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

Sun Dec 9 17:23:37 CET 2007

On Dec 9, 2007, at 3:02 AM, Prof Brian Ripley wrote:

> 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.
>

It is the "experimental" Leopard quad-arch nightly build and yes,  
changing the default package type is a good idea. I'll look into this.

Thanks,
Simon

>
> 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