[BioC] Problems with packages: annaffy, GO, KEGG, golubEsets

[Robert Gentleman]

On Dec 15, 2004, at 9:24 PM, Vitalina Komashko wrote:

> Hello All!
> I'm running R-2.0.1 and I tried to download and install annaffy, KEGG,
> GO, golubEsets packages, but it seems to be a problem. Here is an
> exact mesage:


   Hi,
     It looks like you have installed R-2.0.1 over an existing version  
of R and so you are picking up older versions of the packages.  
Unfortunately that won't work.

     If you start R and go library("affydata") do you get the same error  
message? If so, you need to remove all old packages and install new  
ones that have been build using R 2.0.0 or newer. This was a decision  
made by the R team.

   I did just try install.packages2("KEGG") and got warned that KEGG was  
built with R 2.0.0 and I have 2.0.1 (on windows). We will be building  
new versions of all packages in early January so that warning should go  
away then.

   Robert

>
> Loading required package: reposTools
> [1] TRUE
> Error in library(package, character.only = TRUE, logical = TRUE,  
> warn.conflicts
> = warn.conflicts,  :
>         'affydata' is not a valid package -- installed < 2.0.0?
> Execution halted
> /usr/local/lib/R/bin/INSTALL: line 1:  6558 Broken pipe
> cat "/usr/lo
> cal/lib/R/library/affyPLM/R/affyPLM"
> ERROR: execution of package source for 'affyPLM' failed
> ** Removing '/usr/local/lib/R/library/affyPLM'
> ** Restoring previous '/usr/local/lib/R/library/affyPLM'
> [1] "Attempting to download annaffy from
> http://www.bioconductor.org/repository/
> release1.5/package/Source"
> [1] "Download complete."
> [1] "Installing annaffy"
> * Installing *source* package 'annaffy' ...
> ** R
> ** data
> ** inst
> ** save image
> [1] TRUE
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
>          Vignettes contain introductory material.  To view,
>          simply type: openVignette()
>          For details on reading vignettes, see
>          the openVignette help page.
> Loading required package: GO
> Loading required package: KEGG
> Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc =  
> lib.loc)
> :
>         'KEGG' is not a valid package -- installed < 2.0.0?
> Execution halted
> /usr/local/lib/R/bin/INSTALL: line 1:  6663 Broken pipe
> cat "/usr/lo
> cal/lib/R/library/annaffy/R/annaffy"
> ERROR: execution of package source for 'annaffy' failed
> ** Removing '/usr/local/lib/R/library/annaffy'
> ** Restoring previous '/usr/local/lib/R/library/annaffy'
> [1] "Attempting to download edd from
> http://www.bioconductor.org/repository/rele
> ase1.5/package/Source"
> [1] "Download complete."
> [1] "Installing edd"
> * Installing *source* package 'edd' ...
> ** R
> ** inst
> ** save image
> [1] TRUE
> Loading required package: golubEsets
> Error in library(pkg, character.only = TRUE, logical = TRUE, lib.loc =  
> lib.loc)
> :
>         'golubEsets' is not a valid package -- installed < 2.0.0?
> Execution halted
> /usr/local/lib/R/bin/INSTALL: line 1:  6752 Broken pipe
> cat "/usr/lo
> cal/lib/R/library/edd/R/edd"
> ERROR: execution of package source for 'edd' failed
> ** Removing '/usr/local/lib/R/library/edd'
> ** Restoring previous '/usr/local/lib/R/library/edd'
>> From URL:   
>> http://www.bioconductor.org/repository/release1.5/package/Source
>         affyPLM version 1.2.5
>         annaffy version 1.0.11
>         edd version 1.5.0
>
> You have downloaded a default set of packages.
> If you wish to see other download options, please go to the URL:
> http://www.bioconductor.org/faq.html#getBioC
> Warning messages:
> 1: Installation of package affyPLM had non-zero exit status in:
> installPkg(fileN                                            ame, pkg,
> pkgVer, type, lib, repEntry, versForce)
> 2: Installation of package annaffy had non-zero exit status in:
> installPkg(fileN                                            ame, pkg,
> pkgVer, type, lib, repEntry, versForce)
> 3: Installation of package edd had non-zero exit status in:
> installPkg(fileName,                                             pkg,
> pkgVer, type, lib, repEntry, versForce)
>
> What can I do?
> Thank you very much for your help.
> Vitalina.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
          |
| Head, Program in Computational Biology   fax:  (206) 667-1319   |
| Division of Public Health Sciences       office: M2-B865               
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| Fred Hutchinson Cancer Research Center                                 
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| email: rgentlem at fhcrc.org                                              
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