On Tue, Mar 19, 2013 at 12:59 AM, Stefanie Tauber <stefanie.tau...@univie.ac.at> wrote: > > 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... >
Try removing import(RJSONIO) from NAMESPACE. Dan > Best, > Stefanie > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
