[BioC] oligo on R 2.4.1?

[drnevich at uiuc.edu]

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?

:)
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