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

[정 태훈]

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, 오전 2:11, Simon Urbanek 작성:

>
> On Dec 6, 2007, at 9:40 PM, 정 태훈 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