[BioC] oligo on R 2.4.1?

[James W. MacDonald]

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
> 
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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


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