[BioC] [Spam:8.0] Re: R command history on unix version
Kasper Daniel Hansen
khansen at stat.Berkeley.EDU
Thu Jun 15 04:27:28 CEST 2006
Jianping: your Sun system may or may not have compiled with readline.
If you want to make sure do this:
# R RHOME
this will give you the location of R. Change to this directory, look
in the config.log file (search eg. for Source by doing /Source in
less) for something like
R is now configured for x86_64-unknown-linux-gnu
Source directory: .
Installation directory: /usr/local
C compiler: gcc -g -O2 -std=gnu99
Fortran 77 compiler: g77 -g -O2
C++ compiler: g++ -g -O2
Fortran 90/95 compiler: g77 -g -O2
Interfaces supported: X11, tcltk
External libraries: readline, BLAS(ATLAS)
Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
Options enabled: shared library, R profiling
Recommended packages: yes
Readline should be listed here. If not, your sysadmins need to
recompile. If it is listed you probably have some problems with your
terminal connection. Do your arrow keys work in the shell?
Running R from ESS/Emacs is of course the best way to go, but if you
are new to Emacs get ready fro a rough ride. It _will_ take quite
some time to get comfortable doing this... Note that in your case you
will be running R remotely inside a local Emacs, which is slightly
different than what most guides talk about (which is running local R
in local Emacs).
How to setup X(Emacs) and ESS is off-topic for this list. Try the ESS
help list.
/Kasper
On Jun 14, 2006, at 12:14 PM, James W. MacDonald wrote:
> Jianping Jin wrote:
>> readline is available on our server side. Do I need to ask a system
>> administer to re-compile R with adding readline?
>
> I don't think so. If readline was installed when R was compiled, I
> think
> you should be good.
>
>>
>>> use up and down arrows just like on win32. However, running at a
>>> terminal
>>> is IMO really not the way to do things. I much prefer to use
>>> Xemacs/ESS
>>> with R as an inferior process. In that case you can use M-p and M-n
>>> (Alt-p and Alt-n for non-(X)emacs folks) to go up and down in the
>>> history.
>>
>>
>> I added Xemacs to my account on the server and was able to
>> initiate the
>> Xemacs:*scratch* window. But I do not know how to run R from within
>> Xemacs. I can type commands and initiate xterm window. It gave me an
>> error message, however, when I tried to run R on the Xemacs Shell
>> command: "fatal error: you must specify '--save', '--no-save' or
>> '--vanilla'".
>>
>
> Do you have ESS installed in your Xemacs? See here for more
> information:
>
> http://ess.r-project.org/
>
>>>
>>> On win32, adding this to my init.el file makes the up and down
>>> arrows
>>> work just like the Rgui, but doesn't seem to work on Linux.
>>
>>
>> On my desktop computer I did not find any file called init.el to
>> which I
>> can add your script. Is this an alternative to the two ways described
>> above?
>
> This file doesn't exist until you make one. John Fox has been nice
> enough to make a very detailed instruction manual for win32 here:
>
> http://socserv.mcmaster.ca/jfox/Books/Companion/ESS/
>
> Best,
>
> Jim
>
>
>>
>> I greatly appreciate your help!
>>
>> Jianping
>>
>>>
>>> (eval-after-load
>>> "comint"
>>> '(progn
>>> (setq comint-scroll-to-bottom-on-output 'others) ; not
>>> current
>>> ;;=default: (setq comint-scroll-to-bottom-on-input nil)
>>> (setq comint-scroll-show-maximum-output t) ;;; this is the
>>> key
>>> (define-key comint-mode-map [up]
>>> 'comint-previous-matching-input-from-input)
>>> (define-key comint-mode-map [down]
>>> 'comint-next-matching-input-from-input)
>>>
>>> (define-key comint-mode-map "\C-a" 'comint-bol)))
>>>
>>> HTH,
>>>
>>> Jim
>>>
>>>
>>>>
>>>> Thanks in advance!
>>>>
>>>> Jianping
>>>>
>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>> x Jianping Jin Ph.D. x
>>>> x Bioinformatics scientist x
>>>> x Center for bioinformatics x
>>>> x 3133 Bioinformatics Building x
>>>> x CB# 7104 x
>>>> x University of North Carolina x
>>>> x Chapel Hill, NC 27599 x
>>>> x Tel: (919)843-6105 x
>>>> x Fax: (919)843-3103 x
>>>> x E-mail: jjin at email.unc.edu x
>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>
>>> --
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> Affymetrix and cDNA Microarray Core
>>> University of Michigan Cancer Center
>>> 1500 E. Medical Center Drive
>>> 7410 CCGC
>>> Ann Arbor MI 48109
>>> 734-647-5623
>>>
>>>
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and
>>> should not
>>> be used for urgent or sensitive issues.
>>
>>
>>
>>
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> x Jianping Jin Ph.D. x
>> x Bioinformatics scientist x
>> x Center for bioinformatics x
>> x 3133 Bioinformatics Building x
>> x CB# 7104 x
>> x University of North Carolina x
>> x Chapel Hill, NC 27599 x
>> x Tel: (919)843-6105 x
>> x Fax: (919)843-3103 x
>> x E-mail: jjin at email.unc.edu x
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and
> should not be used for urgent or sensitive issues.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/
> gmane.science.biology.informatics.conductor
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