[Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

hi, one of the recent changes in the devel IRanges has been to defunct the 'ifelse' method for 'Rle' objects. This was warned during the previous devel cycle and so it does with current release. One of the affected functions is the VRanges object constructor, 'VRanges()'. Since I use this

Re: [Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

News to me. Why was this deprecated? Why can't the ifelse() method just do what it is now telling the user to do? Is it to make the inefficiency of the implementation more obvious? The goal with Rle was to make it behave as conveniently and as vector-like as possible. On Wed, Oct 21, 2015 at

[Bioc-devel] question regarding change to release version of package

Dear Bioc-devel users, One of the authors of our package realized that the first letter of her last name was not capitalized in the description file of the package. Would it be okay to update the release version of the package to change something small like this so we don't have to wait 6

Re: [Bioc-devel] question regarding change to release version of package

Samuel, Only documentation and bug fixes should be back-ported to the release branch. This issue would classify as a documentation fix so would be a valid change. The naming ambiguities can be resolved by specifying an `Authors@R` block in your DESCRIPTION file. ``` Authors@R:

Re: [Bioc-devel] question regarding change to release version of package

The person() function that Jim uses in Authors@R allows for specification of first name, middle name etc. Kasper On Wed, Oct 21, 2015 at 11:34 AM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Samuel E Zimmerman" > > To:

Re: [Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

That sucks. I was thinking we could easily make R smarter about sub-assignment, so that base::ifelse would just work with value Rle, as would [<- in general. The C code would just call as.vector() on the object. The problem is that S4 objects are seen by that code as "scalar" and are wrapped in a

Re: [Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

On 10/21/2015 03:36 PM, Michael Lawrence wrote: That sucks. I was thinking we could easily make R smarter about sub-assignment, so that base::ifelse would just work with value Rle, as would [<- in general. The C code would just call as.vector() on the object. The problem is that S4 objects are

Re: [Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

Ok, thanks. That's what R (in my working copy) basically does now. Since internal sub-assignment is vector-based, it just calls as.vector(). That vector may be subsequently "promoted" given the type of "x" and "value" (like integer to real, real to character, etc). So it could be optimized, but it

Re: [Bioc-devel] VariantAnnotation::VRanges() & defunct ifelse method for Rle objects in devel IRanges

Hi Michael, On 10/21/2015 07:09 AM, Michael Lawrence wrote: News to me. Why was this deprecated? Why can't the ifelse() method just do what it is now telling the user to do? Is it to make the inefficiency of the implementation more obvious? There was some discussion about this here:

Re: [Bioc-devel] test coverage in Release packages

Hi Dan, On Tue, 20-10-2015, at 23:56, Dan Tenenbaum wrote: > Hi Ramon, > > - Original Message - >> From: "Ramon Diaz-Uriarte" >> To: "bioc-devel" >> Cc: "ramon diaz" >> Sent: Sunday, October