[BioC] oligo on R 2.4.1?

[Xinxia Peng]

Hi Jenny,

Under Linux, you can install a local copy of both R and related packages
yourself anywhere inside your home directory. I got both packages
installed.

Best,
Xinxia
    

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of
drnevich at uiuc.edu
Sent: Thursday, February 08, 2007 11:44 AM
To: bioconductor at stat.math.ethz.ch; bcarvalh at jhsph.edu
Subject: [BioC] oligo on R 2.4.1?

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.U
TF-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_ID
ENTIFICATION=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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