Re: [Bioc-devel] Dependency on devtools in biocLite()

On 01/17/2017 07:15 AM, Andrzej Oleś wrote: Thanks Martin! I see your point - then I suggest that at least the call to `devtools::install` is guarded by a customized more informative error massage, something along the lines: Package 'devtools' missing: please install it (e.g., by a call to

Re: [Rd] unlicense

I was looking at https://www.r-project.org/Licenses/ which is first when you google for "R licenses". Silly me. Kurt says I should have been looking at share/licenses/license.db in the R source tree. Thanks. I'm satisfied now. I don't have any CRAN packages with "Unlimited" on them, but I do

Re: [Bioc-devel] Code quality and bug reports

Hi, On 01/14/2017 03:01 AM, Lluís Revilla wrote: > Dear Valerie and all, > > If I understood the page you kindly linked correctly, a package is deprecated: > 1) When it fails to build and check (unless it is fixed). > 2) When the maintainer asks for it. > 3) If the maintainer is unresponsive (I

Re: [Rd] unlicense

> Charles Geyer writes: > In that case, perhaps the question could be changed to could CC0 be > added to the list of R licences. Right now the only CC licence that > is in the R licenses is CC-BY-SA-4.0. Hmm, I see Name: CC0 FSF: free_and_GPLv3_compatible

Re: [Rd] unlicense

Probably, one side of the issue is that people are unaware of the dangers of overly permissive statements, like the infamous "collection copyright" which originally applied to collections of medieval music by anonymous composers, but extends to the individual items, so that you can't (say)

Re: [Rd] unlicense

In that case, perhaps the question could be changed to could CC0 be added to the list of R licences. Right now the only CC licence that is in the R licenses is CC-BY-SA-4.0. On Wed, Jan 18, 2017 at 7:23 AM, Brian G. Peterson wrote: > > On Tue, 2017-01-17 at 22:46 -0500,

[R-pkg-devel] R CMD Check: package dependencies

Hello: I am working on uploading my first R package to CRAN and running into a problem with package dependencies with R CMD check using win-builder (I am not having this problem on my mac). I am getting: “Package required but not available: ‘grasp2db’” Best I can tell this is because

Re: [Rd] unlicense

On Tue, 2017-01-17 at 22:46 -0500, Kevin Ushey wrote: > It appears that Unlicense is considered a free and GPL-compatible > license; however, the page does suggest using CC0 instead (which is > indeed a license approved / recognized by CRAN). CC0 appears to be > the primary license recommended by

Re: [R-pkg-devel] package API change

Another solution is to start a new package. This is what Hadley did with the ggplot package (https://cran.r-project.org/src/contrib/Archive/ggplot/). The new version (ggplot2) would break existing code. Users were informed that the old package is not longer maintained. So the user has the choice

Re: [R-pkg-devel] package API change

On 18/01/2017 5:31 AM, Berry Boessenkool wrote: What's good practice to inform users about an API change? The package in question is extremeStat. Apparently, people actually use it. I don't have a userbase like Hadley, but I do receive emails with feature requests and code change

Re: [Bioc-devel] Alternative Hypothesis Specification For edgeR

Ah - sorry - upon re-reading your message, I realized I misunderstood your question. So basically you want to make your LRT p-value one-sided; I can see how that would be useful, e.g., when comparing to negative controls in ChIP-seq or other technologies. I've been doing it fairly simply,

Re: [Bioc-devel] Alternative Hypothesis Specification For edgeR

Hi Dario, I guess so - it would be a fairly easy extension of glmLRT - but why? I can't think of many situations where a non-zero log-fold change is expected under the null hypothesis. Mixture experiments, or correcting for gene dosage due to copy number variants, perhaps. Cheers, Aaron On

[R-pkg-devel] package API change

What's good practice to inform users about an API change? The package in question is extremeStat. Apparently, people actually use it. I don't have a userbase like Hadley, but I do receive emails with feature requests and code change suggestions. Since the change is rather big (going from