I removed it from the namespace file, still the same warning, (btw gridSVG depends on RJSONIO)
best, Stefanie Am 19.03.2013 um 15:31 schrieb Dan Tenenbaum <dtene...@fhcrc.org>: > 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 >> DI Stefanie Tauber Center for Integrative Bioinformatics Vienna (CIBIV) (CIBIV is a joint institute of Vienna University and Medical University) Max F. Perutz Laboratories (MFPL) Campus Vienna Biocenter 5 (VBC5), Ebene 1, Room 1812.2 Dr. Bohr Gasse 9 A-1030 Wien, Austria Phone: ++43 +1 / 42772-4030 Fax: ++43 +1 / 42772-4098 email: stefanie.tau...@univie.ac.at www.cibiv.at [[alternative HTML version deleted]]
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