On 6/12/19 08:26, Vincent Carey wrote: > remedied by installation of latest S4Vectors/SummarizedExperiment from git
Good. I just fixed this in git/github 5 min ago: https://github.com/Bioconductor/SummarizedExperiment/commit/01aa07a87b72b7423bea38028fffba4e896fdcf3 H. > > 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 >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel