Re: [Bioc-devel] TabixFileList() constructor broken in devel

2017-01-04 Thread Martin Morgan
On 12/29/2016 12:25 PM, Vincent Carey wrote: A while ago Martin and I discussed the possibility of idempotence for TabixFile ... this seemed to make sense and so TabixFile function (file, index = paste(file, "tbi", sep = "."), ..., yieldSize = NA_integer_) { if (is(file, "TabixFile"))

Re: [Rd] seq.int/seq.default

2017-01-04 Thread Mick Jordan
On 1/4/17 8:15 AM, Mick Jordan wrote: Here is another difference that I am guessing is unintended. > y <- seq.int(1L, 3L, length.out=2) > typeof(y) [1] "double" > x <- seq.default(1L, 3L, length.out=2) > typeof(x) [1] "integer" The if (by == R_MissingArg) branch at line 842 doesn't contain a

Re: [Rd] seq.int/seq.default

2017-01-04 Thread Mick Jordan
On 1/4/17 1:26 AM, Martin Maechler wrote: Mick Jordan on Tue, 3 Jan 2017 07:57:15 -0800 writes: > This is a message for someone familiar with the implementation. > Superficially the R code for seq.default and the C code for seq.int > appear to be

[Bioc-devel] Code quality and bug reports

2017-01-04 Thread Lluís Revilla
Dear Guangchuang and all, Quality of the packages has been a preoccupation of the project from the beginning (see https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005810.html for more references and other discussions about bug reports.) Despite not being in a goal of the project, it is

Re: [Bioc-devel] How to get further assessment for newly submitted package?

2017-01-04 Thread Martin Morgan
On 01/04/2017 04:13 AM, Jurat Shayidin wrote: Dear Lori : I still didn't get any updated action from reviewer on our packages. We've planned to complete package submission process by fixing possible issue raised from Bioconductor team and proceed publication accordingly.we only need brief,

Re: [Rd] seq.int/seq.default

2017-01-04 Thread Martin Maechler
> Mick Jordan > on Tue, 3 Jan 2017 07:57:15 -0800 writes: > This is a message for someone familiar with the implementation. > Superficially the R code for seq.default and the C code for seq.int > appear to be semantically very similar. My question

Re: [Bioc-devel] How to get further assessment for newly submitted package?

2017-01-04 Thread Jurat Shayidin
Dear Lori : I still didn't get any updated action from reviewer on our packages. We've planned to complete package submission process by fixing possible issue raised from Bioconductor team and proceed publication accordingly.we only need brief, general evaluation on this package and make sure we