remedied by installation of latest S4Vectors/SummarizedExperiment from git On Wed, Jun 12, 2019 at 10:53 AM Vincent Carey <st...@channing.harvard.edu> wrote:
> my installation of Bioc 3.10 passes valid() > > > > ee = SummarizedExperiment(assay=data.matrix(mtcars)) > > > ee > > class: SummarizedExperiment > > dim: 32 11 > > metadata(0): > > assays(1): '' > > rownames(32): Mazda RX4 Mazda RX4 Wag ... Maserati Bora Volvo 142E > > rowData names(0): > > colnames(11): mpg cyl ... gear carb > > colData names(0): > > > colnames(ee)[1] = "foo" > > *Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : * > > * object 'normalize_names_replacement_value' not found* > > > > sessionInfo() > > R version 3.6.0 Patched (2019-05-06 r76460) > > Platform: x86_64-apple-darwin15.6.0 (64-bit) > > Running under: macOS Sierra 10.12.6 > > > Matrix products: default > > BLAS: > /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib > > LAPACK: > /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > > attached base packages: > > [1] parallel stats4 stats graphics grDevices utils datasets > > [8] methods base > > > other attached packages: > > [1] SummarizedExperiment_1.15.1 DelayedArray_0.11.0 > > [3] BiocParallel_1.19.0 matrixStats_0.54.0 > > [5] Biobase_2.45.0 GenomicRanges_1.37.10 > > [7] GenomeInfoDb_1.21.1 IRanges_2.19.9 > > [9] S4Vectors_0.23.11 BiocGenerics_0.31.4 > > [11] rmarkdown_1.13 > > > loaded via a namespace (and not attached): > > [1] Rcpp_1.0.1 knitr_1.23 XVector_0.25.0 > > [4] zlibbioc_1.31.0 lattice_0.20-38 tools_3.6.0 > > [7] grid_3.6.0 xfun_0.7 htmltools_0.3.6 > > [10] digest_0.6.19 Matrix_1.2-17 startup_0.12.0 > > [13] GenomeInfoDbData_1.2.1 BiocManager_1.30.4 bitops_1.0-6 > > [16] RCurl_1.95-4.12 evaluate_0.14 compiler_3.6.0 > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel