Trouble with affy version 1.2.1
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Isaac Neuhaus ▴ 360
@isaac-neuhaus-22
Last seen 8.8 years ago
United States
I am running R 1.5.1 and I have installed the affy package version 1.2.1. When I start R and select library affy I get the following error. Any help? Isaac P.S. I have installed HDF5 and rhdf5. ---------------------------------------------------------------------- ----------------------- > library(affy) Loading required package: Biobase Loading required package: methods Expanding the signature to include omitted arguments in definition: j = "missing" Attaching package `Biobase': The following object(s) are masked from package:base : split ************* affy: development version (...this is usable...) ************* demo(affy.tour) will eventually work and give an overview... ************* If you have tkWidgets and rhdf5 installed, try expresso(widget=T, hdf5=T) for a real thrill... Loading required package: eda -->detecting normalization methods from naming convention -->detecting expression value methods from naming convention -->detecting background correction methods from naming convention -->initCdf -->initCel -->initCel.container Loading required package: rhdf5 Attaching package `rhdf5': The following object(s) are masked from package:base : is.finite is.matrix -->initPPSet -->initPPSet.container -->initPlob Error in setMethod("abstract", "Plob", function(object) abstract(object@description), : No existing definition for function "abstract" Error in library(affy) : .First.lib failed
Normalization rhdf5 tkWidgets affy Normalization rhdf5 tkWidgets affy • 1.1k views
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Isaac Neuhaus ▴ 360
@isaac-neuhaus-22
Last seen 8.8 years ago
United States
Thanks. Yes that fixed it. Isaac Laurent Gautier wrote: > The use of the 'devel' version of the package Biobase should keep R > happy. > > Let us know if it not the case. > > Hopin' it helps, > > Laurent > > On Wed, Sep 04, 2002 at 05:17:38PM -0400, Isaac Neuhaus wrote: > > I am running R 1.5.1 and I have installed the affy package version > > 1.2.1. When I start R and select library affy I get the following error. > > Any help? > > > > Isaac > > > > P.S. I have installed HDF5 and rhdf5. > > ------------------------------------------------------------------ --------------------------- > > > > > library(affy) > > Loading required package: Biobase > > Loading required package: methods > > Expanding the signature to include omitted arguments > > in definition: j = "missing" > > > > Attaching package `Biobase': > > > > > > The following object(s) are masked from package:base : > > > > split > > > > ************* > > affy: development version (...this is usable...) > > ************* > > demo(affy.tour) will eventually work and give an overview... > > ************* > > If you have tkWidgets and rhdf5 installed, try > > expresso(widget=T, hdf5=T) > > for a real thrill... > > Loading required package: eda > > -->detecting normalization methods from naming convention > > -->detecting expression value methods from naming convention > > -->detecting background correction methods from naming convention > > -->initCdf > > -->initCel > > -->initCel.container > > Loading required package: rhdf5 > > > > Attaching package `rhdf5': > > > > > > The following object(s) are masked from package:base : > > > > is.finite is.matrix > > > > -->initPPSet > > -->initPPSet.container > > -->initPlob > > Error in setMethod("abstract", "Plob", function(object) > > abstract(object@description), : > > No existing definition for function "abstract" > > Error in library(affy) : .First.lib failed > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > -------------------------------------------------------------- > Laurent Gautier CBS, Building 208, DTU > PhD. Student DK-2800 Lyngby,Denmark > tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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Laurent Gautier ★ 2.3k
@laurent-gautier-29
Last seen 9.6 years ago
The use of the 'devel' version of the package Biobase should keep R happy. Let us know if it not the case. Hopin' it helps, Laurent On Wed, Sep 04, 2002 at 05:17:38PM -0400, Isaac Neuhaus wrote: > I am running R 1.5.1 and I have installed the affy package version > 1.2.1. When I start R and select library affy I get the following error. > Any help? > > Isaac > > P.S. I have installed HDF5 and rhdf5. > -------------------------------------------------------------------- ------------------------- > > > library(affy) > Loading required package: Biobase > Loading required package: methods > Expanding the signature to include omitted arguments > in definition: j = "missing" > > Attaching package `Biobase': > > > The following object(s) are masked from package:base : > > split > > ************* > affy: development version (...this is usable...) > ************* > demo(affy.tour) will eventually work and give an overview... > ************* > If you have tkWidgets and rhdf5 installed, try > expresso(widget=T, hdf5=T) > for a real thrill... > Loading required package: eda > -->detecting normalization methods from naming convention > -->detecting expression value methods from naming convention > -->detecting background correction methods from naming convention > -->initCdf > -->initCel > -->initCel.container > Loading required package: rhdf5 > > Attaching package `rhdf5': > > > The following object(s) are masked from package:base : > > is.finite is.matrix > > -->initPPSet > -->initPPSet.container > -->initPlob > Error in setMethod("abstract", "Plob", function(object) > abstract(object@description), : > No existing definition for function "abstract" > Error in library(affy) : .First.lib failed > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
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