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. 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]]
_______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel