Thanks David! I got a solution, though maybe not optimal.  In the zzz.r file
of the R package, I include the folloing code:

.onLoad <- function(libname,pkgname) {
    myoptions <- list(ngs.python="sage -python",ngs.macs="macs14")
    if(exists("myoptions",.GlobalEnv))
        options(.GlobalEnv$myoptions)
    else
        options(myoptions)
}
If user save his options in the myoptions list, by loading saved image he
does not need to set the option again. However, I still believe there is a
more elegant way to let user save his options. Hope someone could come up
with a better solution :-)

Thanks!


Xue




On Sat, May 7, 2011 at 5:47 AM, David Winsemius <dwinsemius@comcast.net>wrote:

>
> On May 6, 2011, at 8:59 PM, xwang14 wrote:
>
> Hi,
>>
>> Could anyone help me with the following problem? After I finished a R
>> session and modified some options (for example, set
>> options(editor="neditor")), I want save these modifications so that after
>> I
>> load the saved R data I do not need to modify these options again. What is
>> the best way to do this? Is there a way without using an external file? I
>> tried save.image. However, only default setting is perserved.
>>
>
> You need to read about your options about setting options at startup. You
> can find information in the Installation Manual or by typing: ?Startup
>
> (I cannot think of a manner in which this can be tied to a data file being
> loaded.)
>
> --
>
> David Winsemius, MD
> West Hartford, CT
>
>

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