Hi Kasper,

Thanks !

I'm afraid *remove.packages(pkgs="name of the package")* doesn't remove the
names of the packages from the list generated by PACKAGES > LOAD PACKAGES in
R.

Moreover, regarding the startup script you've mentioned, if you are
referring to the "tcltk"-part, I don't know how I actually got that in the
past ! Neither do I know its functionality nor do I use it !! Also, I start
R normally, without any customized way.
After I received your mail, I tried to remove it using *remove.packages
(pkgs="*tcltk*")*, now this is what I'm getting :

R version 2.6.0 (2007-10-03)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Loading required package: tcltk
Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc=
lib.loc) :
  'tcltk' is not a valid package -- installed < 2.0.0?

> sessionInfo()
R version 2.6.0 (2007-10-03)
i386-pc-mingw32

locale:
- - - - - - -

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

loaded via a namespace (and not attached):
[1] tools_2.6.0


Kathy


= = = = = =  == = = = = = =


On Tue, Apr 1, 2008 at 6:56 AM, Kasper Daniel Hansen <
khansen@stat.berkeley.edu> wrote:

> What about uninstalling the packages using (for example)
> R> packages.remove()
>
> You are using a custom startup script that loads everything in all you
> libraries. This is pretty bad (IMHO) for several reasons, amongst them
> 1) you may have a conflict with loading two packages containing
> functions with the same name.
> 2) It is bad for debugging, especially if you want help from other
> people.
> 3) when you install a package, you are installing over something you
> have already loaded.
>
> Kasper
>
>
> On Mar 30, 2008, at 6:41 PM, Kathy Duncan wrote:
>
> > Hi !
> >
> > I previously tried unsuccessfully to install packages like
> > "marrayInput",
> > "marrayClasses",
> > "marrayNorm" from their respective webpages. But later I came to know
> > (courtesy: Sean Davis) that those packages are no longer available
> > in newer
> > releases of bioconductor, and have been consolidated into "marray".
> >
> > Now, I'm wondering whether I can remove the names of such (defunct !)
> > packages from the list generated by PACKAGES > LOAD PACKAGES in R.
> >
> > Kathy
> >
> >
> >
> > = = = = = =  ==  = = =
> >
> > R version 2.6.0 (2007-10-03)
> > Copyright (C) 2007 The R Foundation for Statistical Computing
> > ISBN 3-900051-07-0
> >
> > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > You are welcome to redistribute it under certain conditions.
> > Type 'license()' or 'licence()' for distribution details.
> >
> >  Natural language support but running in an English locale
> >
> > R is a collaborative project with many contributors.
> > Type 'contributors()' for more information and
> > 'citation()' on how to cite R or R packages in publications.
> >
> > Type 'demo()' for some demos, 'help()' for on-line help, or
> > 'help.start()' for an HTML browser interface to help.
> > Type 'q()' to quit R.
> >
> > Loading required package: tcltk
> > Loading Tcl/Tk interface ... done
> > Warning messages:
> > 1: '\A' is an unrecognized escape in a character string
> > 2: unrecognized escape removed from ";for Options\AutoIndent: 0=Off,
> > 1=follow language scoping and 2=copy from previous line\n"
> > 3: In grep(paste("[{]TclEval ", topic, "[}]", sep = ""),
> > tclvalue(.Tcl("dde
> > services TclEval {}")),  :
> >  argument 'useBytes = TRUE' will be ignored
> > Loading required package: svMisc
> > Loading required package: R2HTML
> >
> >> local({pkg <- select.list(sort(.packages(all.available = TRUE)))
> > + if(nchar(pkg)) library(pkg, character.only=TRUE)})
> > Error in library(pkg, character.only = TRUE) :
> >  'marrayNorm' is not a valid package -- installed < 2.0.0?
> >
> >> sessionInfo()
> > R version 2.6.0 (2007-10-03)
> > i386-pc-mingw32
> >
> > locale:
> >
> > - - - - - - - -  -
> >
> >
> > attached base packages:
> > [1] stats     graphics  grDevices datasets  tcltk     utils
> > methods
> > base
> >
> > other attached packages:
> > [1] svSocket_0.9-5 svIO_0.9-5     R2HTML_1.58    svMisc_0.9-5
> > svIDE_0.9-5
> >
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.6.0
> >
> >       [[alternative HTML version deleted]]
> >

	[[alternative HTML version deleted]]

