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
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