[BioC] oligo on R 2.4.1?

Thu Feb 8 21:49:31 CET 2007

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?

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=en_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.UTF-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
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>
>
>-- 
>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