[R-SIG-Mac] 64-bit R and package installation question

Prof Brian Ripley ripley at stats.ox.ac.uk
Sun Dec 9 09:02:07 CET 2007 

The fix is to install source packages: use argument type="source", 
including AFAICS as an argument to biocLite(). Or set
options(pkgType="source").

Simon: it is unclear to me what build this is, but could the default not 
be pkgType="source" for off-CRAN builds?  I don't think we should be 
expecting third parties to support architectures the CRAN build does not.


On Sun, 9 Dec 2007, Á¤ ÅÂÈÆ wrote:

> The binaries in http://r.research.att.com/ worked great!
> Thanks a lot for the tip.
>
> However, when I tried to install bioconductor libraries using
> biocLite, I got the following error message:
>
> bash-3.2$ R --arch=x86_64
>
> R version 2.6.1 Patched (2007-12-06 r43615)
> Copyright (C) 2007 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
> > source("http://www.bioconductor.org/biocLite.R")
> > biocLite(lib="~/Library/R64")
> Running biocinstall version 2.1.8 with R version 2.6.1
> Your version of R requires version 2.1 of Bioconductor.
> Will install the following packages:
>  [1] "affy"         "affydata"     "affyPLM"      "annaffy"
> "annotate"
>  [6] "Biobase"      "Biostrings"   "DynDoc"       "gcrma"
> "genefilter"
> [11] "geneplotter"  "hgu95av2"     "limma"        "marray"
> "matchprobes"
> [16] "multtest"     "ROC"          "vsn"          "xtable"
> "affyQCReport"
> Please wait...
>
> trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/affy_1.16.0.tgz'
> Content type 'application/x-gzip' length 1683130 bytes (1.6 Mb)
> opened URL
> ==================================================
> downloaded 1.6 Mb
>
> ... < skip > ...
>
> trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/affyQCReport_1.16.0.tgz'
> Content type 'application/x-gzip' length 145478 bytes (142 Kb)
> opened URL
> ==================================================
> downloaded 142 Kb
>
>
> The downloaded packages are in
>         /var/folders/T0/T0X1+9S9ExGTArjMjd98hk+++TI/-Tmp-//Rtmp90AT9K/
> downloaded_packages
> > library(affy, lib="~/Library/R64")
> Error: package 'affy' is not installed for 'arch=x86_64'
>
> Is there any special way to install any packages for 64-bit compatible
> manner?
>
> Thanks in advance,
>
> 2007. 12. 08, ¿ÀÀü 2:11, Simon Urbanek ÀÛ¼º:
>
>>
>> On Dec 6, 2007, at 9:40 PM, Á¤ ÅÂÈÆ wrote:
>>
>>> Hi, All;
>>>
>>> I've compiled and installed successfully "presumably" 64-bit R on
>>> Leopard.
>>> But when I tried to run R, I got the following error:
>>>
>>> /usr/bin/R: line 179: /Library/Frameworks/R.framework/Resources/etc/
>>> i386/ldpaths: No such file or directory
>>>
>>
>> I'm pretty sure that your /usr/bin/R comes from a different build.
>> Make sure you remove old scripts.
>>
>> FWIW: dual 32-bit and 64-bit binaries of current R 2.6.1 patched and
>> R-devel for Leopard are available from
>> http://r.research.att.com/
>> They support all four architectures. To start 64-bit Intel R use R --
>> arch=x86_64, for 64-bit ppc it is R --arch=ppc64.
>>
>> Cheers,
>> Simon
>>
>>
>>> Here is the configuration I used:
>>>
>>> CONFIG_SHELL=/bin/bash ../R-devel/configure r_arch=x86_64 LDFLAGS="-
>>> L/
>>> usr/local/lib64 -L/usr/X11R6/lib" CC='gcc-4.2 -g -O3' CXX='g++-4.2 -
>>> g -
>>> O3' F77='gfortran -g -O3' FC='gfortran -g -O3' --with-blas='-
>>> framework
>>> vecLib' --with-lapack
>>>
>>> Thanks in advance
>>>
>>> Tae-Hoon Chung
>>>
>>> Korea Centers for Disease Control & Prevention (KCDC)
>>> Korea National Institute of Health (KNIH)
>>> Center for Genome Sciences, Biobank for Health Sciences
>>>
>>> 194 Tongil-ro, Eunpyoung-gu, Seoul, 122-701, Korea
>>>
>>> Tel		82-2-380-2252
>>> Fax		82-2-354-1078
>>> Mobile	82-10-8011-1036
>>>
>>>
>>> 	[[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>
>
> Tae-Hoon Chung
>
> Korea Centers for Disease Control & Prevention (KCDC)
> Korea National Institute of Health (KNIH)
> Center for Genome Sciences, Biobank for Health Sciences
>
> 194 Tongil-ro, Eunpyoung-gu, Seoul, 122-701, Korea
>
> Tel		82-2-380-2252
> Fax		82-2-354-1078
> Mobile	82-10-8011-1036
>
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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