[BioC] can't get limma for R 2.12.0 x64?
Jenny Drnevich
drnevich at illinois.edu
Wed Nov 10 23:41:17 CET 2010
Hi Hervé,
Maybe same problem as before, but now for
IRanges? I don't know that I use this package
directly, but I use affycoretools extensively,
and it won't load properly without IRanges:
> biocLite("IRanges")
Using R version 2.12.0, biocinstall version 2.7.4.
Installing Bioconductor version 2.7 packages:
[1] "IRanges"
Please wait...
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘IRanges’ is not available
> library(affycoretools)
Error in library.dynam(lib, package, package.lib) :
DLL 'IRanges' not found: maybe not installed for this architecture?
Error: package/namespace load failed for 'affycoretools'
> 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 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices
datasets utils methods base
other attached packages:
[1]
limma_3.6.6 lattice_0.19-13
made4_1.24.0 scatterplot3d_0.3-31 gplots_2.8.0
[6]
caTools_1.10 bitops_1.0-4.1
gdata_2.8.0 gtools_2.6.2 RColorBrewer_1.0-2
[11]
ade4_1.4-16 KEGG.db_2.4.5
GO.db_2.4.5 RSQLite_0.9-3 DBI_0.2-5
[16] AnnotationDbi_1.12.0
affy_1.28.0 Biobase_2.10.0 RWinEdt_1.8-2
loaded via a namespace (and not attached):
[1]
affyio_1.18.0 annaffy_1.22.0
annotate_1.28.0 biomaRt_2.6.0 Category_2.16.0
[6]
genefilter_1.32.0 GOstats_2.16.0
graph_1.28.0 GSEABase_1.12.0 preprocessCore_1.12.0
[11]
RBGL_1.26.0 RCurl_1.4-4.1
splines_2.12.0 survival_2.35-8 tools_2.12.0
[16] XML_3.2-0.1 xtable_1.5-6
>
Thanks,
Jenny
At 09:16 AM 11/10/2010, Jenny Drnevich wrote:
>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
>
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