[BioC] oligo on R 2.4.1?

James W. MacDonald jmacdon at med.umich.edu
Thu Feb 8 22:53:42 CET 2007


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=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 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.



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