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7 messages · Gerald Jurasinski, Kieran Healy, mwtoews at sfu.ca +2 more

Original
Gerald Jurasinski
# 
Hello Maintainers,

I just wanted to mention, that the new GUI (ref 3141), which was  
recommended as an update when updating to R 2.3.0 still exhibits some  
undesired behaviour. So i can't save images from the quartz device as  
pdf anymore. The programme wants to save as Quartz image. So i can do  
this and then later open the file in preview and saving it as a pdf.  
but before it was much more convenient. Maybe it is a general problem  
with the Quartz devices: Often i got two of them automatically and  
one is always empty and it's not possible to get rid of it. This  
doesn't cause any further problem it is just a bit nagging.
However, i greatly appreciate your effort of bringing R to Aqua, and  
i am happy that i finally found R and learned (beginner stage) how to  
use it. One wish: The status region at the bottom of the console  
window could be a bit bigger (or growing, to always display the whole  
function usage) and the font used there could be a bit bigger (or  
adjustable).

Thank you
Gerald Jurasinski

P.S. Does anybody know a programme or package capable of producing  
two-dimensional correlograms (Oden & Sokal 1986)?
??????????????????

gerald jurasinski
biogeography
university of bayreuth
95440 bayreuth
gerald.jurasinski at uni-bayreuth.de
Jean Thioulouse
# 
Hello,

Sorry to bother you, but I have a problem installing R-2.3.0 from source. 
'configure' and 'make' produce no error, and the R executable seems to run
fine (particularly, R --version does work), but 'make install' fails with
the following error message :

% sudo make install
Password:
make[1]: Nothing to be done for `install'.
make[1]: Nothing to be done for `install'.
installing doc ...
help2man: can't get `--version' info from ../bin/R
make[1]: *** [R.1] Error 22
make: *** [install] Error 1

R-2.2.1 compiles and installs without problem. Using MacOS 10.4.6 on a
powerMac G5 with XCode 2.2.1.

Thank you,
Jean
Kieran Healy
# 
Hi -

I posted a little while ago about the same problem, as did Michael  
Toews. I've tried to follow this up. The short answer is that R  
2.3.0's version string doesn't conform to what the help2man.pl  
utility expects. The help2man.pl script gets version information from  
R --version and makes a man page from it. Here is the relevant line  
of the Makefile inside the doc/ directory of the R-2.3.0 source code  
bundle:
The help2man script wants the version information in a specific form  
Here is 2.3.0's version info (without the copyright message, which  
doesn't matter for the error):
And here is 2.2.1:
The extra word 'version' is what does it.

The roots of this issue are in src/main/version.c, which contains the  
code that produces the text of the version message. It has changed  
since 2.2.1. The changed code includes a function whose comments say,  
more or less, "this is a workaround designed to make GNU tools like  
help2man happy," together with information about how the version  
message will change in the next version of R. So I guess the authors  
of the code are aware of this issue, but for whatever reason it still  
arises on some macs. I'm afraid I don't' know C, so I can't diagnose  
any further.

As a short-term, completely ad hoc workaround, I ran the help2man  
command in the Makefile directly, but pointed it at my already- 
installed version of R (2.2.1) instead. I.e., from inside the doc/  
directory in the R 2.3.0 sources, and assuming you have R 2.2.1  
already installed, do
(This should all be one line.) This produces a file called R.1  
containing version information, which is the desired goal, but with  
version info from R.2.2.1 instead of 2.3.0. You can edit the first  
line of the file to make the version number correct if you like. Then  
you can comment out the equivalent section in  doc/Makefile, viz,
Doing 'sudo make install' as usual (from the top-level source  
directory) will then work, as the R.1 file is now present in the doc  
directory. Of course this doesn't change the usual output of R -- 
version (you'd have to edit version.c to do that), just the  
information in the man page.

Obviously is not any kind of proper solution, but I'm afraid I don't  
know C, or the ins-and-outs of R's source code in great detail. I'm  
not sure why this issue only appears on some macs (e.g., my iBook)  
and not others (e.g., by G5 tower).

Best,

Kieran
On May 16, 2006, at 1:32 AM, Jean Thioulouse wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      mwtoews at sfu.ca
    

    

      
      #
    

  


  

      
Hi,
The problem is actually R's inability to print the version number  
normally .. for instance typing: './bin/R --version' produces the  
proper output, but './bin/R --version | cat' does not produce any  
output ('help2man' reads an empty strings, and throws an error).

The only solution for now is to download a pre-compiled version from  
CRAN, since it works perfectly (including 'R --version | cat').

However, I have tracked down the vulnerability to:
sys-std.c: In function 'pushReadline':
sys-std.c:497: warning: passing argument 2 of  
'rl_callback_handler_install' from incompatible pointer type
sys-std.c: In function 'popReadline':
sys-std.c:513: warning: passing argument 2 of  
'rl_callback_handler_install' from incompatible pointer type

The source file ./src/unix/sys-std.c refers to Apple's ReadLine on OS  
X 10.4-pre, and how it needs to be forced to flush the stdout to make  
it visible (this is exactly the problem described above from  
help2man). Simon fixed this almost a year ago (svn r33778), but it  
appears this problem has re-surfaced for some proportions of Macs.
I can provide a complete log from './configure', 'make' and 'sudo  
make install' to anyone interested in seeing.

+mt

        
On 2006-May-16, at 01:32 , Jean Thioulouse wrote:

        

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
Michael,

thanks for tracking this down, excellent work!
The reason for CRAN R binary working is simply that it uses GNU  
readline instead of Apple's libedit (which is disguised as readline  
btw).  A simple work-around is therefore to install GNU readline (see  
the R for Mac OS X FAQ for details, don't forget -DNEED_EXTERN_PC).

I think I may be able to reproduce this on my laptop, I'll try that  
tomorrow and see if I can fix it.

Cheers,
Simon

        
On May 16, 2006, at 12:27 PM, Michael Toews wrote:

        

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jean Thioulouse
    

    

      
      #
    

  


  

      
Simon,

Thanks for the message. I installed GNU readline 5.1, but i still get
the help2man error.

Jean

        
At 22:12 -0400 16/05/06, Simon Urbanek wrote:

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Jean Thioulouse
    

    

      
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Hi Kieran,

This works for me, thanks. It will allow me to wait until Simon can fix
the problem (hopefully).

Jean

        
At 6:45 -0700 16/05/06, Kieran Healy wrote: