Hi, I am currently working on new BioC package. R CMD build, check and INSTALL are successfully passed. I just always get the following warning (when installing the package):
Warning in .simpleDuplicateClass(def, prev) : the specification for S3 class “AsIs” in package ‘RJSONIO’ seems equivalent to one from package ‘BiocGenerics’ and is not turning on duplicate class definitions for this class Here are the relevant slots from my Description file: Depends: R (>= 2.15.3), BiocGenerics, ggplot2, gridSVG (>= 1.0-0) Imports: BiocGenerics, gridSVG, gridExtra, GenomicRanges, GenomicFeatures, biomaRt, knitr, fractaldim, xtable, IRanges And my Namespace File: import(BiocGenerics) import(ggplot2) import(gridSVG) import(gridExtra) import(GenomicRanges) import(GenomicFeatures) import(biomaRt) import(knitr) import(fractaldim) import(xtable) import(IRanges) This is my SessionInfo when loading my package: > sessionInfo() R Under development (unstable) (2013-02-27 r62087) 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] grid parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] fractalQC_0.99 gridSVG_1.0-0 XML_3.95-0.2 RJSONIO_1.0-1 [5] ggplot2_0.9.3.1 BiocGenerics_0.5.6 loaded via a namespace (and not attached): [1] AnnotationDbi_1.21.16 Biobase_2.19.3 biomaRt_2.15.1 [4] Biostrings_2.27.11 bitops_1.0-5 BSgenome_1.27.1 [7] colorspace_1.2-1 DBI_0.2-5 dichromat_2.0-0 [10] digest_0.6.3 evaluate_0.4.3 formatR_0.7 [13] fractaldim_0.8-1 GenomicFeatures_1.11.16 GenomicRanges_1.11.38 [16] gridExtra_0.9.1 gtable_0.1.2 IRanges_1.17.37 [19] knitr_1.1 labeling_0.1 MASS_7.3-24 [22] munsell_0.4 plyr_1.8 proto_0.3-10 [25] RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape2_1.2.2 [28] Rsamtools_1.11.25 RSQLite_0.11.2 rtracklayer_1.19.11 [31] scales_0.2.3 stats4_3.0.0 stringr_0.6.2 [34] tools_3.0.0 xtable_1.7-1 zlibbioc_1.5.0 What can I do so that the warning gets resolved? Best, Stefanie _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel