Rscript ggplot - ggsave problem

Question

I am using the following code to draw a graph and print it to a PDF:

ggplot(agg_data_cl, aes( as.Date(date), avg_entries, color = classification ) ) +
  geom_point()

ggsave(file = "output.pdf")

This works fine when I execute the script in TextMate.

But when I call it from the commandline via RScript I get the following error:

Error in all.vars(as.formula(.$facets)) : 
  could not find function "as.formula"
Calls: print ... <Anonymous> -> <Anonymous> -> <Anonymous> -> all.vars
Execution halted

I use the following header in my RScrpipt file:

#! /usr/local/bin/Rscript --vanilla --default-packages=utils

Any ideas what could be the problem?

Here is my command line session information:

R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] grid  utils base 

other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2   

loaded via a namespace (and not attached):
[1] grDevices_2.13.1 graphics_2.13.1  stats_2.13.1

In textmate sessionInfo() gives me more attached base packages:

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base

I have no idea why this the case.

Answer 1

Two things:

1) Make sure you have library(ggplot2) _in_your_script_

2) Make sure you print() or plot() the ggplot object. (See the FAQ 7.22) This may not be the problem in this instance, since you are gg-saving, but it is a common problem with lattice or ggplot graphics from Rscript sessions.

Answer 2

The problem was the --vanilla option when calling Rscript.

Here is what Rscript --help says about its options

--save              Do save workspace at the end of the session
--no-environ        Don't read the site and user environment files
--no-site-file      Don't read the site-wide Rprofile
--no-init-file      Don't read the user R profile
--restore           Do restore previously saved objects at startup
--vanilla           Combine --no-save, --no-restore, --no-site-file
                    --no-init-file and --no-environ

..and --vanilla basically means that Rscriptshould forget everything before it starts executing R commands, including some of the installed packages.

Answer 3

as.formula is in the stats package. Not sure why it isn't being loaded, but see if manually including library(stats) at the start of your script fixes the issue.