Hi Martin, Well that looks like it should help me out. I had tried something similar, but I was trying it on the GOHyperGParams class, and that kept dying on me, so I didn't see it. So this will work: > setClass("H", + contains="HyperGParams", + prototype=prototype(annotation="GO")) [1] "H" > H1 <- new("H") > H1 A H instance category: annotation: GO > setClass("I", + contains="H", + representation=representation(numrep="numeric"), + prototype=prototype(numrep=1)) [1] "I" > I1 <- new("I") > I1 A I instance category: annotation: GO But, I can't do it from the GOHyperGParam directly, and this is what was tripping me up earlier. I didn't think to go back a step and put in a default. > setClass("H", + contains="GOHyperGParams", + prototype=prototype(annotation="GO")) Loading required package: .db Error in DatPkgFactory(annotation) : annotation package '.db' not available In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called '.db' And this is due to the DatPkgFactory function needing some kind of default annotation. Ok, weird, but I think I can make it work. Thanks, -Robert On Thu, Dec 23, 2010 at 14:33, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: > Hi Robert -- > > On 12/23/2010 09:48 AM, Robert M. Flight wrote: >> Hi All, >> >> I am trying to make my own package a little easier to use, and want to >> extend some of the Category parameter classes. I can easily extend the >> primary virtual class without any problems, but I run into >> difficulties if I first extend the virtual class, and then try and >> extend that, or extend any of the other classes already built on it. I >> want to add just one slot to the classes, but would rather not >> redefine a bunch of stuff if the previously defined classes already >> have what I need (which is what I would do if I extended the >> HyperGParams class directly). >> >> Two examples should illustrate what I am trying to do and the problem. >> >> >> Extend the VIRTUAL class "HyperGParams", works as expected >> >>> setClass("T1", >> + ? ? ? ? ?contains="HyperGParams", >> + ? ? ? ? ?representation=representation(numrep="numeric"), >> + ? ? ? ? ?prototype=prototype(numrep=1)) >> [1] "T1" > > not quite -- > >> new("T1") > Loading required package: .db > Error in DatPkgFactory(annotation) : > ?annotation package '.db' not available > In addition: Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, ?: > ?there is no package called '.db' > > And simpler > >> setClass("H", "HyperGParams") > [1] "H" >> new("H") > Loading required package: .db > Error in DatPkgFactory(annotation) : > ?annotation package '.db' not available > In addition: Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, ?: > ?there is no package called '.db' > > A solution is to provide a default for the 'annotation' slot, along the lines of > >> setClass("H", "HyperGParams", > + ? ? ? ? ?prototype=prototype(annotation="GO")) > [1] "H" >> new("H") > A H instance > ?category: > annotation: GO > > Martin > >> >> >> Now lets extend it to something like the "GOHyperGParams" >> >>> setClass("GOT1", >> + contains="T1", >> + ? ? ? ? representation=representation(ontology="character", >> + ? ? ? ? ? ? ? ? ? ? ? ? conditional="logical"), >> + ? ? ? ? prototype=prototype(categoryName="GO", >> + ? ? ? ? ? ?conditional=FALSE)) >> Loading required package: .db >> Error in DatPkgFactory(annotation) : >> ? annotation package '.db' not available >> In addition: Warning message: >> In library(package, lib.loc = lib.loc, character.only = TRUE, >> logical.return = TRUE, ?: >> ? there is no package called '.db' >> >> >> This behavior seems to be caused by the DatPkgFactory function in >> Category, but I can't figure out how to get around it in the class >> definition >> >> >> Ok, what about trying to extend the GOHyperGParams directly then? >> >>> setClass("T2", >> + ? ? ? ? ?contains="GOHyperGParams", >> + ? ? ? ? ?representation=representation(numrep="numeric"), >> + ? ? ? ? ?prototype=prototype(numrep=1)) >> Loading required package: .db >> Error in DatPkgFactory(annotation) : >> ? annotation package '.db' not available >> In addition: Warning message: >> In library(package, lib.loc = lib.loc, character.only = TRUE, >> logical.return = TRUE, ?: >> ? there is no package called '.db' >> >> Same problem. Is this expected behavior? Is there a way to get around >> this? I would really appreciate any insight someone might have into >> this. >> >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] GOstats_2.16.0 ? ? ? RSQLite_0.9-3 ? ? ? ?DBI_0.2-5 >> [4] graph_1.28.0 ? ? ? ? Category_2.16.0 ? ? ?AnnotationDbi_1.12.0 >> [7] Biobase_2.10.0 >> >> loaded via a namespace (and not attached): >> ?[1] annotate_1.28.0 ? genefilter_1.32.0 GO.db_2.4.5 ? ? ? GSEABase_1.12.1 >> ?[5] RBGL_1.26.0 ? ? ? splines_2.12.0 ? ?survival_2.36-1 ? tools_2.12.0 >> ?[9] XML_3.2-0.2 ? ? ? xtable_1.5-6 >> >> >> Regards, >> >> -Robert >> >> Robert M. Flight, Ph.D. >> University of Louisville Bioinformatics Laboratory >> University of Louisville >> Louisville, KY >> >> PH 502-852-0467 >> EM robert.flight at louisville.edu >> EM rflight79 at gmail.com >> >> Williams and Holland's Law: >> ? ? ? ?If enough data is collected, anything may be proven by >> statistical methods. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 >