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

Completely agree on the importance of disambiguating class references in the long term. However I still think that just because we have a mechanism to disambiguate means we shouldn't make an effort to avoid name clashes, especially when the name clash is easy to avoid, like in the case discussed

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

Dear Michael, Thanks, that fixed the problem. The new version hasn’t shown up in a call to biocLite, but I was able to get it from the github repository and check it; also our package is now clearing bioconductor checks. Just to note, our package has always gotten messages about the class

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

On 04/14/2018 07:21 AM, Vincent Carey wrote: But Annotated is defined in S4Vectors and RNeXML; the latter is not a Bioconductor package. The likelihood of collisions among class names defined in different packages seems pretty high as S4 adoption grows. So requiring a systematic approach to

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

But Annotated is defined in S4Vectors and RNeXML; the latter is not a Bioconductor package. The likelihood of collisions among class names defined in different packages seems pretty high as S4 adoption grows. So requiring a systematic approach to disambiguating class references seems inevitable.

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

How about renaming Annotated? Isn't having 2 classes around with the same name fundamentally a bad situation? No amount of workarounds will change that. H. On 04/12/2018 04:06 PM, Michael Lawrence wrote: Yea, good idea, I was thinking of supporting :: in class names and parsing them out. In

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

Hi Michael, Thanks for looking into this. Can you or someone with push permission to S4Vectors implement the workaround that you mentioned? Happy to create a pull request on Github if that helps. We’re trying to solve this to fix the clusterExperiment package build on Bioc-devel. Thanks,

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

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 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

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

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

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

Hello, Our package clusterExperiment has suddenly started producing errors in the bioconductor devel branch because our unit tests are failing, even though we haven’t pushed any changes and they passed previously. We first noticed this on April 5th. I believe the source of these errors