drnevich at uiuc.edu wrote: > Thanks Jim, Xinxia and Seth for the good suggestion! I wondered about > doing it, and Jim's line-by-line directions were VERY helpful. > Everything appeared to configure and build correctly, but adding > "export PATH=/home/jdrnevich/R-devel/bin:$PATH" to my .bashrc file is > not working to find my local install of R. Any other suggestions of > what to try? I usually just get all red in the face and kick it a couple of times, and then things start to work ;-D Did you add the path to your .bashrc and _then_ open a shell, or are you using an existing shell? Your .bashrc file is only read when you open a shell, so if you have an existing one, it won't see the new path. On *nix I find emacs/ess to be the only way to go, even if it requires lots of teeth gnashing at the outset. Best, Jim > > Thanks, Jenny > > ---- Original message ---- > >> Date: Thu, 08 Feb 2007 15:13:17 -0500 From: "James W. MacDonald" >> <jmacdon at="" med.umich.edu=""> Subject: Re: [BioC] oligo on R 2.4.1? To: >> drnevich at uiuc.edu Cc: bioconductor at stat.math.ethz.ch >> >> Hi Jenny, >> >> drnevich at uiuc.edu wrote: >> >>> Hi again, >>> >>> I'm having trouble making a data package for my Affy tiling array >>> - it's not related to the arguments for makePDpackages, but >>> because of memory limitations and the inability to install the >>> oligo package on R 2.4.0. I have R 2.5.0 (the devel. version) >>> installed on my PC, along with all the necessary compilers, but I >>> don't have enough memory to make the package. I also have access >>> to R on a server with more memory, but it's only R 2.4.0 and I >>> doubt I could get them to install R 2.5.0 on it until it's the >>> released version. R CMD INSTALL failed for the oligo package >>> because it says it requires 2.5.0, but the makePlatformDesign >>> package installed fine. I thought I would be able to make the >>> package on the server then install it back on my PC, but >>> according to the warnings and errors below, the oligo package is >>> required. Is there any way for me to get around this, or am I >>> SOL? >> >> I doubt you are SOL, unless the sysadmin has restricted your home >> directory to a thimbleful of disk. If you have a reasonable amount >> of disk space you can simply download the current devel version of >> R (the tar.gz), then configure and build right in your home >> directory. >> >> You don't have to go any farther than >> >> tar xvfz R-devel_blahblahblah.tar.gz cd R-devel ./configure make >> >> Then maybe add >> >> export PATH=/home/jdrnevich/R-devel/bin:$PATH >> >> to your .bashrc file so you will find your local R install first. >> Alternatively you can set your init.el file to use that directory >> if you use emacs for running R. >> >> You can then fire up your new R-devel, run biocLite() and rock on! >> >> Best, >> >> Jim >> >> >> >>> :) Jenny >>> >>> >>> >>> >>>> library(makePlatformDesign) >>> >>> Loading required package: oligo >>> >>> Attaching package: 'makePlatformDesign' >>> >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> complementSeq >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> longestConsecutive >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> matchprobes >>> >>> The following object(s) are masked from package:matchprobes : >>> >>> reverseSeq >>> >>> Warning messages: 1: there is no package called 'oligo' in: >>> library(package, lib.loc = lib.loc, character.only = TRUE, >>> logical = TRUE, 2: The oligo package could not be loaded thus the >>> platformDesign class is not defined. in: f(libname, pkgname) >>> >>> >>>> >>>> makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap", type="tiling", >>>> genomebuild="mg33") >>> >>> affymetrix tiling The package will be called pdmmpromprv01ncbiv35 >>> Array identified as having 914 rows and 914 columns. Error in >>> getClass(Class, where = topenv(parent.frame())) : >>> "platformDesign" is not a defined class >>> >>> >>>> sessionInfo() >>> >>> R version 2.4.0 (2006-10-03) x86_64-unknown-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> >>> attached base packages: [1] "splines" "tools" "methods" >>> "stats" "graphics" "grDevices" [7] "utils" "datasets" >>> "base" >>> >>> other attached packages: makePlatformDesign affyQCReport >>> simpleaffy made4 "0.99.20" "1.12.0" >>> "2.8.0" "1.8.0" scatterplot3d ade4 >>> affyPLM gcrma "0.3-24" "1.4-2" "1.10.0" >>> "2.6.0" matchprobes affydata affycoretools >>> biomaRt "1.6.0" "1.10.0" "1.6.0" "1.8.0" >>> RCurl XML GOstats Category "0.8-0" >>> "1.2-0" "2.0.4" "2.0.3" genefilter survival >>> KEGG RBGL "1.12.0" "2.29" "1.14.1" >>> "1.10.0" annotate GO graph limma >>> "1.12.0" "1.14.1" "1.12.0" "2.9.1" affy >>> affyio Biobase "1.12.1" "1.2.0" "1.12.2" >>> >>> >>> >>> Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics >>> Specialist Roy J. Carver Biotechnology Center University of >>> Illinois, Urbana-Champaign >>> >>> 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 >>> >>> ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu >>> >>> _______________________________________________ Bioconductor >>> mailing list Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >>> archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> >> -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA >> Microarray Core University of Michigan Cancer Center 1500 E. >> Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >> >> >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and >> should not be used for urgent or sensitive issues. > > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist > Roy J. Carver Biotechnology Center University of Illinois, > Urbana-Champaign > > 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 > > ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Dear Jenny, > Thanks Jim, Xinxia and Seth for the good suggestion! I wondered about > doing it, and Jim's line-by-line directions were VERY helpful. > Everything appeared to configure and build correctly, but adding > "export PATH=/home/jdrnevich/R-devel/bin:$PATH" to my .bashrc file is > not working to find my local install of R. Any other suggestions of > what to try? As an alternative to editing PATH, I find it convenient to create a little file (shell script) in my $HOME/bin directory, of the name "R" and with contents like #!/bin/sh exec /home/huber/R-2.4.1/bin/R $* On many systems, $HOME/bin is already in the PATH. That way you can easily juggle between different versions of R, set environment variables like "LD_LIBRARY_PATH" locally just for this R (not interfering with other software), prepend "nice -n 19" etc. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber