make own CDF package probelm, error "installed < 2.0.0"
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Liqun He ▴ 30
@liqun-he-1253
Last seen 10.5 years ago
Dear there, I am creating own chip CDF and probe package file with a window R 2.0.1 version. The make.cdf.package works fine, > make.cdf.package(chip.CDF); Reading CDF file. Creating CDF environment Creating package in E:/chipcdf I installed this CDF package in R and try to load it to run makeProbePackage, and then come the error message, > library(chipcdff) Error in library(chipcdf) : 'chipcdf' is not a valid package -- installed < 2.0.0? I have tried google, but can not get the right solution. Could any one help me to solve the trouble? Thanks a lot! Kind regards, Liqun [[alternative HTML version deleted]]
cdf probe cdf probe • 883 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Liqun He wrote: > > Dear there, > > I am creating own chip CDF and probe package file with a window R 2.0.1 > version. > > The make.cdf.package works fine, > >>make.cdf.package(chip.CDF); > > Reading CDF file. > Creating CDF environment > Creating package in E:/chipcdf > > I installed this CDF package in R and try to load it to run > makeProbePackage, and then come the error message, > > library(chipcdff) > Error in library(chipcdf) : 'chipcdf' is not a valid package -- > installed < 2.0.0? What exactly did you do to install this package? > > I have tried google, but can not get the right solution. Could any one > help me to solve the trouble? > Thanks a lot! > > Kind regards, > Liqun > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald 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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Hi, After I used the command "make.cdf.package(chip.CDF)", it produced a cdf package subdirectory "chipcdf". When I checked the R package installation instruction for Windows, it required a zipped local file. So, I put the whole subdirectory into a linux system, and used the command "zip -r chipcdf chipcdf", it produced the zip file "chipcdf.zip" Then I used the R window bottom, Packages->Install Packages from local zipped files, and selected the file chipcdf.zip. It showed the following without error message. >install.packages(choose.files('',filters=Filters[c('zip','All'),]), .libPaths()[1], CRAN = NULL) updating HTML package descriptions Then I was trying to load the package, it gived the error message: > library(chipcdf) Error in library(chipcdf) : 'chipcdf' is not a valid package -- installed < 2.0.0? I am a beginner here, there must be something wrong with my procedure. But I don't the right way to do it. Could someone provide a help? Some web pages say using the function make.cdf.env to create CDF environment directly. >Chipcdf=make.cdf.env(chip.CDF) But I don't known in this case, how should the makeProbePackage command be used. I am trying to create the required packages to run the GCRMA? Could someone help with this? Thanks a lot! Kind regards, Liqun -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of James W. MacDonald Sent: Tuesday, May 17, 2005 2:57 PM To: Liqun He Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] make own CDF package probelm, error "installed < 2.0.0" Liqun He wrote: > > Dear there, > > I am creating own chip CDF and probe package file with a window R 2.0.1 > version. > > The make.cdf.package works fine, > >>make.cdf.package(chip.CDF); > > Reading CDF file. > Creating CDF environment > Creating package in E:/chipcdf > > I installed this CDF package in R and try to load it to run > makeProbePackage, and then come the error message, > > library(chipcdff) > Error in library(chipcdf) : 'chipcdf' is not a valid package -- > installed < 2.0.0? What exactly did you do to install this package? > > I have tried google, but can not get the right solution. Could any one > help me to solve the trouble? > Thanks a lot! > > Kind regards, > Liqun > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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Liqun He wrote: > Hi, > > After I used the command "make.cdf.package(chip.CDF)", it produced a cdf > package subdirectory "chipcdf". > When I checked the R package installation instruction for Windows, it > required a zipped local file. So, I put the whole subdirectory into a > linux system, and used the command "zip -r chipcdf chipcdf", it produced > the zip file "chipcdf.zip" Yeah, I thought you had done something like that. Unfortunately, installing packages on Windows is not quite that simple. You will need some tools and you will also need to follow the instructions in the README.packages in your rw2001 directory *exactly* as written. They are a bit terse, but everything you need to know is right there. First look here and follow the links to the murdoch-sutherland website http://cran.r-project.org/bin/windows/base/rw-FAQ.html#Can-I-install- packages-into-libraries-in-this-version_003f Note that you will only need the 'Essentials' from Duncan Murdoch's webpage. The other tools listed there are nice if you want to build things like compiled HTML help, but are not completely necessary. Note too, that if you have access to R on a Unix-alike, installing packages is quite simple (but cross-compiling for Windows is not). All it takes is an R CMD INSTALL at a terminal prompt. HTH, Jim > Then I used the R window bottom, Packages->Install Packages from local > zipped files, and selected the file chipcdf.zip. It showed the following > without error message. > -- James W. MacDonald 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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