[BioC] can't load affycoretools because GOstats is broken. Can I load affycoretools without dependencies to use some functions?

Sun Feb 11 01:37:21 CET 2007

Robert,

I seem to be getting nowhere fast. I am having trouble with biocLite. 
The error message I get below with biocLite(GOstats) I get with any 
other BioC package I try to install.

I have also regularly been getting this message:

 > update.packages(repos=biocReposList(), dependencies=TRUE)
Warning: unable to access index for repository 
http://bioconductor.org/packages/2.0/monograph/bin/windows/contrib/2.5

at the beginning of each session as I have this code as part of my 
.Rprofile to make sure I keep up to date. Despite this code, which Seth 
suggested I ignore, I have been getting updates.

Perhaps I have a corrupted package somewhere? I would be willing to 
install all my packages from scratch if that is what it takes.

Unfortunately, I have not yet learned how to build from source and am 
dependent on the Windows binaries.

What command would I use to install all of BioC? I used to know it, now 
I've forgotten and couldn't find it on the website.

Mark

 > setRepositories()
 > utils:::menuInstallPkgs()
Warning: unable to access index for repository 
http://www.bioconductor.org/bin/windows/contrib/2.5
Error in install.packages(NULL, .libPaths()[1], dependencies = NA, type 
= type) :
         no packages were specified
 > source("http://bioconductor.org/getBioC.R")
 >
 > biocLite <- function(pkgs, groupName="lite", ...)
+ {
+     if (missing(pkgs))
+         getBioC(groupName=groupName, ...)
+     else
+         getBioC(pkgs=pkgs, groupName=groupName, ...)
+ }
 > biocLite(GOstats)
Running getBioC version 0.1.8 with R version 2.5.0
Running biocinstall version 2.0.2 with R version 2.5.0 (under development)
Your version of R requires version 2.0 of Bioconductor (under 
development too).
Error in install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
         object "GOstats" not found

  sessionInfo()
R version 2.5.0 Under development (unstable) (2007-02-09 r40677)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
   RWinEdt     limma      affy    affyio   Biobase
   "1.7-5"   "2.9.9" "1.13.14"   "1.3.3" "1.13.37"

Robert Gentleman wrote:
> Hi Mark,
>  It looks like you were installing GOstats from a local copy, are you 
> sure that is up to date?  One thing you might try is to update all 
> packages, using update.packages, or to reinstall with biocLite - as I 
> said, it worked for me
> 
> Again, it is not sufficient to do this for files on your hard disk, you 
> are going to need updated versions of many of them from the bioc website.
> 
>  best wishes
>    Robert
> 
> Mark W Kimpel wrote:
>> Robert,
>>
>> I deleted GOstats from my R library and re-downloaded the latest GOstats
>> Win binary from BioC-devel. I deleted my .Rprofile that was preloading 
>> some packages like affy. So I had a "virgin" instance of R running. I 
>> get the same error message. I did not debug this time as it looks like 
>> the same problem I was having before.
>>
>> Thanks for your continued help. Below is my output.
>> Mark
>>
>>
>> R version 2.5.0 Under development (unstable) (2007-02-09 r40677)
>> 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.
>>
>>  > utils:::menuInstallLocal()
>> package 'GOstats' successfully unpacked and MD5 sums checked
>> updating HTML package descriptions
>>  > require(GOstats)
>> Loading required package: GOstats
>> Loading required package: graph
>> Loading required package: Biobase
>> Loading required package: tools
>>
>> Welcome to Bioconductor
>>
>>     Vignettes contain introductory material. To view, type
>>     'openVignette()' or start with 'help(Biobase)'. For details
>>     on reading vignettes, see the openVignette help page.
>>
>> Loading required package: GO
>> Loading required package: annotate
>> Loading required package: RBGL
>> Loading required package: Category
>> Loading required package: KEGG
>> Loading required package: genefilter
>> Loading required package: survival
>> Loading required package: splines
>> Error in expMethods[[i]] <- allMethodLists[ii] :
>>         more elements supplied than there are to replace
>> [1] FALSE
>> sessionInfo()
>> R version 2.5.0 Under development (unstable) (2007-02-09 r40677)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
>> States.1252;LC_MONETARY=English_United 
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" 
>> "utils"     "datasets"  "methods"   "base"
>>
>> other attached packages:
>>   Category genefilter   survival       KEGG       RBGL   annotate    
>> GO    Biobase      graph
>>   "2.1.15"   "1.13.8"     "2.31"   "1.15.1"   "1.11.4"   "1.13.6" 
>> "1.15.1"  "1.13.37"   "1.13.6"
>>  >
>>
>>
>> Robert Gentleman wrote:
>>> Have you tried to reinstall GOstats? Please, do so,
>>>
>>> eg
>>>
>>> biocLite("GOstats")
>>>
>>> and then
>>> library(GOstats)
>>>
>>> and then report exactly what comes across the screen for all steps,
>>> thanks
>>>  Robert
>>>
>>>
>>> Mark W Kimpel wrote:
>>>> GOstats is broken in BioC 2.0, and I think in 1.9. Seth and Robert 
>>>> are working on a fix but are en-route to New Zealand for a 
>>>> conference. Can I load affycoretools without one or more 
>>>> dependencies? I just want to use the venn diagram functions.
>>>>
>>>> Mark
>>>
>>
> 

-- 
Mark W. Kimpel MD
Neuroinformatics
Department of Psychiatry
Indiana University School of Medicine