Summary re: read.table on Mac OS 10

Thanks to all who responded.  Not all of the advice
helped me with that particular problem, but, I have
learned a lot just from your answers.

1.  R for Mac 10 (Carbon version) uses the Mac
convention of using ":" for the usual Unix "/" and thanks
to Dr. Lumley for that since I'm new to R, Mac10, Macs
in general, and Unix.
2.  Interestingly, Dr. Ripley suggested to me not to use
spaces in the path as R wouldn't be able to read them.
I've found that on my Mac, spaces often come as
default in file names.  As long as I use the ":" (see 1) I
can also use a space.  I'm not sure of the Darwin/
Xwinows version of R.  Looks like another Mac
convention though.
3.  The problem is partially solved:  I never was able to
read the data set I made with Mac's TextEdit.  But, on
entering the data at R's runtime window, I was able to
write.table to an external file, shut down R and/or the
computer, and come back later to read.table ... no
problem.  Perhaps TextEdit throws some extra code in,
not sure <although I did save the data as simple text
and fixed width format, really the only two options I
could manipulate in TextEdit>  I'll try Mac SimpleText (a
Developer Tool) and emacs to see what happens with
them.
4.  Having fun with R!

Thanks again for the help, if things with the text editors
and read.table change I'll post my findings.

Cheers,
Jason Boyd
graduate student
University of Georgia
College of Pharmacy

600 MHz 128 Mb iBook Mac OS 10.1, Fink & DevTools
Carbonized R1.4.0

***original message follows***
From: Ben Bolker <ben at zoo.ufl.edu>
Date: Tue Feb 19, 2002  09:28:37 X US/Eastern
To: Jason Boyd <BOYDJ at mail.rx.uga.edu>
Cc: R help list <r-help at stat.math.ethz.ch>
Subject: Re: [R] error in read.table on Mac OS 10 ... request for help
Reply-To: <bolker at zoo.ufl.edu>


  I haven't seen any answers to this, so I'll try to provide some other
things to try (although I don't really know what's going on).

  Try getwd() to see how paths appear to be specified internally.  You
could also try setwd("/Users/Shared/rm140_FULL/work") before
read.table("...").  Also try list.files() to check out the file names.

  It does seem you've been pretty thorough.

  good luck,
   Ben Bolker

On Fri, 15 Feb 2002, Jason Boyd wrote:

Hello,
I'm a new user of R, and unsure of why I'm getting an
error reading external files on my Mac OS 10 machine.
I've read through posts that would seem related (and 'R
Import/Export' and 'Introduction to R' as well as
pertinent sections in V&R's 'Modern Applied Statistics
with S-Plus') but to no avail.    If anyone has any
suggestions, I'd be very grateful.  Here's the problem:

When I enter the command:

idusc <- read.table(file = "/Users/Shared/

rm140_FULL/work/ioddupb.txt")

I get the message:

Error in file(file, "r") : cannot open file `/Users/Shared/
rm140_FULL/work/ioddupb.txt'

This is the correct path according to my Finder
window's "path" tab (that is, as far as Users is a folder
under /) and also according to the command line
interface (shell).  I'm not sure why it can't read the file.
I'm new to Unix systems also, so perhaps I've
misunderstood paths (though I've been reading over
Unix tutorials enough not to scare me). Other info:

1.  the file was created in simple text mode in Mac
TextEdit and saved fixed width text format.

2.  when I save the file to another working directory
under a different user, I also cannot read.table

3.  I checked the priveleges of the .txt file, they were
Read & write for the owner and Read for everyone else
so that would seem to take care of R being able to copy
it.

4.  I also tried read.fwf with the same type error
message.

5.  The tutorials and examples as well as libraries all
work fine, I can read data in the libraries, use add-on
functions, and plot so it doesn't seem to be a problem
with R itself.

I'm sure this is just a simple matter but I'm perplexed.
Thanks for any suggestions,

Jason Boyd

graduate student
University of Georgia
College of Pharmacy
boydj at mail.rx.uga.edu

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--
318 Carr Hall                                bolker at zoo.ufl.edu
Zoology Department, University of Florida    
http://www.zoo.ufl.edu/bolker
Box 118525                                   (ph)  352-392-5697
Gainesville, FL 32611-8525                   (fax) 352-392-3704

I am having the same problem (#3) with read.table on Darwin. The edit()
function is not a work-around for me since I have to read an enormous
text file. I tried copying the data from TextEdit and pasting it into vi
and Project Builder, but that didn't help at all. I wonder if this is
related to the MacOS convention of ending lines with "\l" instead of
"\n".

The strange thing is that read.delim() seems to work fine.

On Tuesday, February 19, 2002, at 06:22 †, Jason Boyd wrote:

Thanks to all who responded.  Not all of the advice
helped me with that particular problem, but, I have
learned a lot just from your answers.

1.  R for Mac 10 (Carbon version) uses the Mac
convention of using ":" for the usual Unix "/" and thanks
to Dr. Lumley for that since I'm new to R, Mac10, Macs
in general, and Unix.
2.  Interestingly, Dr. Ripley suggested to me not to use
spaces in the path as R wouldn't be able to read them.

On Wed, 20 Feb 2002, David R. Bickel wrote:

I am having the same problem (#3) with read.table on Darwin. The edit()
function is not a work-around for me since I have to read an enormous
text file. I tried copying the data from TextEdit and pasting it into vi
and Project Builder, but that didn't help at all. I wonder if this is
related to the MacOS convention of ending lines with "\l" instead of
"\n".

It's CR (ctrl-J, \r) as far as I know.

Neither of you have anywhere told us what the actual error message was
in problem number 3.

Prof. Ripley,

I encountered the read.table problem in the Darwin version using
as.is=TRUE, but not with as.is=FALSE. It gives different results than
the Carbon version does. The output for each version follows; 'temp'
is a two-line text file with three tab-delimited columns.

Prof. Ripley,

I encountered the read.table problem in the Darwin version using
as.is=TRUE, but not with as.is=FALSE. It gives different results than
the Carbon version does. The output for each version follows; 'temp' is
a two-line text file with three tab-delimited columns.

UNDER DARWIN:

 > read.table('temp')

               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11

 > read.table('temp',as.is=TRUE)

stack imbalance in internal type.convert, 26 then 25stack imbalance in
Internal, 25 then 24
stack imbalance in if, 19 then 18
stack imbalance in <-, 17 then 16
stack imbalance in {, 15 then 14
stack imbalance in for, 8 then 7
stack imbalance in {, 6 then 5
               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11
Error: unprotect(): stack imbalance

UNDER CARBON:

 > read.table('temp')

               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11

 > read.table('temp',as.is=TRUE)

               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11

Best regards,
David


On Thursday, February 21, 2002, at 02:13 X, Prof Brian Ripley wrote:

Neither of you have anywhere told us what the actual error message was
in problem number 3.

http://www.mcg.edu/research/biostat/bickel.html

David R. Bickel, PhD
Assistant Professor
Medical College of Georgia
Office of Biostatistics and Bioinformatics
1120 Fifteenth St., AE-3037
Augusta, GA 30912-4900

Tel.: 706-721-4697; Fax: 706-721-6294
E-mail: dbickel at mail.mcg.edu or bickel at prueba.info

That's not the current version of R.  When you update to 1.4.1 you'll
see the bug fix list includes this.

It transpired that the posting earlier today about the speed of 
read.table
on Darwin vs Carbon was also a difference in R version (1.4.0 vs 1.3.1).

Please do tell us the R version(s) you are using when posting.
Installing 1.x.1 to replace 1.x.0 is highly recommended, for all values 
of
x.

On Thu, 21 Feb 2002, David R. Bickel wrote:

Prof. Ripley,

I encountered the read.table problem in the Darwin version using
as.is=TRUE, but not with as.is=FALSE. It gives different results than
the Carbon version does. The output for each version follows; 'temp' is
a two-line text file with three tab-delimited columns.

UNDER DARWIN:

read.table('temp')

               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11

read.table('temp',as.is=TRUE)

stack imbalance in internal type.convert, 26 then 25stack imbalance in
Internal, 25 then 24
stack imbalance in if, 19 then 18
stack imbalance in <-, 17 then 16
stack imbalance in {, 15 then 14
stack imbalance in for, 8 then 7
stack imbalance in {, 6 then 5
               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11
Error: unprotect(): stack imbalance

UNDER CARBON:

read.table('temp')

               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11

read.table('temp',as.is=TRUE)

               V1   V2   V3
1 AFFX-BioB-5_at -214 -139
2 AFFX-BioB-M_at  -49  -11

Best regards,
David


On Thursday, February 21, 2002, at 02:13 X, Prof Brian Ripley wrote:

Neither of you have anywhere told us what the actual error message was
in problem number 3.

--
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272860 (secr)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595