Re: [Rd] R 2.1 dies when some text() arguments are NULL (PR#7477)

[MSchwartz]

On Fri, 2005-01-07 at 04:44 +0100, [EMAIL PROTECTED] wrote:
> 
> [My very deepest apologies in advance if this is not plain text; I am 
> recently at a new job in a windows-based environment and have 
> not yet set up my favorite old (pine) system. I have tried my best to 
> strip all formatting from the message..]
> 
> I'm overlaying plots of tree locations mapped before and after 
> logging activities and checking my matched individuals using 
> several arguments to text() which plot tree attributes by or 
> near their (x,y) locations. R 2.1 dies when a coding error on 
> my part results in a null data.frame...
> 
> Example: 
> 
> plot(1)
> text(NULL ~ NULL, label=NULL)
> 
> This happens for me under Windows 98 and XP. Andrew Robinson 
> was kind enough to try it for me on FreeBSD with the same result. 
> The code returns nothing for me under R 1.9 on Windows 98 and 
> XP (same win. machines).  The version details of the three 
> are as follows:
> 
> # FreeBSD:
> 
> >version
>  _  
> platform i386-portbld-freebsd5.3
> arch i386   
> os   freebsd5.3 
> system   i386, freebsd5.3   
> status  
> major2  
> minor0.1
> year 2004   
> month11 
> day  15 
> language R  
> 
> # Windows XP:
> 
> > version
>  _  
> platform i386-pc-mingw32
> arch i386   
> os   mingw32
> system   i386, mingw32  
> status  
> major2  
> minor0.1
> year 2004   
> month11 
> day  15 
> language R   
> 
> # Windows 98:
> 
> > version
>  _  
> platform i386-pc-mingw32
> arch i386   
> os   mingw32
> system   i386, mingw32  
> status  
> major2  
> minor0.1
> year 2004   
> month11 
> day  15 
> language R   
> 
> Please let me know if I can add any more details-
> 
> Thank you,
> 
> Rob 

Your subject line and body refer to R version 2.1, which technically
does not exist as 2.1.0 is the current development version. 

However, your output above indicates that R version 2.0.1 is what you
have installed on the three platforms. That is the current released
version.

In either case, using:

Version 2.0.1 Patched (2005-01-02)

I get the following:

> plot(1)
> text(NULL ~ NULL, label=NULL)
Error in text(xy.coords(x, y, recycle = TRUE), labels, adj, pos,
offset,  :
no coordinates were supplied


Same thing with:

> plot(1)
> text(NULL, NULL, label = NULL)
Error in text.default(NULL, NULL, label = NULL) :
x and y lengths differ in text().


No crash.


There is the following note in the NEWS file for 2.0.1 patched:

"text()'s default method could segfault if passed 0-length coordinates."

So I believe that this fixes the issue that you have posted about.


A patched version for Windows is available via CRAN:

http://www.cran.mirrors.pair.com/bin/windows/base/rpatched.html

and a source code tarball is available for the *nix versions via the FTP
link under the R Sources link:

ftp://ftp.stat.math.ethz.ch/Software/R/

HTH,

Marc Schwartz

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[Rd] R 2.1 dies when some text() arguments are NULL (PR#7477)

[Robert_Keefe]

[My very deepest apologies in advance if this is not plain text; I am 
recently at a new job in a windows-based environment and have 
not yet set up my favorite old (pine) system. I have tried my best to 
strip all formatting from the message..]

I'm overlaying plots of tree locations mapped before and after 
logging activities and checking my matched individuals using 
several arguments to text() which plot tree attributes by or 
near their (x,y) locations. R 2.1 dies when a coding error on 
my part results in a null data.frame...

Example: 

plot(1)
text(NULL ~ NULL, label=NULL)

This happens for me under Windows 98 and XP. Andrew Robinson 
was kind enough to try it for me on FreeBSD with the same result. 
The code returns nothing for me under R 1.9 on Windows 98 and 
XP (same win. machines).  The version details of the three 
are as follows:

# FreeBSD:

>version
 _  
platform i386-portbld-freebsd5.3
arch i386   
os   freebsd5.3 
system   i386, freebsd5.3   
status  
major2  
minor0.1
year 2004   
month11 
day  15 
language R  

# Windows XP:

> version
 _  
platform i386-pc-mingw32
arch i386   
os   mingw32
system   i386, mingw32  
status  
major2  
minor0.1
year 2004   
month11 
day  15 
language R   

# Windows 98:

> version
 _  
platform i386-pc-mingw32
arch i386   
os   mingw32
system   i386, mingw32  
status  
major2  
minor0.1
year 2004   
month11 
day  15 
language R   

Please let me know if I can add any more details-

Thank you,

Rob 

_

Rob Keefe

Cooperative Forestry Research Unit
University of Maine

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Re: [Rd] Standalone Mathlib, C++ and ISNAN()

[Bill Northcott]

On 06/01/2005, at 10:16 PM, Martyn Plummer wrote:
I think the workaround is supposed to look like this:
#define _GLIBCPP_USE_C99 1
#include 
#undef _GLIBCPP_USE_C99
#include 
using __gnu_cxx::isnan;
I thought I had tried that, but I was not sure.  So I tried again this 
morming, and it definitely does not work on MacOS X.  The problem being 
that the undefs in cmath are unconditional.

I presume it works on Linux because isnan is a function.
Bill Northcott
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Re: [Rd] Broken Link for gregmisc_2.0.0.zip

[Duncan Murdoch]

On Thu, 6 Jan 2005 13:06:51 +0100, [EMAIL PROTECTED] wrote
>
>Not really ... we had the webmaster address on almost all pages of
>CRAN until 2 or 3 years ago. I removed it deliberately from most
>places because way too many people confused it with r-help.

How about a "Contact Us" link on each page, which goes to a page that
lists the various possible contact addresses, with r-help first?  We
wouldn't want to put in the r-help submission address there; it should
be a link to  or
some other page that tells people what to expect, and lets them search
the archives.

Duncan Murdoch

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RE: [Rd] Broken Link for gregmisc_2.0.0.zip

[Warnes, Gregory R]

> Sorry, my fault. I included the index building in a cron job and that
> was broken. Should work now.
> 

Seems to work now.


>   > Uwe
> 
>   >> 
>   >>> Also, could the appropriate email address for reporting 
> web site problems
>   >>> please be added to the website in some conspicous place?
>   >> 
>   >> 
>   >> Good idea.
>   >> 
> 
> Not really ... we had the webmaster address on almost all pages of
> CRAN until 2 or 3 years ago. I removed it deliberately from most
> places because way too many people confused it with r-help.
> 
> And I doubt that people like Greg really have problems finding out how
> to contact Kurt or me ;-)
> 

The broken link was reported to my by users, who weren't really savvy, and
they would be unlikely to know..


> Best.
> Fritz
> 


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Re: [Rd] Broken Link for gregmisc_2.0.0.zip

[Friedrich . Leisch]

> On Thu, 06 Jan 2005 08:50:44 +0100,
> Uwe Ligges (UL) wrote:

  > Peter Dalgaard wrote:
  >> "Warnes, Gregory R" <[EMAIL PROTECTED]> writes:
  >> 
  >> 
  >>> The link from
  >>> http://cran.r-project.org/src/contrib/Descriptions/gregmisc.html to the
  >>> windows package  gregmisc_2.0.0.zip is broken.  
  >> 
  >> 
  >> Looks like a generic errors in mirroring the windows packages. Has
  >> happened before.

  > Not quite, Windows packages are mirrored correctly, but all (?) links to 
  > Windows *and* Mac OS X binary packages in the packages' Descriptions on 
  > CRAN are broken.

Sorry, my fault. I included the index building in a cron job and that
was broken. Should work now.

  > Uwe

  >> 
  >>> Also, could the appropriate email address for reporting web site problems
  >>> please be added to the website in some conspicous place?
  >> 
  >> 
  >> Good idea.
  >> 

Not really ... we had the webmaster address on almost all pages of
CRAN until 2 or 3 years ago. I removed it deliberately from most
places because way too many people confused it with r-help.

And I doubt that people like Greg really have problems finding out how
to contact Kurt or me ;-)

Best.
Fritz

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Re: [Rd] Standalone Mathlib, C++ and ISNAN()

[Martyn Plummer]

On Thu, 2005-01-06 at 08:29 +1100, Bill Northcott wrote:
> On 06/01/2005, at 6:53 AM, Thomas Lumley wrote:
> >
> > I believe (with a little Googling) the suggested C++ approach is to 
> > use std::isnan if  is included.
> >
> I tried that too, but without any success.  I even tried 
> __gnu_cxx::isnan.
> 
> It was suggested by one of the gcc people, but I could find no 
> documentation about it.  The ISO C++ docs do not include isnan as a 
> symbol provided by cmath within the std namespace.  I looked at the gcc 
> source code and could see no reason why it should work.

I think the workaround is supposed to look like this:

#define _GLIBCPP_USE_C99 1
#include 
#undef _GLIBCPP_USE_C99
#include 

using __gnu_cxx::isnan;

I don't know whether this solves the problem on MacOs X but it is valid
on Linux.  But do you really want to write code that is specific to gcc?
I don't.

Martyn

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Re: [Rd] Standalone Mathlib, C++ and ISNAN()

[Bill Northcott]

On 06/01/2005, at 3:31 PM, John W. Eaton wrote:
What I finally decided to do for Octave was to use a C language
autoconf test for isnan, then provide a function declared "extern C"
that is a wrapper around the C isnan function (if it exists).  I also
use this method for other functions that may be easier to call from C
than directly from C++.
Thanks for confirming my suspicions.
As far as I can see that is just what R has done with the R_IsNaN 
function.  I am just asking that it be included in the standalone Rmath 
library.

Bill Northcott
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Re: [Rd] install.packages and bundles

[Uwe Ligges]

Warnes, Gregory R wrote:
Hi All,
Since I changed the gregmisc package into a bundle, I almost daily questions
asking how to get the individual packages contained in the bundle.  

The standard example arises when someone attempts to install and then use my
'genetics' package which depends on the 'gdata' package contained within the
'gregmisc' bundle.  The install succedes, but when the user does
library(genetics) they get the error message:
	> library(genetics)
	Loading required package: gdata 
	Error: package 'gdata' could not be loaded

The user then attempts to install the package 'gdata' not realizing that it
is part of the (e.g.) gregmisc bundle, and can't find it.  For example
> install.packages("gdata")
trying URL
`http://cran.r-project.org/bin/windows/contrib/2.0/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 24149 bytes
opened URL
downloaded 23Kb
	Warning message: 
	No package "gdata" on CRAN. in: download.packages(pkgs, destdir =
tmpd, 
	available = available,  

Now the user is in trouble and sends me an error message asking how to get
the 'gdata' package.
A couple of minor changes to the package installation/listing tools would
help alleviate this and some related problems.
1) Modify install.packages() so that the by default "dependencies=TRUE",
since this knows how to find dependencies within bundles.  
	(Why is this FALSE by default anyway?  In normal circumstances, is
there any
 reason to install a package without installing its
dependencies?)

2) Modify install.packages() to check if a requested package is contained in
a bundle, and install the bundle if so.
This is already done, at least in R-2.0.1 if "dependencies" is set to 
"TRUE".


3) Modify CRAN.packages() to list packages contained within bundles as well
as independent packages, so that the windows "install packages from CRAN"
menu item will properly show bundled packages.
You already get the packages in bundles in the "Contains" column with
  CRAN.packages()[,"Contains"]
Uwe

Comments?
Gregory R. Warnes
Associate Director, Non-Clinical Statistics
Pfizer Global Research and Development

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