[BioC] can't get limma for R 2.12.0 x64?
Hervé Pagès
hpages at fhcrc.org
Wed Nov 10 00:39:40 CET 2010
Hi Jenny, Martha,
Thanks for reporting this problem.
Because of a problem we had recently with our build system, the
Windows binary of limma that is currently available thru biocLite()
is single arch only (it has the 32-bit part but is missing the 64-bit
part). A new binary containing the 2 archs will be available in a few
minutes. Please reinstall with biocLite().
Other packages might have the same problem but we'll need to wait
after the next build cycle is finished in order to do a more systematic
check.
Cheers,
H.
On 11/09/2010 01:21 PM, mkbehnke at gmail.com wrote:
> 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
>
> [[alternative HTML version deleted]]
>
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
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