[BioC] Remove from package-list

[Kasper Daniel Hansen]

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]]
>
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