[BioC] cannot install SNPlocs.Hsapiens.dbSNP.20090506

[James W. MacDonald]

Hi Dan,

Dan Strumpf wrote:
> Hi,
> received these messagages when trying to install
> 
> SNPlocs.Hsapiens.dbSNP.20090506
> 
> Any tips?

Where do you get that package name? I only see versions from 2007 and 2008:

 > suppressMessages(library(Biobase))
 > z <- biocReposList()
 > a <- available.packages(paste(a[2], "/src/contrib", sep =""))
 > grep("SNPlocs.Hsapiens", row.names(a), value = TRUE)
[1] "SNPlocs.Hsapiens.dbSNP.20071016" "SNPlocs.Hsapiens.dbSNP.20080617"
 > sessionInfo()
R version 2.10.0 Patched (2009-11-05 r50317)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] Biobase_2.6.1

loaded via a namespace (and not attached):
[1] tools_2.10.0

Best,

Jim


> 
> Thanks,
> 
> Dan
> 
>  > source("http://bioconductor.org/biocLite.R")
> Warning messages:
> 1: In safeSource() : Redefining ‘biocinstall’
> 2: In safeSource() : Redefining ‘biocinstallPkgGroups’
> 3: In safeSource() : Redefining ‘biocinstallRepos’
>  > biocLite("SNPlocs.Hsapiens.dbSNP.20090506")
> Using R version 2.10.0, biocinstall version 2.5.10.
> Installing Bioconductor version 2.5 packages:
> [1] "SNPlocs.Hsapiens.dbSNP.20090506"
> Please wait...
> 
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
>   package ‘SNPlocs.Hsapiens.dbSNP.20090506’ is not available
> 
>  > sessionInfo()
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252 
> LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Canada.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BSgenome_1.14.2     Biostrings_2.14.10  IRanges_1.4.9 
> org.Hs.eg.db_2.3.6  RSQLite_0.8-1       DBI_0.2-5 AnnotationDbi_1.8.0
> [8] Biobase_2.6.0
> 
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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