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automating some tasks

5 messages · Denis Chabot, Ulises M. Alvarez, stefano iacus +2 more

Original
Denis Chabot
# 
Hi, I have a few questions as a new user to R and some wishes for the 
interface.

First, is a way to specify which packages should be opened 
automatically when one starts R? Ideally a pane of the preferences 
would show the packages that are installed, like the "Packages/Package 
Manager" command does, but the boxes that would be checked there would 
be remembered and this list would be opened each time R starts. 
Obviously this is not implemented now, so is there an alternative that 
exists now, maybe a command file that is automatically read when R 
starts and where I could specify packages to be loaded automatically?

Second, I don't know what to think of the Help menu. Because I got no 
result from using it except a slowing down of my computer, I opened the 
Process Viewer (I think it is called this in English, it is Moniteur 
d'activit? in French). I should precise that I am working on a 700 MHz 
iMac with 768 Mo RAM and OS X 10.3.4. With no application other than 
Finder, Mail, and Process Viewer, around 90% of the Processor Time is 
available. Launching R does not change this much.

For this test, the first thing I did in R was selecting "Help/R Help", 
the R Console says this:

 > help.start()
Making links in per-session dir ...
If /usr/bin/open is already running, it is *not* restarted, and you 
must switch to its window.
Otherwise, be patient ...
 >

But nothing else of use happens. What is /usr/bin/open? How can I 
switch to its window? There is not a Open application that appears in 
the dock for me to switch to its window.
At this point my Mac becomes sluggish, the processor activity jumped 
from about 10 to 100%, and the two culprit are kernel_task (user Root) 
and Open (user chabotd), with each about 45% of CPU time. Quitting R 
does not stop these tasks. Indeed, after restarting R and choosing Help 
again, I now have one kernel_task but two Open tasks! And still no 
help!

I also tried the "Help/R for Mac OS X FAQ", but all that did is start 
the hated rainbow spinning ball. This opened another "Open task". while 
I typed this paragraph, R froze and I cannot go back to it, I can only 
force quit it. I just did but the kernel_Task and the two Open tasks 
still hug my CPU, so I'll have to force quite them as well!

I don't know Process Viewer very well, but it has an export button. If 
you are interested, I used this button before launching Help from R and 
after. I opened those plist files with TextWrangler and the information 
is not in a format I can use easily, but maybe it is usable by whoever 
will look in this matter. I will be pleased to email these 2 files on 
request.

Is Help working better for others or is this just a growing pain of the 
new Aqua interface for R?

Thanks in advance,

Sincerely,

Denis Chabot
Ulises M. Alvarez
# 
Hi!
?.First

Take a careful look at. Now type:
?options

On the other hand, '/usr/bin/open' or 'open' for short is a MacOX command 
which open files  using the default application associated with its 
extension. In my iBook the RHelp opens the Safari browser. Can you tell 
which is your default browser?

Why don't you try with the recently released R.dmg? (browse the 
list files). It seems to me like something is wrong with your current 
installation of R. 

Good look.
On Fri, 9 Jul 2004, Denis Chabot wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      stefano iacus
    

    

      
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please remove libxml2 from /usr/local/lib and the help will work.
stefano

        
On Jul 9, 2004, at 2:37 PM, Denis Chabot wrote:

        

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    
2 days later

    

      
      

        


  

        

      Ingmar Visser
    

    

      
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Hi All,

I am building a package on Mac OS X using C++ and Fortran.
I am getting a "Trace/BPT trap" error which means nothing to me I'm afraid.

I am using the gcc compilers, g++ and g77 to compile, these are invoked by
calling R CMD INSTALL etc.

Can anyone help me with this particular error and/or point me to strategies
for debugging C++ code when building packages fo R.

Any suggestions are welcome,

ingmar visser

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
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On Jul 12, 2004, at 12:19 PM, Ingmar Visser wrote:

        

            

      
      
      
    

        
The error isn't helpful usually. If there is really no further messages 
(about libraries, symbols etc.), then you may want to run R in a 
debugger. For example you can use gdb - start R like this:

R -d gdb

then type
run

after messing around with your library to get the error you can get a 
stack trace with
bt

for details see the help command in the gdb.

(Alternative way of attaching a gdb into a running R process is to run 
gdb and type "attach R.bin")

I hope it helps...
Simon