[BioC] Installation errors for DESeq, Genomic Ranges etc.

[Martin Morgan]

On 02/18/2012 04:18 PM, Alpesh Querer wrote:
> Hi all,
>
> I`m trying to install some packages like DESeq, GenomicRanges etc with R
> 2.14.
> I am getting error like the following. Same with dependent packages like
> RCurl, rtracklayer.
> Can someone help me with correct installation instructions here?
>
>
>>      source("http://www.bioconductor.org/biocLite.R")
>>      biocLite("GenomicRanges")
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'GenomicRanges'
> also installing the dependency ‘IRanges’
>
> trying URL '
> http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/IRanges_1.12.5.zip
> '
> Error in download.file(url, destfile, method, mode = "wb", ...) :
>    cannot open URL '
> http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/IRanges_1.12.5.zip

I'm not sure exactly why you're seeing this, but the problem is that the 
current version of IRanges is 1.12.6, but biocLite is pointing you 
toward 1.12.5. I would suggest starting a new R session and trying 
again. In particular, open a DOS prompt and run

   Rgui --vanilla

perhaps proving the full path to Rgui, along the lines of

   "c:\Program Files\R\R-2.14.1\bin\i386\Rgui.exe" --vanilla

Martin

> '
> In addition: Warning message:
> In download.file(url, destfile, method, mode = "wb", ...) :
>    cannot open: HTTP status was '404 Not Found'
> Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
>    download of package ‘IRanges’ failed
> trying URL '
> http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/GenomicRanges_1.6.6.zip
> '
> Error in download.file(url, destfile, method, mode = "wb", ...) :
>    cannot open URL '
> http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/GenomicRanges_1.6.6.zip
> '
> In addition: Warning message:
> In download.file(url, destfile, method, mode = "wb", ...) :
>    cannot open: HTTP status was '404 Not Found'
> Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
>    download of package ‘GenomicRanges’ failed
>
>
>
>> sessionInfo()
> R version 2.14.1 (2011-12-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
>   [1] Biostrings_2.22.0   locfit_1.5-6        lattice_0.20-0
>   akima_0.5-7         DEXSeq_1.0.2        Biobase_2.14.0
>   GenomicRanges_1.6.7 IRanges_1.12.6
>   [9] edgeR_2.4.3         limma_3.10.2        BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1 grid_2.14.1    hwriter_1.3    plyr_1.7.1
> statmod_1.4.14 stringr_0.6    tools_2.14.1   zlibbioc_1.0.0
>
> Many thanks
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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