[BioC] Error : package slot missing from signature for generic
Mark Cowley
m.cowley at garvan.org.au
Fri Aug 3 06:14:58 CEST 2012
any ideas fellow bioconductors?
cheers, Mark
On 01/08/2012, at 9:41 AM, Mark Cowley wrote:
> Dear guRu's,
> please help me escape dependency hell...
> in my package foo, i'm trying to replace the 'sampleNames<-' method from package lumi. This works well, ie I can install foo, and execute the updated code.
>
> However, if my package foo imports oligoClasses, (or as it turns out, a chain of dependencies which lead to oligoClasses), I get this error during INSTALL
> * installing to library Œ/Library/Frameworks/R.framework/Versions/2.15/Resources/library‚
> * installing *source* package Œfoo‚ ...
> ** R
> ** preparing package for lazy loading
> Warning: replacing previous import Œimage‚ when loading Œgraphics‚
> Warning: replacing previous import Œdensity‚ when loading Œstats‚
> Warning: replacing previous import Œresiduals‚ when loading Œstats‚
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> *** arch - i386
> Warning: replacing previous import Œimage‚ when loading Œgraphics‚
> Warning: replacing previous import Œdensity‚ when loading Œstats‚
> Warning: replacing previous import Œresiduals‚ when loading Œstats‚
> Error : package slot missing from signature for generic ŒsampleNames<-‚
> and classes LumiBatch, ANY
> cannot use with duplicate class names (the package may need to be re-installed)
> Error: loading failed
> Execution halted
> *** arch - x86_64
> Warning: replacing previous import Œimage‚ when loading Œgraphics‚
> Warning: replacing previous import Œdensity‚ when loading Œstats‚
> Warning: replacing previous import Œresiduals‚ when loading Œstats‚
> Error : package slot missing from signature for generic ŒsampleNames<-‚
> and classes LumiBatch, ANY
> cannot use with duplicate class names (the package may need to be re-installed)
> Error: loading failed
> Execution halted
> ERROR: loading failed for Œi386‚, Œx86_64‚
> * removing Œ/Library/Frameworks/R.framework/Versions/2.15/Resources/library/foo‚
> * restoring previous Œ/Library/Frameworks/R.framework/Versions/2.15/Resources/library/foo‚
>
> The message tells me its a problem with my 'sampleNames<-' method, however it looks fine to me:
> 1) foo installs just fine when I don't import oligoClasses
> 2) My sampleNames<- code can be pasted into an R session just fine
> 3) the error appears as soon as I add a import(oligoClasses) or importFrom(oligoClasses,'sampleNames<-') to foo's NAMESPACE
>
> I've had a look at oligoClasses, and it seems to be playing by the rules: it importMethodsFrom(Biobase, "sampleNames<-") and exportMethods("sampleNames<-") for a 'RangedDataCNV' class. It doesn't import lumi, nor does it know about sampleNames<-,LumiBatch,ANY-method
>
> i've spent a few days trying to work this one out, so can anyone point me in the right direction?
>
> cheers,
> Mark
>
> foo/R/LumiBatch-methods.R:
> #' @name LumiBatch-methods
> #' @title a collection of LumiBatch manipulators
> #' @description \code{sampleNames<-}: set sampleNames in LumiBatch objects,
> #' including the QC, vstParameter, transformFun and controlData slots
> #'
> #' @note code came from lumi_2.8.0 & modified by MJC to set the controlData slot
> #' properly
> #'
> #' @param object an \code{LumiBatch} object
> #' @param value a character vector of column names
> #' @return a \code{LumiBatch} object
> #' @rdname LumiBatch-methods
> #' @aliases sampleNames<-,LumiBatch,ANY-method
> #' @export
> #' @importMethodsFrom Biobase "sampleNames<-"
> #' @importMethodsFrom lumi "sampleNames<-"
> #' @import oligoClasses
> setMethod("sampleNames<-",
> signature=signature("LumiBatch", "ANY"),
> function(object, value) {
> object <- callNextMethod()
> ddim <- dim(object)
> if (!is.null(object at QC)) {
> QC <- object at QC
> if (!is.null(QC$sampleSummary))
> if (ncol(QC$sampleSummary) == ddim[2])
> colnames(QC$sampleSummary) <- value
> if (!is.null(QC$BeadStudioSummary))
> if (nrow(QC$BeadStudioSummary) == ddim[2])
> rownames(QC$BeadStudioSummary) <- value
> object at QC <- QC
> }
> if (!is.null(attr(object, "vstParameter"))) {
> vstParameter <- attr(object, "vstParameter")
> if (!is.null(nrow(vstParameter))) {
> if (nrow(vstParameter) == ddim[2]) {
> rownames(vstParameter) <- value
> transformFun <- attr(object, "transformFun")
> names(transformFun) <- value
> attr(object, "vstParameter") <- vstParameter
> attr(object, "transformFun") <- transformFun
> }
> }
> }
> if (nrow(object at controlData) > 0) {
> # modified by MJC
> colnames(controlData(object)) <- c("controlType", "ProbeID", value)
> }
> return(object)
> }
> )
>
>
> foo/NAMESPACE:
> exportMethods("sampleNames<-")
> import(oligoClasses)
> importMethodsFrom(Biobase,"sampleNames<-")
> importMethodsFrom(lumi,"sampleNames<-")
>
>
> foo/DESCRIPTION:
> Package: foo
> Maintainer: Mark Cowley <m.cowley at garvan.org.au>
> License: GPL-2
> Title: Quicktest package for rapid development with testthat facilities
> Author: Mark Cowley <m.cowley at garvan.org.au>
> Description: A lightweight library for rapid iterative development of new
> code and test suites. Once code is confirmed to work, you should move it out
> to a dedicated package.
> Version: 0.1
> Date: 2012-08-01
> Depends:
> R (>= 2.0),
> methods,
> Biobase,
> lumi
> Suggests:
> roxygen2,
> testthat,
> Imports:
> Biobase,
> lumi,
> oligoClasses
> Collate:
> 'LumiBatch-methods.R'
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] lumi_2.8.0 nleqslv_1.9.3 methylumi_2.2.0 ggplot2_0.9.1
> [5] reshape2_1.2.1 scales_0.2.1 Biobase_2.16.0 BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
> [1] affy_1.34.0 affyio_1.24.0 annotate_1.34.1
> [4] AnnotationDbi_1.18.1 bigmemory_4.2.11 BiocInstaller_1.4.7
> [7] Biostrings_2.24.1 bitops_1.0-4.1 BSgenome_1.24.0
> [10] colorspace_1.1-1 DBI_0.2-5 dichromat_1.2-4
> [13] digest_0.5.2 DNAcopy_1.30.0 GenomicRanges_1.8.9
> [16] genoset_1.6.0 grid_2.15.1 hdrcde_2.16
> [19] IRanges_1.14.4 KernSmooth_2.23-8 labeling_0.1
> [22] lattice_0.20-6 MASS_7.3-19 Matrix_1.0-6
> [25] memoise_0.1 mgcv_1.7-19 munsell_0.3
> [28] nlme_3.1-104 plyr_1.7.1 preprocessCore_1.18.0
> [31] proto_0.3-9.2 RColorBrewer_1.0-5 RCurl_1.91-1
> [34] Rsamtools_1.8.5 RSQLite_0.11.1 rtracklayer_1.16.3
> [37] stats4_2.15.1 stringr_0.6.1 tools_2.15.1
> [40] XML_3.9-4 xtable_1.7-0 zlibbioc_1.2.0
>
>
>
> [[alternative HTML version deleted]]
>
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