[BioC] can't get limma for R 2.12.0 x64?

[mkbehnke at gmail.com]

I had the same problem but was too busy to pursue it at the time - I'm interested in the response too!
Martha

Sent from my Verizon Wireless BlackBerry

-----Original Message-----
From: Jenny Drnevich <drnevich at illinois.edu>
Sender: bioconductor-bounces at stat.math.ethz.ch
Date: Tue, 09 Nov 2010 15:15:39 
To: <bioconductor at stat.math.ethz.ch>
Subject: [BioC] can't get limma for R 2.12.0 x64?

Hi all,

I'm just now getting around to upgrading to R 2.12.0.  Last month I 
got a fancy new laptop, 64-bit Windows 7, and I was able to install R 
x64 2.11.1 from the separate binary and then use biocLite() just 
fine. With the new release of R 2.12.0, it seems they changed the way 
the R x64 is handled (from the Change Log):

>
>64-bit NEWS
>

>The 32- and 64-bit distributions have been merged:
>
>There is a combined installer (called 'R-<version>-win.exe'). When 
>used under 32-bit Windows this works as before and installs 32-bit 
>R. When used under 64-bit Windows there are options to install 
>either or both of 32- and 64-bit R: the default is to install both.
>
>The default package type is "win.binary" on both 32- and 64-bit 
>builds: a single repository contains binary packages for both 
>architectures. This is in place for CRAN, CRANextras and BioC: type 
>= "win64.binary" can still be used for any repositories which follow 
>the R 2.11.x convention. With the default filters (see 
>?available.packages) packages will only be offered if they are 
>available for the current architecture.
>
>The default personal library, e.g. '~/R/win-library/2.12' is now the 
>same for both 32- and 64-bit R.

I'm thinking it's great that I can easily have both 32-bit and 64-bit 
versions of R. I use the combined installer and install both 32- and 
64-bit versions. I plan on primarily using the 64-bit version, so I 
first go into that and use biocLite(), but I got a warning message 
that package 'limma' is not available:

 > source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
 > biocLite()
Using R version 2.12.0, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
  [1] "affy"          "affydata"      "affyPLM"       "affyQCReport"
  [5] "annaffy"       "annotate"      "Biobase"       "biomaRt"
  [9] "Biostrings"    "DynDoc"        "gcrma"         "genefilter"
[13] "geneplotter"   "GenomicRanges" "hgu95av2.db"   "limma"
[17] "marray"        "multtest"      "vsn"           "xtable"
Please wait...

#skipped a bunch of output

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
   packages 'GenomicRanges', 'limma' are not available

 > biocLite("limma")
Using R version 2.12.0, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] "limma"
Please wait...

Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
   package 'limma' is not available

 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/x64 (64-bit)

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 utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.12.0


The current page for limma says the windows binary is 32- & 64-bit:
http://bioconductor.org/help/bioc-views/release/bioc/html/limma.html

So then I went into the 32-bit R and used biocLite(), and it 
installed everything just fine, and I can load limma:

 > library(limma)
 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)

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 utils     datasets  methods   base

other attached packages:
[1] limma_3.6.6

loaded via a namespace (and not attached):
[1] tools_2.12.0


If I go back to the x-64 R and try to load limma, I now get this message:

 > library(limma)
Error: package 'limma' is not installed for 'arch=x64'


I have no idea how the shared library for both 32- and 64-bit 
installations is going to work. I looked at both the R and BioC 
mailing lists, but no one seemed to post this problem yet, so I'm 
wondering what I'm doing wrong. Shouldn't it "just work", or do I 
need to get the 64-bit toolchain and compile limma from source for my 
64-bit R?

Thanks,
Jenny

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