[Bioc-devel] Setup for pushing changes in unifiedWMWqPCR to bioconductor git.

Hi all, For the package unifiedWMWqPCR I want to push some updates on the documentation, but apparently I don't have access to the bioconductor git any longer. I had to completely reinstall my system here, so probably either my key got lost, or I'm using the wrong account to push. I tried to

Re: [Bioc-devel] iGraph depending packages failing on Windows build machines

Petr, Yesterday I installed R 3.5.0 beta on the devel Windows builder (tokay2). The report has not posted yet but I checked on the build of PharmacoGx and it is clean. It looks like the CRAN 'maps' package was updated on April 4. It's possible that during the nightly builds, the new version

Re: [Bioc-devel] Setup for pushing changes in unifiedWMWqPCR to bioconductor git.

Hi, On 04/12/2018 03:02 AM, Joris Meys wrote: Hi all, For the package unifiedWMWqPCR I want to push some updates on the documentation, but apparently I don't have access to the bioconductor git any longer. I had to completely reinstall my system here, so probably either my key got lost, or I'm

Re: [Bioc-devel] Suggested edits to support site posting guide

Hi Mike, I just added a few comments to your google doc. Thanks for doing this! Best, Leo On Thu, Apr 12, 2018 at 11:23 AM, Michael Love wrote: > > > dear all, > > I've edited the text from the posting guide >

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Yea it's basically library(S4Vectors) library(RNeXML) is(1:5, "Annotated") # Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors' # Also defined by ‘RNeXML’ # [1] FALSE But can be worked around: > is(1:5, getClass("Annotated",

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Just to follow up on my previous post. I am able to replicate the problem in the problem like in the github post from 2 years ago (https://github.com/epurdom/clusterExperiment/issues/66 ) only now it is not the SummarizedExperiment class

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Well, it's not really SingleCellExperiment's problem, either. library(S4Vectors) DataFrame(1:5) # Silent, okay. library(RNeXML) DataFrame(1:5) # Prints out the message ## Found more than one class "Annotated" in cache; using the first,  from namespace 'S4Vectors' ## Also defined by ‘RNeXML’

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

If we need to disambiguate class references, perhaps an operator could help? Along the lines of base::"::" ... "%c%" <- function(package,class) { pk = as.character(substitute(package)) cl = as.character(substitute(class)) getClass(cl, where=getNamespace(pk)) } Biobase %c%

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Hi Davide, We can get this fixed soon, but I was hoping to hear e.g. Herve's opinion first if he has one. Michael On Thu, Apr 12, 2018 at 12:53 PM, Davide Risso wrote: > Hi Michael, > > Thanks for looking into this. > > Can you or someone with push permission to

Re: [Bioc-devel] problem with class definitions between S4Vectors and RNeXML in using Summarized Experiment

Yea, good idea, I was thinking of supporting :: in class names and parsing them out. In code is better. Maybe %::%? It wouldn't have to get a class object (for one thing, a class might not exist), because the methods package supports a 'package' attribute on the character vector, abstracted by

[Bioc-devel] Suggested edits to support site posting guide

dear all, I've edited the text from the posting guide to update it a bit. For example, some of the text still referred to the mailing list ​: ​ "Compose a new message with a new subject line". ​Mostly, though, I wanted to emphasize