emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
From: Daniel Drake <silophophe@gmail.com>
To: Eric Schulte <eric.schulte@gmx.com>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: [0][babel][R] Undesired conversion of integers to floats in R code block output
Date: Sat, 18 Feb 2012 23:02:43 -0800	[thread overview]
Message-ID: <4F409E93.5010800@gmail.com> (raw)
In-Reply-To: <87boowrtyv.fsf@gmx.com>

On 02/18/2012 08:23 AM, Eric Schulte wrote:
> Daniel Drake<silophophe@gmail.com>  writes:
>> Hi All,
>> I'm using R in org-mode/babel to analyze data from a psychological
>> study.  The subjects in this study are identified by nine digit integers
>> (e.g., 987654321) that I treat as strings (or factors) in my R data
>> frames.
>> Tables output by an R code block that contain these subject IDs are
>> not formatted properly: the subject IDs seem to be treated as numbers
>> and a decimal point and a trailing zero are appended.  For example,
>> what should be
>> |   subj.id |
>> |-----------|
>> | 987654321 |
>> becomes
>> |     subj.id |
>> | 987654321.0 |
>> (I've included real, self-contained code below.)
>> When I write the data frames directly to a file from within the R code
>> block (using a write.table function call that mimics the one in
>> ob-R.el), the integer IDs are preserved; but when code from ob-R.el
>> writes them out, the values get reformated as floats.
>> I've noticed that eight digit integers are not modified in the same
>> way, which makes me wonder if there is a 'digits' threshold I could
>> modify to prevent this from happening.
>> I've pretty much ruled out the possibility that this transformation
>> occurs in R; however I'm not proficient enough in elisp to follow the
>> operations that happen after the data frame is written to a file in
>> the org-babel-R-write-object-command.
>> Any pointers to help me figure this out would be very appreciated!
>> (I've seen this thread:
>> http://comments.gmane.org/gmane.emacs.orgmode/31373, but do not know
>> if the conversion to calc has been made already or if it is the source
>> of the problem.)
> Hi Dan,
> When I launch Emacs without any personal configuration (emacs -Q),
> evaluate ob-R.el to add R support, and then execute your code blocks I
> get the following behavior.
> I would recommend installing the latest version of Org-mode from source
> as that tends to fix many problems, and will at least ensure that we are
> both working from the same code base moving forward.  See
> http://orgmode.org/worg/org-faq.html#Keeping-current
> Best,

Hi Eric,
First of all, thanks for your reply.

Just to be safe, I nuked my org-mode directory and re-cloned from the 
git repository: I'm now at release_7.8.03.386.g2239d (I was at 
release_7.8.03-351-g47eb3 previously).  Is there a more recent version? 
  I also removed the org directory that came with the packaged version 
of emacs, just in case.

I start emacs with the following options:
$ emacs -Q -eval '(setq load-path (cons 
"~/share/emacs/site-lisp/org-mode/lisp" load-path))' -eval "(require 
'ob-R)" test.org

I get the same behavior as before.  I was a little puzzled when I saw 
this happen, as I've been working on this study for over a year in org 
and it's the first time I've seen this behavior.  I went back and tried 
previous versions (e.g., 7.4), and now I see the same thing.

I wonder if Arch (a rolling release linux distribution that tries to be 
close to the leading edge) has updated an underlying library that 
impacts the babel code in some odd way.  (Granted, I don't see how this 
could be, as the emacs environment seems pretty well insulated from the 
underlying OS; PEBKAC just as likely.)

In any event, since you can't reproduce the behavior (thanks again for 
trying), I don't expect it's anything you can fix.  Maybe it will show 
up in other distributions as they update to more current versions.  In 
the mean time, I'll try to improve my elisp skills and figure out where 
the extraneous formatting occurs.


- GNU Emacs 23.4.1 (i686-pc-linux-gnu, GTK+ Version 2.24.9) of 
2012-02-01 on shirley.hoetzel.info
- Org-mode version 7.8.03 (release_7.8.03.386.g2239d)

  reply	other threads:[~2012-02-19  7:05 UTC|newest]

Thread overview: 11+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2012-02-16 19:07 [0][babel][R] Undesired conversion of integers to floats in R code block output Daniel Drake
2012-02-18 16:23 ` Eric Schulte
2012-02-19  7:02   ` Daniel Drake [this message]
2012-02-19 16:48     ` Eric Schulte
2012-02-19 17:40       ` Daniel Drake
2012-02-19 18:28         ` Daniel Drake
2012-02-19 19:27           ` Daniel Drake
2012-02-19 20:46             ` Eric Schulte
2012-02-19 21:19               ` Daniel Drake
2012-02-19 21:35               ` Achim Gratz
2012-02-20 17:36                 ` Achim Gratz

Reply instructions:

You may reply publicly to this message via plain-text email
using any one of the following methods:

* Save the following mbox file, import it into your mail client,
  and reply-to-all from there: mbox

  Avoid top-posting and favor interleaved quoting:

  List information: https://www.orgmode.org/

* Reply using the --to, --cc, and --in-reply-to
  switches of git-send-email(1):

  git send-email \
    --in-reply-to=4F409E93.5010800@gmail.com \
    --to=silophophe@gmail.com \
    --cc=emacs-orgmode@gnu.org \
    --cc=eric.schulte@gmx.com \


* If your mail client supports setting the In-Reply-To header
  via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line before the message body.
Code repositories for project(s) associated with this public inbox


This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).