[Bioc-devel] Found more than one class "Annotated" in cache
Michael Lawrence
lawrence.michael at gene.com
Fri Apr 29 20:38:40 CEST 2016
Thanks, will fix.
On Fri, Apr 29, 2016 at 10:26 AM, davide risso <risso.davide at gmail.com> wrote:
> Hi all,
>
> when running R CMD check on our package, we get the following warning:
>
> checking whether the namespace can be unloaded cleanly ... WARNING
> ---- unloading
> Error in .getClassFromCache(what, resolve.confl = "all") :
> argument "where" is missing, with no default
> Calls: unloadNamespace ... <Anonymous> -> .removeSuperclassBackRefs ->
> .getClassFromCache
> Execution halted
>
> Is this warning related to the message mentioned earlier in this thread? If
> so, should I expect this warning to go away once the bug in the class import
> is fixed?
>
> Here for the full Travis CI report:
> https://travis-ci.org/epurdom/clusterExperiment/builds/126175973
>
> Thanks,
> Davide
>
>
> On Mon, Apr 25, 2016 at 2:00 PM davide risso <risso.davide at gmail.com> wrote:
>>
>> 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
>>> >>>
>>> >>
>>> >> _______________________________________________
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>>> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>> >>
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