[BioC] can't get limma for R 2.12.0 x64?
Hervé Pagès
hpages at fhcrc.org
Wed Nov 10 02:00:01 CET 2010
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
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