64-bit R and package installation question
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, ?? 2:11, Simon Urbanek ??:
On Dec 6, 2007, at 9:40 PM, ? ?? 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]]
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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