[Bioc-devel] Problem accessing annotation packages in R2.4.0

[Herve Pages]

Hi Keith,

As James W. MacDonald posted here recently:

    The binary metaData packages are typically not built until close to
    release time for the devel branch. For those using
    R-devel/BioC-devel, a
    certain level of expertise is assumed, which (in this case) includes
    the
    ability to compile source packages.

You might try to use BioC 1.8 windows binary versions of the annotation packages with
R 2.4.0 though and they will probably work... (but we can't guarantee it)

Best,

H.


Keith Satterley wrote:
> I need to access annotation packages under R2.4.0 to test my program.
> I have just installed the latest R2.4.0 binary available for Windows. I 
> also had the same problem with a vesion of R2.4.0 I installed in May 
> this year.
>
> I run the following code under R2.3.1 and R2.4.0
>  >===========
> cu=contrib.url(Biobase::biocReposList())
> cu
> ap<-available.packages(contriburl=cu)
> length(ap)
> mi<-match("mouse4302",ap[,"Package"])
> mi
> sessionInfo()
>  >============
>
> Output Using R2.3.1
>
>  > cu=contrib.url(Biobase::biocReposList())
>  > cu
> [1] "http://bioconductor.org/packages/1.8/bioc/bin/windows/contrib/2.3" 
>
> [2] 
> "http://bioconductor.org/packages/1.8/data/annotation/bin/windows/contrib/2.3"
> [3] 
> "http://bioconductor.org/packages/1.8/data/experiment/bin/windows/contrib/2.3"
> [4] 
> "http://bioconductor.org/packages/1.8/omegahat/bin/windows/contrib/2.3" 
>
> [5] 
> "http://bioconductor.org/packages/1.8/lindsey/bin/windows/contrib/2.3" 
>
> [6] "http://cran.fhcrc.org/bin/windows/contrib/2.3" 
>
>  > ap<-available.packages(contriburl=cu)
>  > length(ap)
> [1] 14517
>  > mi<-match("mouse4302",ap[,"Package"])
>  > mi
> [1] 619
>  > sessionInfo()
> Version 2.3.1 (2006-06-01)
> i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils" 
> "datasets"  "base"
>
> ---------------
>
> Output Using R2.4.0
>
>  > cu=contrib.url(Biobase::biocReposList())
>  > cu
> [1] "http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4" 
>
> [2] 
> "http://bioconductor.org/packages/1.9/data/annotation/bin/windows/contrib/2.4"
> [3] 
> "http://bioconductor.org/packages/1.9/data/experiment/bin/windows/contrib/2.4"
> [4] 
> "http://bioconductor.org/packages/1.9/omegahat/bin/windows/contrib/2.4" 
>
> [5] 
> "http://bioconductor.org/packages/1.9/monograph/bin/windows/contrib/2.4" 
>
> [6] "http://cran.fhcrc.org/bin/windows/contrib/2.4" 
>
>  > ap<-available.packages(contriburl=cu)
> Warning: unable to access index for repository 
> http://bioconductor.org/packages/1.9/monograph/bin/windows/contrib/2.4
>  > length(ap)
> [1] 8676
>  > mi<-match("mouse4302",ap[,"Package"])
>  > mi
> [1] NA
>  > sessionInfo()
> R version 2.4.0 Under development (unstable) (2006-08-14 r38872)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils" 
> "datasets"  "base"
>  >
> -------------
>
> Questions:
> 1. Is the warning from R2.4.0 being unable to access the monograph 
> repository expected.
>
> 2. I do not have any of the annotation packages in the output from 
> R2.4.0, whereas I do under R2.3.1. Can the windows binary versions of 
> these packages be made available?
>
> 3. Alternatively will the R2.3.1 windows binary versions of the 
> annotation packages work for R2.4.0?
>
> Note also that when running bioclite(), it reports:
> Warning: unable to access index for repository 
> http://bioconductor.org/packages/1.9/monograph/bin/windows/contrib/2.4
> dependency ''hgu95av2'' is not available
>
> thanks for any response,
>
> Keith Satterley
> Bioinformatics
> WEHI
>
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>   


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