Re: [Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Andrew McDavid
Hi Caleb, Hopefully Herve will chime in regarding SummarizedExperiment, but yes, I think you can and should inherit from that. The `assays` slot must be an object of type `Assays`, but that does appear to include a sparse Matrix. See the comments at the top of Assays-class.R in the tarball for

Re: [Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Bemis, Kylie
Hi Caleb, Per your question on sparse on-disk matrices: is your experimental data coming in some pre-defined text or binary file format, or are you looking to convert to a new, custom format to take advantage of the sparsity? I need to start working on an on-disk sparse matrix implementation

[Bioc-devel] Reading and storing single cell ATAC data

2016-09-23 Thread Caleb Lareau
Hi everyone— I’m working with a team that’s generating single cell ATAC data in large amounts and am designing the framework of an S4 object to facilitate analyses in R. I have a couple of high-level questions that I wanted to pose early to hopefully attain some community guidance in the

Re: [Bioc-devel] Invalid biocViews terms

2016-09-23 Thread Martin Morgan
On 09/23/2016 12:15 PM, Martin Morgan wrote: Bioc Developers! biocViews are an important way for users to navigate to your package. The following packages have incorrect biocViews terms. To update terms in your package, visit http://bioconductor.org/packages/devel/BiocViews.html#___Software

[Bioc-devel] Invalid biocViews terms

2016-09-23 Thread Martin Morgan
Bioc Developers! biocViews are an important way for users to navigate to your package. The following packages have incorrect biocViews terms. To update terms in your package, visit http://bioconductor.org/packages/devel/BiocViews.html#___Software check the 'Develoeprs: check this box...'

Re: [Bioc-devel] JAGS 4.X.Y not installed on Windows (tokay1)

2016-09-23 Thread Hervé Pagès
Hi Yu, On 09/23/2016 06:57 AM, Yu Kong wrote: Hi Hervé, Thank you so much for help. My package uses JAGS thru the rjags package. Good. Thanks for clarifying. So can you please remove the SystemRequirements line from the DESCRIPTION file of your package? I just installed JAGS on tokay1.

Re: [Bioc-devel] Package warning due to function replacement

2016-09-23 Thread Michael Lawrence
You'll need to either `importFrom(Biobase, only, the, symbols, needed)` or use the `except="combine"` argument to `import()`. On Fri, Sep 23, 2016 at 4:59 AM, THEVENOT Etienne 207099 wrote: > Dear Bioc Team, > > First of all thanks a lot again for all the time you spend

Re: [Bioc-devel] Package warning due to function replacement

2016-09-23 Thread Kasper Daniel Hansen
In general you can assume this to be the case for core functionality like the stuff in Biobase. What you should do however, since combine() is an S4 method, is import the S4 method from BiocGenerics. In fact, it is a good idea to check which generics are defined in BiocGenerics and consider

[Bioc-devel] Package warning due to function replacement

2016-09-23 Thread THEVENOT Etienne 207099
Dear Bioc Team, First of all thanks a lot again for all the time you spend developing and maintaining the Bioc repository. I recently added 'Biobase' as "suggests" in the 'biosigner' package in order to have the biosign method work on 'ExpressionSet' objects (devel version of 'biosigner').

Re: [Bioc-devel] platforms "some" on devel?

2016-09-23 Thread Ramon Diaz-Uriarte
Yes, that was the strange thing (for me at least): some packages showed "all" and some showed "some" and a cursory look did not reveal any pattern. R. On Fri, 23-09-2016, at 08:26, Hervé Pagès wrote: > On 09/22/2016 11:09 PM, Ramon Diaz-Uriarte wrote: >> Hi Hervé, >> >>

Re: [Bioc-devel] JAGS 4.X.Y not installed on Windows (tokay1)

2016-09-23 Thread Hervé Pagès
Hi Yu, On 09/22/2016 02:15 PM, Yu Kong wrote: Dear BioConductor community, My package (MADSEQ) passed the build on Linux (*malbec1*) and Mac (*morelia*) build servers. However it fails on Windows (tokay1) server for multiple days. Our package is a Bayesian model depends on JAGS sampler. The

Re: [Bioc-devel] platforms "some" on devel?

2016-09-23 Thread Hervé Pagès
On 09/22/2016 11:09 PM, Ramon Diaz-Uriarte wrote: Hi Hervé, Thanks for the clarification; (what I was surprised about was that some say "some" and others said "all", Oh really? I went directly to the landing page of your package, saw the "some", and didn't mind checking other package landing