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

[Jenny Drnevich]

Got it installed. Thanks Hervé!

Jenny

At 07:00 PM 11/9/2010, Hervé Pagès wrote:
>On 11/09/2010 03:39 PM, Hervé Pagès wrote:
>>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().
>
>The new limma binary (bi-arch) is now available:
>
>D:\biocbld\bbs-2.7-bioc>R\bin\R
>
>R version 2.12.0 RC (2010-10-11 r53293)
>Copyright (C) 2010 The R Foundation for Statistical Computing
>ISBN 3-900051-07-0
>Platform: x86_64-pc-mingw32/x64 (64-bit)
>[...]
> > source("http://bioconductor.org/biocLite.R")
>BioC_mirror = http://www.bioconductor.org
>Change using chooseBioCmirror().
> > biocLite("limma")
>Using R version 2.12.0, biocinstall version 2.7.4.
>Installing Bioconductor version 2.7 packages:
>[1] "limma"
>Please wait...
>
>trying URL 
>'http://www.bioconductor.org/packages/2.7/bioc/bin/windows/contrib/2.12/limma_3.6.6.zip'
>Content type 'application/zip' length 1280462 bytes (1.2 Mb)
>opened URL
>downloaded 1.2 Mb
>
>package 'limma' successfully unpacked and MD5 sums checked
>
>The downloaded packages are in
>C:\Users\biocbuild2\AppData\Local\Temp\2\RtmpYU9pzb\downloaded_packages
> > library(limma)
> > sessionInfo()
>R version 2.12.0 RC (2010-10-11 r53293)
>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
>
>other attached packages:
>[1] limma_3.6.6
>
>loaded via a namespace (and not attached):
>[1] tools_2.12.0
> >
>
>Also to answer your question about how the shared library for both
>32- and 64-bit installations is working: bi-arch Windows packages
>that contain native code are compiled for the 2 archs and the
>resulting DLLs are put under <pkgtopdir>/libs/i386 and
><pkgtopdir>/libs/x64 respectively. In addition those packages
>have an Archs field in their DESCRIPTION file that lists the
>supported archs, e.g.:
>
>Archs: i386, x64
>
>Packages that don't contain native code don't have the Archs field.
>Note that this field is not something the developer needs to be
>dealing with: it is automatically added when the binary package is
>built (hence you won't find any documentation about it in the
>"Writing R Extensions" manual).
>
>Please let me know if you have any question.
>
>H.
>
>
>>
>>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
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319