Re: [Bioc-devel] Coverage test badge not updating

2015-11-23 Thread Leonardo Collado Torres
Thank you for fixing this Jim! I noticed it working now on devel. However, I believe that is still not working for the release branch. Cheers, Leo On Fri, Nov 20, 2015 at 3:37 PM, Jim Hester wrote: > The coverage tests were inadvertently not running, but they are now > re-enabled. > > Please let

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

2015-11-23 Thread Vincent Carey
On Mon, Nov 23, 2015 at 1:11 PM, Morgan, Martin < martin.mor...@roswellpark.org> wrote: > I would rather mapIds() continue to operate on a single column, return a > named character vector, and by default provide a 1:1 relationship between > input and output. multiVals=CharacterList does actually r

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

2015-11-23 Thread Morgan, Martin
I would rather mapIds() continue to operate on a single column, return a named character vector, and by default provide a 1:1 relationship between input and output. multiVals=CharacterList does actually return a 1:many mapping in a way that retains parallel structure (I guess, maybe module limit

Re: [Bioc-devel] Behavior of select function in AnnotationDbi

2015-11-23 Thread James W. MacDonald
Hi Hervé, Hmmm. Persuasive arguments. I like it! I'm pretty close to thinking you are right about this. However there is one small stumbling block. While select() allows for the look up of multiple columns simultaneously, mapIds() does not. But I do like your idea of having a function that guaran

Re: [Bioc-devel] PANTHER.db GOSLIM_ID hosed?

2015-11-23 Thread Jim Hester
Panther has been updated to the new 1.03, which should resolve this issue. Let us know if there are any further updates. On Fri, Nov 20, 2015 at 5:29 AM, Julius Müller wrote: > Dear Steve, > > thanks a lot for pointing out the error! The problem Martin described is > exactly the problem addresse