[BioC] Remove from package-list

Wed Apr 2 00:41:22 CEST 2008

Hi Kathy,

The function that populates the list you are talking about is 
packages(), which simply looks in your local library directory and then 
lists all packages that are there that also have a DESCRIPTION file with 
a valid version field. See ?.packages for more information.

So what that says to me is that there are remnants of the marrayNorm, 
etc packages in your library directory. If there are only remnants of 
the packages there, then remove.packages() will not do anything. 
Instead, you will have to go in there (you can find out where this is by 
typing .libPaths() at an R prompt) and remove all the marrayNorm, etc 
directories you find there.

In addition, you should probably do

install.packages("tcltk")

as well to fix your evidently busted tcltk package.

OR, better yet, since R-2.6.0 is obsolete, you might just install 
R-2.6.2 and run biocLite() to get a shiny new installation that should 
Just Work(tm).

Best,

Jim

Kathy Duncan wrote:
> 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 at 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]]
> 
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-- 
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623