[BioC] problem with 'biomaRt' package installation: Error in loadNamespace(i, c(lib.loc, .libPaths()))

[Glazko, Galina V]

Dan,

Genius! Thank you, it worked fine! Though do not understand why.

Best regards
Galina

-----Original Message-----
From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] 
Sent: Wednesday, April 11, 2012 9:59 AM
To: Glazko, Galina V
Cc: bioconductor at r-project.org
Subject: Re: [BioC] problem with 'biomaRt' package installation: Error in loadNamespace(i, c(lib.loc, .libPaths()))

On Wed, Apr 11, 2012 at 6:54 AM, Glazko, Galina V <GVGlazko at uams.edu> wrote:
> Dear list,
>
> I was trying to install biomaRt package.
>>  biocLite('biomaRt')
>
> Everything worked, but I had this warning:
>
> Warning: unable to move temporary installation 'C:\Program Files\R\R-2.15.0\library\file77847d9453b\XML' to 'C:\Program Files\R\R-2.15.0\library\XML'
>
> However,:
> package 'biomaRt' successfully unpacked and MD5 sums checked
>
> Then, when I was trying to load the library I had the following error:
>>  library(biomaRt)
> Error in loadNamespace(i, c(lib.loc, .libPaths())) :
>  there is no package called 'XML'
> Error: package/namespace load failed for 'biomaRt'
>
> Enigmatically, there is no such directory 'file77847d9453b' in 'C:\Program Files\R\R-2.15.0\library'
> I would appreciate an advise how to fix this error!
>
> Best regards
> Galina

Try starting a fresh R session with
R --vanilla
then
library(BiocInstaller)
biocLite(c("XML","biomaRt"))

Dan


>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> 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
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BSgenome_1.24.0     GenomicRanges_1.8.3 Biostrings_2.24.1   IRanges_1.14.2      BiocGenerics_0.2.0  edgeR_2.6.0         limma_3.12.0
> [8] BiocInstaller_1.4.3
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1.1 stats4_2.15.0  tools_2.15.0
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