On Mo, 18.03.2013, 17:39, Dan Tenenbaum wrote: > On Mon, Mar 18, 2013 at 5:39 AM, Stefanie Tauber > <stefanie.tau...@univie.ac.at> wrote: >> 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? > > You could put RJSONIO and BiocGenerics in Depends even though you > don't depend directly on RJSONIO (and you can remove BiocGenerics from > Imports and NAMESPACE). > > This is caused by the fact that RJSONIO and BiocGenerics use > setOldClass on the same 'old' S3 classes; The behavior is probably a > bug in R. > > Dan > > >> >> Best, >> Stefanie >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >
Hi, Thanks for your help, I changed my description and namespace file accordingly. DESCRIPTION File: Depends: R (>= 2.15.3), BiocGenerics, RJSONIO, ggplot2, gridSVG (>= 1.0-0) Imports: gridExtra, GenomicRanges, GenomicFeatures, biomaRt, knitr, fractaldim, xtable, IRanges Namespace File: import(RJSONIO) import(ggplot2) import(gridSVG) import(gridExtra) import(GenomicRanges) import(GenomicFeatures) import(biomaRt) import(knitr) import(fractaldim) import(xtable) import(IRanges) Still, I get the same warning: 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 I mean, everything is working fine. I just would prefer a clean installation procedure... Best, Stefanie _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
