[R-SIG-Mac] 64-bit R and package installation question
hoontaechung at gmail.com
Sun Dec 9 08:11:02 CET 2007
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
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.
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:
 "affy" "affydata" "affyPLM" "annaffy"
 "Biobase" "Biostrings" "DynDoc" "gcrma"
 "geneplotter" "hgu95av2" "limma" "marray"
 "multtest" "ROC" "vsn" "xtable"
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)
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)
downloaded 142 Kb
The downloaded packages are in
> 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
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
>> 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
> 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.
>> Here is the configuration I used:
>> CONFIG_SHELL=/bin/bash ../R-devel/configure r_arch=x86_64 LDFLAGS="-
>> 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='-
>> 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
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
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