Re: [Bioc-devel] Python package dependency loading problem on malbec1 builder

2020-01-28 Thread Pages, Herve
Hi Will, Let's keep this on the mailing list. On 1/13/20 16:00, William Chen wrote: > Hi Herve, > > Thanks for this reply. I have been looking into the R CMD CHECK error > that has been thrown by the tokay1 builder and am still unsure how to > potentially mitigate the error message given. >

[Bioc-devel] Problems on BiocCredentials account_activation

2020-01-28 Thread Danrley Fernandes
Hi, I'm the developer of the package rSWeeP, and I'm trying to activate my account at Bioconductor Git Credentials ( https://git.bioconductor.org/BiocCredentials/account_activation/) and I keep receiving the message " danrle...@gmail.com is not associated with a maintainer of a Bioconductor

[Bioc-devel] Updating R-devel on Bioconductor builders

2020-01-28 Thread Shepherd, Lori
We will be updating R-devel on the Bioconductor devel builders this afternoon (malbec2 and tokay2). This may mean some intermittent download on the Single Package Builder. It should not affect the build report for today. We appreciate your understanding. Lori Shepherd Bioconductor Core

Re: [Bioc-devel] New SE or new assay in SE?

2020-01-28 Thread Tim Triche, Jr.
Assume the object is backed by an HDF5 or Zarr array, for the sake of argument and because that’s kind of how it works these days for many people. Also assume the “SE*” may not actually be an SE, but rather some wacky subclass of SE. If you return a new SE*, you need to copy all the metadata,

[Bioc-devel] New SE or new assay in SE?

2020-01-28 Thread Laurent Gatto
Dear all, Assume we have a SummarizedExperiment object `se` that contains raw count data, and a method `doProcess` that processes the data to produce a matrix of identical dimensions (for example log-transformation, normalisation, imputation, ...). What are the opinions in favour or against