Re: [Bioc-devel] adding methods to BiocGenerics

2017-05-19 Thread Stephanie M. Gogarten
On 5/19/17 12:15 PM, Michael Lawrence wrote: That could work, also. On Fri, May 19, 2017 at 10:27 AM, Martin Morgan wrote: On 05/19/2017 12:14 PM, Michael Lawrence wrote: Since SeqArray already imports SummarizedExperiment and VariantAnnotation, why can't it

Re: [Bioc-devel] adding methods to BiocGenerics

2017-05-19 Thread Michael Lawrence
That could work, also. On Fri, May 19, 2017 at 10:27 AM, Martin Morgan wrote: > On 05/19/2017 12:14 PM, Michael Lawrence wrote: >> >> Since SeqArray already imports SummarizedExperiment and >> VariantAnnotation, why can't it just move them to Depends and use >>

Re: [Bioc-devel] Build problem with malbec2

2017-05-19 Thread Hervé Pagès
Hi Roel, It looks like Michael fixed rtracklayer yesterday and that MutationalPatterns 1.2.1 could finally propagate: http://bioconductor.org/checkResults/release/bioc-LATEST/MutationalPatterns/malbec2-buildsrc.html The landing page should get updated soon:

Re: [Bioc-devel] adding methods to BiocGenerics

2017-05-19 Thread Martin Morgan
On 05/19/2017 12:14 PM, Michael Lawrence wrote: Since SeqArray already imports SummarizedExperiment and VariantAnnotation, why can't it just move them to Depends and use their generics? do they need to be moved to Depends? Or simply import the generic export the new method(s) (and generic)?

Re: [Bioc-devel] adding methods to BiocGenerics

2017-05-19 Thread Michael Lawrence
Since SeqArray already imports SummarizedExperiment and VariantAnnotation, why can't it just move them to Depends and use their generics? On Fri, May 19, 2017 at 8:39 AM, Stephanie M. Gogarten wrote: > Dear Core Team, > > What do you think about adding the following

Re: [Bioc-devel] adding methods to BiocGenerics

2017-05-19 Thread Laurent Gatto
On 19 May 2017 15:39, Stephanie M. Gogarten wrote: > Dear Core Team, > > What do you think about adding the following generics to BiocGenerics? > > colData > rowRanges > ref > alt > qual Currently exists in MSnbase with signature setGeneric("qual", function(object) standardGeneric("qual"))

[Bioc-devel] adding methods to BiocGenerics

2017-05-19 Thread Stephanie M. Gogarten
Dear Core Team, What do you think about adding the following generics to BiocGenerics? colData rowRanges ref alt qual filt header fixed info geno They are currently defined by both VariantAnnotation/SummarizedExperiment and SeqArray. Given the increasingly widespread use of VCF files, it

Re: [Bioc-devel] Build problem with malbec2

2017-05-19 Thread Janssen-10, R.R.E.
Dear Valerie, Could we maybe do a manual build for the package, so that the bugfixed version can be propagated to users? Kind regards, Roel Janssen From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Janssen-10, R.R.E.