Entering edit mode
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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