[Bioc-devel] normalize_names_replacement_value error with colnames<- on SummarizedExperiment

[Vincent Carey]

remedied by installation of latest S4Vectors/SummarizedExperiment from git

On Wed, Jun 12, 2019 at 10:53 AM Vincent Carey <stvjc using 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
>

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