[Bioc-devel] sort(RangedSummarizedExperiment) fails

[Martin Morgan]

Thanks, fixed in version 1.5.7. Martin

On 02/18/2017 04:20 PM, Vincent Carey wrote:
> after example(RangedSummarizedExperiment)
>
>> rse1
>
> class: RangedSummarizedExperiment
>
> dim: 200 6
>
> metadata(0):
>
> assays(1): counts
>
> rownames: NULL
>
> rowData names(1): feature_id
>
> colnames(6): A B ... E F
>
> colData names(1): Treatment
>
>> sort(rse1)
>
> Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
>
>   object '.order_GenomicRanges' not found
>
>
> Enter a frame number, or 0 to exit
>
>
> 1: sort(rse1)
>
> 2: sort(rse1)
>
> 3: .local(x, decreasing, ...)
>
> 4: GenomicRanges:::.order_GenomicRanges
>
> 5: get(name, envir = asNamespace(pkg), inherits = FALSE)
>
>
>> sessionInfo()
>
> R Under development (unstable) (2017-02-08 r72142)
>
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> Running under: CentOS release 6.8 (Final)
>
>
> locale:
>
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
>
> [8] methods   base
>
>
> other attached packages:
>
>  [1] SummarizedExperiment_1.5.6 DelayedArray_0.1.7
>
>  [3] matrixStats_0.51.0         Biobase_2.35.0
>
>  [5] GenomicRanges_1.27.22      GenomeInfoDb_1.11.9
>
>  [7] IRanges_2.9.18             S4Vectors_0.13.15
>
>  [9] BiocGenerics_0.21.3        BiocInstaller_1.25.3
>
>
> loaded via a namespace (and not attached):
>
>  [1] lattice_0.20-34         bitops_1.0-6            grid_3.4.0
>
>  [4] zlibbioc_1.21.0         XVector_0.15.2          Matrix_1.2-8
>
>  [7] tools_3.4.0             RCurl_1.95-4.8          compiler_3.4.0
>
> [10] GenomeInfoDbData_0.99.0
>
>
>
> Selection: 0
>
> 	[[alternative HTML version deleted]]
>
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