On 24.06.19 17:35, Andreas Tille wrote:
Hi, On Mon, Jun 24, 2019 at 05:24:09PM +0200, Steffen Möller wrote:I only now learned about https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881317 and the subsequent removal of r-cran-edger from our distro. Sigh. In that thread, the discussion about using a wrapper for installing non-free bits came up. Conda anyone? At the very moment I cannot tell about how essential edgeR may be for seqcluster and the bcbio workflow as a whole - but Debian not offering that package at all - it is a bit weird.I think what is really weird is the license of locfit (see discussion in #731599) and the fact that it seems impossible to reach locfit upstream.
Agreed.
If you ask me there are chances to talk to CRAN / Bioconductor people that they are relying on non-free software (which is as far as I know also against their polica) but nobody has explained that issue clear enough. May be its not to hard to create a locfit alternative.
EdgeR allows locfit to be substituted by other estimators. Once I feel a bit more mentally superior to it all, I am tempted to suggest a free alternative to the edgeR developers as a default. But any such scientifically relevant change should come from upstream, not as an unsuspected patch within Debian. Anyway - from what I oversee, the missing edgeR is not critical for bcbio. Best, Steffen