[Bioc-devel] Add OrgDb class to slot, warning during build

[Martin Morgan]

Hi Jesper --

On 12/22/2012 05:09 PM, Jesper Gådin wrote:
> Hello all,
>
> #I have been attempting to create a slot in my own class foo that is
> supposed to contain an OrgDb object from the AnnotationDbi-package.
> Actually it works, but during my build I get this warning:
>
> ** R
> ** inst
> ** preparing package for lazy loading
> Warning: Class "OrgDb" is defined (with package slot ‘AnnotationDbi’) but
> no metadata object found to revise superClass information---not exported?
> Making a copy in package fooPackage
>
> #Below the parts of the code that may be relevant to solve the problem.
> #My AllClasses file contain these lines:
> setClassUnion("OrgDbOrNULL", c("OrgDb","NULL"))
> setClass("foo",representation(
>
>              OrgDb="OrgDbOrNULL",
>              TxDbUCSC="TranscriptDbOrNULL"
>
>              )
> )
>
> #My NAMESPACE file contain these lines:
> importClassesFrom(AnnotationDbi, AnnotationDb)
> importClassesFrom(GenomicFeatures, TranscriptDb)
>
> #My DESCRIPTION file contain these lines:
> Depends: R (>= 2.15.1), AnnotationDbi
> Imports: methods, BiocGenerics, IRanges, GenomicRanges, GenomicFeatures,
> Rsamtools, AnnotationDbi
>
>
> #To add the TranscriptDb works perfectly(no warnings during build), but not
> the AnnotationDb. I have looked at the source code for AnnotationDb and
> realized it has reference classes. This might be causing the warning during
> build, of the reason that I cannot import the OrgDb class in NAMESPACE, and
> that because it is not exported from AnnotationDbi. Thought putting it in
> the Depends field in the DESCRIPTION would help, but it did not,
> unfortunately. All kinds of help is appreciated.

Thanks for reporting this. I have updated AnnotationDbi to export the OrgDb 
class. This is in AnnotationDbi 1.21.9, in the 'devel' version of Bioconductor 
(available when using the devel version of R). Version 1.21.9 will be available 
with biocLite after about 10am PST Monday.

You will also need to add

   importClassesFrom(AnnotationDbi, AnnotationDb, OrgDb)

to your NAMESAPCE.

Best,

Martin

>
> Sincerely,
> Jesper
>
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] basicASE_1.3         AnnotationDbi_1.18.4 Biobase_2.16.0
> [4] BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-5
>   [4] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
>   [7] GenomicRanges_1.8.13  IRanges_1.14.4        RCurl_1.95-3
> [10] Rsamtools_1.8.6       RSQLite_0.11.2        rtracklayer_1.16.3
> [13] stats4_2.15.1         tools_2.15.1          XML_3.95-0.1
> [16] zlibbioc_1.2.0
>
> 	[[alternative HTML version deleted]]
>
>
>
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>


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