Active=true | |
| Name=knitr spin PDF | |
| Comment=Runs knitr spin to crate an html file. | |
| Exec=/home/dmontaner/bin/000_david/nemo_action_spin_pdf.r %F | |
| Icon-Name=Rlogo | |
| Selection=Single | |
| Extensions=r; |
| #! /usr/local/bin/Rscript --vanilla | |
| ##nemo_action_spin_html.r | |
| ##2014-04-29 dmontaner@cipf.es | |
| ##This script uses knitr::spin to process an R file. | |
| ##Pandoc is may be used to obtain a PDF file. | |
| ## I use hidden variables in this script (names start with dot) | |
| ## so that rm in the compiled script does not clear them. | |
| ## In spin | |
| ## format = "Rmd" -> always creates the file .Rmd | |
| ## knit = TRUE -> creates the file .md | |
| ## report = TRUE -> creates the file .html | |
| ## R.version.string ##"R version 3.0.2 (2013-09-25)" | |
| ## packageDescription ("knitr", fields = "Version") #"1.5" | |
| library (tools) | |
| library (knitr) | |
| opts_chunk$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") |