Dear list, we are developing a new package that defines a class that builds on SummarizedExperiment and also imports the CRAN package phylobase.
The class "Annotated" is defined both in the S4Vectors package (a dependency of SummarizedExperiment) and in the RNeXML package (a dependency of phylobase). Note that we want the former. This causes the following message to be thrown every time we create a new object. Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' A minimal example is the following. > library(SummarizedExperiment)> SummarizedExperiment()class: > SummarizedExperiment dim: 0 0 metadata(0): assays(0): rownames: NULL rowData names(0): colnames: NULL colData names(0):> library(phylobase)> SummarizedExperiment()Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'class: SummarizedExperiment dim: 0 0 metadata(0): assays(0): rownames: NULL rowData names(0): colnames: NULL colData names(0): > sessionInfo()R Under development (unstable) (2016-03-07 r70284) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux stretch/sid locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods [9] base other attached packages: [1] phylobase_0.8.2 SummarizedExperiment_1.1.21 [3] Biobase_2.31.3 GenomicRanges_1.23.23 [5] GenomeInfoDb_1.7.6 IRanges_2.5.39 [7] S4Vectors_0.9.41 BiocGenerics_0.17.3 loaded via a namespace (and not attached): [1] Rcpp_0.12.3 plyr_1.8.3 XVector_0.11.7 iterators_1.0.8 [5] tools_3.3.0 zlibbioc_1.17.0 uuid_0.1-2 jsonlite_0.9.19 [9] nlme_3.1-125 lattice_0.20-33 foreach_1.4.3 DBI_0.3.1 [13] httr_1.1.0 stringr_1.0.0 dplyr_0.4.3 xml2_0.1.2 [17] ade4_1.7-4 grid_3.3.0 rredlist_0.1.0 reshape_0.8.5 [21] data.table_1.9.6 R6_2.1.2 XML_3.98-1.4 RNeXML_2.0.6 [25] reshape2_1.4.1 tidyr_0.4.1 magrittr_1.5 codetools_0.2-14 [29] assertthat_0.1 bold_0.3.5 taxize_0.7.5 ape_3.4 [33] stringi_1.0-1 rncl_0.6.0 lazyeval_0.1.10 rotl_0.5.0 [37] chron_2.3-47 Since we need to import both packages, is there a way to explicitly use the correct definition of "Annotated" or to not import the class "Annotated" from RNeXML? Or is this something that could be addressed in the SummarizedExperiment package? These are our DESCRIPTION and NAMESPACE file (note that we are importing only what we need from phylobase): https://github.com/epurdom/clusterExperiment/blob/develop/DESCRIPTION https://github.com/epurdom/clusterExperiment/blob/develop/NAMESPACE See also Henrik's comment at: https://github.com/epurdom/clusterExperiment/issues/66 Thank you in advance for any help! Best, davide [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
