On Thu, 12 Aug 2010, Blanchette, Marco wrote:
Dear all,
Sorry if this is something totally obvious but I am learning to use
org-mode for my everyday work with R. I just installed the latest
stable release of org-mode (v7.01g) on top of GNU Emacs 23.1.50.1
(x86_64-apple-darwin10.2.0, NS apple-appkit-1038.25). I also
installed the CRAN ascii package v0.7 on top of R v2.11.1. I am
currently working on a MacBook pro with Snow Leopard 10.6.4
Early on today, while reading the org-babel intro, I was able to run
the following example but somehow, later tonight, it started to
break and I spent the last few hours scratching my head to
understand what change and why it now suddenly break. Your help will
be greatly appreciated as I am discovering that org-mode in
collaboration with org-babel have great potential to help us create
more readable report of our daily analysis, as long as I can get
through these early hurdles.
The code you say is "straight from ...org-babel-doc-R.php" is not quite.
Note all the header args:
#+begin_src R :results output code :session ascii
Also note that ascii() does not return an object of class "matrix" or
"data.frame". Try str(ascii( < all the rest > )).
With :results value (the default) you will get a different outcome as
you saw below.
'value' tries to be smart about what it does with .Last.value, but "ascii"
objects are a bit too tricky for it.
'output' on the other hand is pretty simple on the elisp side and
relies on R's print() to get the dispatch for the print method right.
If you want to use ':results value' you will need to form a data.frame
from ascii() yourself, rather than rely on as.data.frame to find a method
to do the conversion. Or you will need to write a method for
as.data.frame.ascii.
HTH,
Chuck
Here is the org buffer that now breaks:
* Two examples of R code that worked when I started the tutorial but suddenly
started to fail...
** some R code that should generate a nice table
#+BEGIN_SRC R
library(ascii)
options(asciiType="org")
d <- as.data.frame(replicate(4,rnorm(100)))
ascii(cor(d),include.rownames=T, include.colnames=T,header=T)
#+END_SRC
** Some code straight from
[[http://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-R.php][org-babel]]
#+BEGIN_SRC R
library(ascii)
options(asciiType="org")
ascii(summary(table(1:4, 1:4)))
#+END_SRC
With the following error recover from the *Org-Babel Error* buffer
Loading required package: proto
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class 'c("ascii", "proto", "environment")' into a data.frame
Calls: write.table ... data.frame -> as.data.frame -> as.data.frame.default
Execution halted
Thanks for the helps.
--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.
Kansas City, MO 64110
Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018
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Charles C. Berry (858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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