[Bioc-devel] Problem with getBioC(develOK=TRUE)

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-----Original Message-----
From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu]
Sent: Wednesday, 13 October, 2004 11:22 AM
To: Goeman, J.J. (MSTAT)
Subject: Re: [BioC] problems with getBioC() and 
getBioC(develOK=TRUE) on
R 2.0.0



On Wed, Oct 13, 2004 at 10:46:15AM +0200, Goeman, J.J. (MSTAT) wrote:

Hi Robert,

I also get errors (different ones) if I try installing the 

develOK branch;

see the second part of the email. 

  Yes, and I suspect that you have installed the wrong version of
  reposTools - so perhaps if you try first doing a remove.packages 
 (you might find this out by starting R, and going 
library(reposTools)  
 and see if that works - it looks like somehow your version is
  interacting badly with getBioC.

  I get:
    packageDescription("reposTools")$Version

   [1] "1.4.11"

  Otherwise, you can take the getBioC script and go through it one
  line at a time, and figure out where it fails, we can fix it given a
  report. 


   Robert

Jelle

http://www.math.leidenuniv.nl/~jgoeman  

-----Original Message-----
From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu]
Sent: Wednesday, 13 October, 2004 10:33 AM
To: Goeman, J.J. (MSTAT)
Cc: 'bioconductor@stat.math.ethz.ch'
Subject: Re: [BioC] problems with getBioC() and 
getBioC(develOK=TRUE) on
R 2.0.0


Yes, and it is rather unfortunate, but actually well
documented. Please, if you want to use Bioconductor with 

R 2.0.0 you

*must* use the devel branch, or you can use R 1.9.1 with 

the release

branch. The next release is a few weeks away, but there 

is a necessary

lag between R releases and BioC releases.

  Robert

On Wed, Oct 13, 2004 at 10:28:50AM +0200, Goeman, J.J. 

(MSTAT) wrote:

Hi,

I'm trying to install Bioconductor on R 2.0.0 (windows 

version). I get some

strange errors

I first try the release version:

source("http://www.bioconductor.org/getBioC.R")
getBioC()

Running getBioC version 1.2.65....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to 

bioconductor@stat.math.ethz.ch.

[1] "Installing reposTools ..."
Loading required package: reposTools 
Error in library(package, character.only = TRUE, logical = TRUE,
warn.conflicts = warn.conflicts,  : 
        'reposTools' is not a valid package -- 

installed < 2.0.0?

Maybe I shouldn't use the release version on 2.0.0? 

Then I try the

developmental version:

getBioC(develOK=TRUE)

Running getBioC version 1.2.65....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found at: www.bioconductor.org/getBioC.R

Please direct any concerns or questions to 

bioconductor@stat.math.ethz.ch.

[1] "Installing reposTools ..."
Loading required package: reposTools 
Loading required package: tools 
[1] "Test:"
NULL
Error in getBioC(develOK = TRUE) : 
default:        targets affy, cdna and exprs.
exprs:          packages Biobase, annotate, genefilter, 

geneploter, edd, 

                ROC, multtest, pamr vsn, and limma.
affy:           packages affy, affydata, annaffy, affyPLM, 

makecdfenv,

                and matchprobes plus 'exprs'.
cdna:           packages marray, vsn, plus 'exprs'.
prog:           packages graph, hexbin, externalVector.
graph:          packages graph, Rgraphviz, RBGL
widgets:        packages tkWidgets, widgetTools, DynDoc.
design:         packages daMA and factDesign
externalData:   packages externalVector and rhdf5.
database:       AnnBuilder, SAGElyzer, Rdbi and RdbiPgSQL.
analyses:       packages Biobase, ctc, daMA, edd, factDesign,
                genefilter, geneplotter, globaltest, 

gpls, limma,

                RMAGEML, multtest, pamr, wvalue, ROC, 

siggenes and

splicegear.
annotation:     packages annotate, AnnBuilder, humanLLMappings
                KEGG, GO, SNPtools, makecdfenv and ontoTools.
proteomics:     packages gpls, PROcess and apComplex.
arrayCGH:       packages aCGH, DNAcopy, repeated, and rmutil.
all:            All of the Bio


Here's my version info:

version

         _              
platform i386-pc-mingw32
arch     i386           
os       mingw32        
system   i386, mingw32  
status                  
major    2              
minor    0.0            
year     2004           
month    10             
day      04             
language R 

What's wrong?

Kind regards,

Jelle Goeman

http://www.math.leidenuniv.nl/~jgoeman

-- 
+-------------------------------------------------------------
--------------+
| Robert Gentleman                 phone : (617) 632-5250     
              |
| Associate Professor              fax:   (617)  632-2444     
              |
| Department of Biostatistics      office: M1B20              
              |
| Harvard School of Public Health  email: 
rgentlem@jimmy.harvard.edu        |
+-------------------------------------------------------------
--------------+

-- 
+-------------------------------------------------------------
--------------+
| Robert Gentleman                 phone : (617) 632-5250     
              |
| Associate Professor              fax:   (617)  632-2444     
              |
| Department of Biostatistics      office: M1B20              
              |
| Harvard School of Public Health  email: 
rgentlem@jimmy.harvard.edu        |
+-------------------------------------------------------------
--------------+