arkas::rowRanges is not compatible with GenomicFeatures::rowRanges

[arcolombo]

if you use library(matrixStats) this will over-write the arkas namespace of rowRanges, and thus rowRanges(arkas.kexp) will fail Argument 'x' must be a matrix or a vector.

GenomicFeatures use of rowRanges is not compatible with arkas::rowRanges for sum reasons

[ttriche]

I think we have to explicitly namespace matrixStats::rowRanges()

At some point I started habitually doing so, as with igraph::graph.data.frame(). It may be worthwhile for BiocGenerics to register a rowRanges generic and promote matrixStats' function thusly

--t

On Tue, Aug 23, 2016 at 5:10 PM, Anthony R. Colombo < notifications@github.com> wrote:

if you use library(matrixStats) this will over-write the arkas namespace of rowRanges, and thus rowRanges(arkas.kexp) will fail Argument 'x' must be a matrix or a vector.

GenomicFeatures use of rowRanges is not compatible with arkas::rowRanges for sum reasons

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[arcolombo]

yes that how I was able to solve using your byMads, with a specific call.

so if someone , a general user, calls library(matrixStats) and it blows out arkas<SummarizedExperiment::rowRanges, is this our problem?

On Tue, Aug 23, 2016 at 5:37 PM, Tim Triche, Jr. notifications@github.com wrote:

I think we have to explicitly namespace matrixStats::rowRanges()

At some point I started habitually doing so, as with igraph::graph.data.frame(). It may be worthwhile for BiocGenerics to register a rowRanges generic and promote matrixStats' function thusly

--t

On Tue, Aug 23, 2016 at 5:10 PM, Anthony R. Colombo < notifications@github.com> wrote:

if you use library(matrixStats) this will over-write the arkas namespace of rowRanges, and thus rowRanges(arkas.kexp) will fail Argument 'x' must be a matrix or a vector.

GenomicFeatures use of rowRanges is not compatible with arkas::rowRanges for sum reasons

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[ttriche]

no it is not, not any more than it's Marc Carlson's problem when it blows away GenomicFeatures' rowRanges method :-)

--t

On Tue, Aug 23, 2016 at 5:38 PM, Anthony R. Colombo < notifications@github.com> wrote:

yes that how I was able to solve using your byMads, with a specific call.

so if someone , a general user, calls library(matrixStats) and it blows out arkas<SummarizedExperiment::rowRanges, is this our problem?

On Tue, Aug 23, 2016 at 5:37 PM, Tim Triche, Jr. <notifications@github.com

wrote:

I think we have to explicitly namespace matrixStats::rowRanges()

At some point I started habitually doing so, as with igraph::graph.data.frame(). It may be worthwhile for BiocGenerics to register a rowRanges generic and promote matrixStats' function thusly

--t

On Tue, Aug 23, 2016 at 5:10 PM, Anthony R. Colombo < notifications@github.com> wrote:

if you use library(matrixStats) this will over-write the arkas namespace of rowRanges, and thus rowRanges(arkas.kexp) will fail Argument 'x' must be a matrix or a vector.

GenomicFeatures use of rowRanges is not compatible with arkas::rowRanges for sum reasons

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