[Bioc-devel] Found more than one class "Annotated" in cache
davide risso
risso.davide at gmail.com
Mon Apr 25 23:00:07 CEST 2016
Thank you Michael and Martin for looking into this!
Best,
davide
On Mon, Apr 25, 2016 at 1:49 PM Michael Lawrence <lawrence.michael at gene.com>
wrote:
> Yes, that's a better fix for this in principle, since it uses the
> information encoded in the extends object, although I think
> getClassFromCache() also needs to be fixed, so that getClassDef() sees
> only the imported classes when only given "where". That's a more
> general fix that works in both load orders.
>
> Maybe the superClass slot of the extends object should store its
> package? Would be convenient, if somewhat redundant. Conceptually, it
> seems the package really belongs on superClass, not on the extends
> object itself (how does a ClassExtends pertain to a package?).
>
> Index: ClassExtensions.R
> ===================================================================
> --- ClassExtensions.R (revision 70547)
> +++ ClassExtensions.R (working copy)
> @@ -316,6 +316,7 @@
> stop(gettextf("the 'replace' argument to setIs() should be a
> function of 2 or 3 arguments, got an object of class %s",
> dQuote(class(replace))), domain = NA)
>
> + packageSlot(to) <- package
> new(extClass, subClass = Class, superClass = to, package = package,
> coerce = coerce, test = test, replace = replace, simple = simple,
> by = by, dataPart = dataPart, distance = distance)
>
>
>
> On Mon, Apr 25, 2016 at 1:24 PM, Martin Morgan
> <martin.morgan at roswellpark.org> wrote:
> >
> >
> > On 04/25/2016 03:53 PM, Michael Lawrence wrote:
> >>
> >> Yea, this is a bug in R, in my opinion. The class cache circumvents
> >> the namespace imports. In my working copy I've fixed it by falling
> >> back to the namespace search when there are multiple hits. That at
> >> least fixes this case.
> >
> >
> > This also fixes it
> >
> > Index: src/library/methods/R/SClasses.R
> > ===================================================================
> > --- src/library/methods/R/SClasses.R (revision 70547)
> > +++ src/library/methods/R/SClasses.R (working copy)
> > @@ -524,7 +524,7 @@
> > superClass <- exti at superClass
> > if(!exti at simple && !is(object, superClass))
> > next ## skip conditional relations that don't hold for this
> > object
> > - superDef <- getClassDef(superClass, where = where)
> > + superDef <- getClassDef(superClass, package = packageSlot(exti))
> > if(is.null(superDef)) {
> > errors <- c(errors,
> > paste0("superclass \"", superClass,
> >
> >
> > There's another problem seen by loading the packages in reverse order
> >
> >> suppressPackageStartupMessages({ library(RNeXML); library(GenomicRanges)
> >> })
> > Found more than one class "Annotated" in cache; using the first, from
> > namespace 'RNeXML'
> > Also defined by 'S4Vectors'
> > ...
> >
> > which is from
> >
> > [[17]]
> > S4Vectors:::setDefaultSlotValue("XRaw", "shared", new("SharedRaw"),
> > where = asNamespace(pkgname))
> >
> > [[18]]
> > resetClass(classname, classdef, where = where)
> >
> > [[19]]
> > completeClassDefinition(Class, classDef, where)
> >
> > [[20]]
> > .completeClassSlots(ClassDef, where)
> >
> > [[21]]
> > isClass(eClass, where = where)
> >
> > [[22]]
> > getClassDef(Class, where)
> >
> > [[23]]
> > .getClassFromCache(Class, where, package = package, resolve.msg =
> > resolve.msg)
> >
> > but I haven't quite got to the bottom of that. Also, I think these are
> both
> > different from but related to
> >
> >> suppressPackageStartupMessages(library(Statomica))
> > Error in .mergeMethodsTable(generic, mtable, tt, attach) :
> > trying to get slot "defined" from an object of a basic class ("list")
> with
> > no slots
> > Error: package or namespace load failed for 'Statomica'
> >
> >
> >>
> >> You can disable the message in the short term by setting the
> >> "getClass.msg" option to FALSE.
> >>
> >> Michael
> >>
> >> On Sun, Apr 24, 2016 at 12:50 PM, davide risso <risso.davide at gmail.com>
> >> wrote:
> >>>
> >>> Dear list,
> >>>
> >>> we are developing a new package that defines a class that builds on
> >>> SummarizedExperiment and also imports the CRAN package phylobase.
> >>>
> >>> The class "Annotated" is defined both in the S4Vectors package (a
> >>> dependency of SummarizedExperiment) and in the RNeXML package (a
> >>> dependency
> >>> of phylobase). Note that we want the former. This causes the following
> >>> message to be thrown every time we create a new object.
> >>>
> >>> Found more than one class "Annotated" in cache; using the first, from
> >>> namespace 'S4Vectors'
> >>>
> >>>
> >>> A minimal example is the following.
> >>>
> >>>> library(SummarizedExperiment)> SummarizedExperiment()class:
> >>>> SummarizedExperiment
> >>>
> >>> dim: 0 0
> >>> metadata(0):
> >>> assays(0):
> >>> rownames: NULL
> >>> rowData names(0):
> >>> colnames: NULL
> >>> colData names(0):> library(phylobase)> SummarizedExperiment()Found
> >>> more than one class "Annotated" in cache; using the first, from
> >>> namespace 'S4Vectors'class: SummarizedExperiment
> >>> dim: 0 0
> >>> metadata(0):
> >>> assays(0):
> >>> rownames: NULL
> >>> rowData names(0):
> >>> colnames: NULL
> >>> colData names(0):
> >>>
> >>>> sessionInfo()R Under development (unstable) (2016-03-07 r70284)
> >>>
> >>> Platform: x86_64-pc-linux-gnu (64-bit)
> >>> Running under: Debian GNU/Linux stretch/sid
> >>>
> >>> locale:
> >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >>> LC_TIME=en_US.UTF-8
> >>> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
> >>> LC_MESSAGES=en_US.UTF-8
> >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> >>> LC_ADDRESS=C
> >>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8
> >>> LC_IDENTIFICATION=C
> >>>
> >>> attached base packages:
> >>> [1] stats4 parallel stats graphics grDevices utils
> >>> datasets methods
> >>> [9] base
> >>>
> >>> other attached packages:
> >>> [1] phylobase_0.8.2 SummarizedExperiment_1.1.21
> >>> [3] Biobase_2.31.3 GenomicRanges_1.23.23
> >>> [5] GenomeInfoDb_1.7.6 IRanges_2.5.39
> >>> [7] S4Vectors_0.9.41 BiocGenerics_0.17.3
> >>>
> >>> loaded via a namespace (and not attached):
> >>> [1] Rcpp_0.12.3 plyr_1.8.3 XVector_0.11.7
> iterators_1.0.8
> >>> [5] tools_3.3.0 zlibbioc_1.17.0 uuid_0.1-2
> jsonlite_0.9.19
> >>> [9] nlme_3.1-125 lattice_0.20-33 foreach_1.4.3 DBI_0.3.1
> >>> [13] httr_1.1.0 stringr_1.0.0 dplyr_0.4.3 xml2_0.1.2
> >>> [17] ade4_1.7-4 grid_3.3.0 rredlist_0.1.0 reshape_0.8.5
> >>> [21] data.table_1.9.6 R6_2.1.2 XML_3.98-1.4 RNeXML_2.0.6
> >>> [25] reshape2_1.4.1 tidyr_0.4.1 magrittr_1.5
> codetools_0.2-14
> >>> [29] assertthat_0.1 bold_0.3.5 taxize_0.7.5 ape_3.4
> >>> [33] stringi_1.0-1 rncl_0.6.0 lazyeval_0.1.10 rotl_0.5.0
> >>> [37] chron_2.3-47
> >>>
> >>>
> >>> Since we need to import both packages, is there a way to explicitly use
> >>> the
> >>> correct definition of "Annotated" or to not import the class
> "Annotated"
> >>> from RNeXML?
> >>>
> >>> Or is this something that could be addressed in the
> SummarizedExperiment
> >>> package?
> >>>
> >>> These are our DESCRIPTION and NAMESPACE file (note that we are
> importing
> >>> only what we need from phylobase):
> >>> https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION
> >>> https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE
> >>>
> >>> See also Henrik's comment at:
> >>> https://github.com/epurdom/clusterExperiment/issues/66
> >>>
> >>> Thank you in advance for any help!
> >>>
> >>> Best,
> >>> davide
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
> >> _______________________________________________
> >> Bioc-devel at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
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