Re: [Bioc-devel] Package download when using functions from affy and oligo

2018-05-04 Thread James W. MacDonald
> >> The warning I get when trying oligo::read.celfiles() on a single CEL file >> right after installing it about the pd.hugene.1.0.st.v1 package. The even >> more annoying thing is that on my machine it insists on building from >> source, whereas on another Windows machine without Rtools, it downl

Re: [Bioc-devel] Package download when using functions from affy and oligo

2018-05-04 Thread James W. MacDonald
I think there are multiple complaints here, so I'll take them one at a time. On Fri, May 4, 2018 at 3:56 PM, Obenchain, Valerie < valerie.obench...@roswellpark.org> wrote: > Joris, > > Sorry I don't have much to offer here. I've cc'd the authors of oligo and > affy who may have some insight. > >

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

2018-05-04 Thread Michael Lawrence
Do you have a reproducible example of this? It's probably a bug in the methods package. Thanks, Michael On Fri, May 4, 2018 at 10:52 AM, Paul Shannon < paul.thurmond.shan...@gmail.com> wrote: > I just discovered a class name collision - AnnotationTrack, in Gviz and my > new package igvR. wish

Re: [Bioc-devel] Package download when using functions from affy and oligo

2018-05-04 Thread Obenchain, Valerie
Joris, Sorry I don't have much to offer here. I've cc'd the authors of oligo and affy who may have some insight. Valerie On 05/02/2018 11:35 AM, Joris Meys wrote: Dear, I've noticed that using certain functions in affy and oligo (eg oligo::read.celfiles and affy::bg.correct) start with downl

Re: [Bioc-devel] class name collision in cache: igvR and Gviz

2018-05-04 Thread Hervé Pagès
Hi Paul, Luckily you caught this only 3 days after the release so renaming the class now is probably ok and shouldn't be disruptive. Cheers, H. On 05/04/2018 10:52 AM, Paul Shannon wrote: I just discovered a class name collision - AnnotationTrack, in Gviz and my new package igvR. wish to g

[Bioc-devel] class name collision in cache: igvR and Gviz

2018-05-04 Thread Paul Shannon
I just discovered a class name collision - AnnotationTrack, in Gviz and my new package igvR. wish to get wise counsel before proceeding with a fix. Here’s the error message: Found more than one class "AnnotationTrack" in cache; using the first, from namespace ‘igvR' Also defined by ‘Gv

Re: [Bioc-devel] DOI information

2018-05-04 Thread Sean Davis
Hi, Felix. I'll take a look. Sean On Fri, May 4, 2018, 7:16 AM Felix Ernst wrote: > Dear BioC-Team, > > > > Just as little bug report. I don't want to make a big deal about it: > > I just imported the citation information for my package tRNAscanImport into > Citavi using the doi number and the

[Bioc-devel] DOI information

2018-05-04 Thread Felix Ernst
Dear BioC-Team, Just as little bug report. I don't want to make a big deal about it: I just imported the citation information for my package tRNAscanImport into Citavi using the doi number and the last name was not imported correctly. Is this due to the middle name(s)? On the package page ever