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

[Pages, Herve]

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 <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
>>
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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