[BioC] org.Hs.eg.db

[James W. MacDonald]

Hi Krakno,

On Monday, September 30, 2013 5:41:04 AM, Krakno [guest] wrote:
>
> Dear all,
>
> I have a problem with the "org.Hs.eg.db" package and would like to ask for some advice on how to get it to work. Currently, the problem I am facing is that R does not seem to recognize the package, see below for the context, error message and the sessionInfo().
>
> I have been able to make "org.Mm.eg.db" and "org.Sc.sgd.db" work, but "org.Hs.eg.db" is not recognized.
>
> I would be grateful for any help.
>
> Thanks in advance.
> /Krakno
>
>   -- output of sessionInfo():
>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("org.Hs.eg.db")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
> Installing package(s) 'org.Hs.eg.db'
> trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/org.Hs.eg.db_2.9.0.zip'
> Content type 'application/zip' length 53311411 bytes (50.8 Mb)
> opened URL
> downloaded 50.8 Mb
>
> Warning: cannot remove prior installation of package ‘org.Hs.eg.db’

^^^^^^^^^^^^^^^ I think that is the hint you were looking for. However, 
there may be more than one reason for the problem. I would first look 
in your package library (use .libPaths() to figure out where your 
packages are located) and see if there is a folder called

OOLOCK-org.Hs.eg.db

If so, delete that and try again.

Best,

Jim


>
> The downloaded binary packages are in
>          C:\Users\<...>\AppData\Local\Temp\RtmpE3cnj9\downloaded_packages
>> library(org.Hs.eg.db)
> Error in library(org.Hs.eg.db) :
>    there is no package called ‘org.Hs.eg.db’
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
> [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
> [5] LC_TIME=Swedish_Sweden.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>   [1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.28.0
>   [3] Biostrings_2.28.0                  GenomicRanges_1.12.5
>   [5] IRanges_1.18.4                     org.Mm.eg.db_2.9.0
>   [7] RSQLite_0.11.4                     DBI_0.2-7
>   [9] AnnotationDbi_1.22.6               Biobase_2.20.1
> [11] BiocGenerics_0.6.0                 BiocInstaller_1.10.3
>
> loaded via a namespace (and not attached):
> [1] stats4_3.0.1 tools_3.0.1
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099