From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Thomas S. Dye" Subject: Re: R code not producing expected results Date: Thu, 12 Aug 2010 20:23:14 -1000 Message-ID: References: Mime-Version: 1.0 (Apple Message framework v936) Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit Return-path: Received: from [140.186.70.92] (port=60703 helo=eggs.gnu.org) by lists.gnu.org with esmtp (Exim 4.43) id 1Ojnfo-000670-9B for emacs-orgmode@gnu.org; Fri, 13 Aug 2010 02:23:25 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.69) (envelope-from ) id 1Ojnfl-0002kO-VO for emacs-orgmode@gnu.org; Fri, 13 Aug 2010 02:23:24 -0400 Received: from oproxy3-pub.bluehost.com ([69.89.21.8]:49635) by eggs.gnu.org with smtp (Exim 4.69) (envelope-from ) id 1Ojnfl-0002hM-Li for emacs-orgmode@gnu.org; Fri, 13 Aug 2010 02:23:21 -0400 In-Reply-To: List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: "Blanchette, Marco" Cc: "emacs-orgmode@gnu.org" Aloha Marco, Here is the code behind the Worg page: #+begin_src R :results output org library(ascii) options(asciiType="org") ascii(summary(table(1:4, 1:4))) #+end_src This works here. The key seems to be the header argument :results output #+BEGIN_SRC R :results output 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 #+results: #+begin_example Welcome to R! |----+------+-------+-------+-------+ | | V1 | V2 | V3 | V4 | |----+------+-------+-------+-------+ | V1 | 1.00 | 0.09 | 0.09 | 0.13 | | V2 | 0.09 | 1.00 | -0.00 | -0.13 | | V3 | 0.09 | -0.00 | 1.00 | 0.18 | | V4 | 0.13 | -0.13 | 0.18 | 1.00 | |----+------+-------+-------+-------+ #+end_example With it added to your other example, it does indeed generate a nice table. I think you are absolutely right about org-mode's babel capabilities helping with your R work. I can't imagine a better environment for working in R. Good luck with your work. All the best, Tom On Aug 12, 2010, at 6:32 PM, 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. > > 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 > > _______________________________________________ > Emacs-orgmode mailing list > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode