Re: [Bioc-devel] Can't see updates from git repo in BioC package

Hi Martin, Ah, thank you for pointing out the build report page and the typo at the top of the vignette. I'll bookmark the page for quick checking in the future. Best,Shraddha On Thu, Feb 1, 2018 at 4:42 PM, Martin Morgan wrote: > > > On 02/01/2018 11:09 AM,

Re: [Bioc-devel] Can't see updates from git repo in BioC package

On 02/01/2018 11:09 AM, Shraddha Pai wrote: Hello BioC group, I've recently moved my package repo from svn to github. Just noticed that the changes in the github repo aren't visible in either the release or devel version of BioC. e.g. I updated the Vignette and the new date on it should be 8

Re: [Rd] as.list method for by Objects

On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler wrote: >> Michael Lawrence >> on Tue, 30 Jan 2018 15:57:42 -0800 writes: > > > I just meant that the minimal contract for as.list() appears to be that > it > > returns a

Re: [Rd] Best practices in developing package: From a single file

On Thu, Feb 1, 2018 at 5:24 AM, Lionel Henry wrote: > On 31 janv. 2018, at 09:08, Gabriel Becker wrote: > > > it *actively discourages* the bits it doesn't directly support. > > It may be discouraging to include Rd syntax in roxygen docs but only >

Re: [Rd] Best practices in developing package: From a single file

On Thu, Feb 1, 2018 at 4:29 AM, Duncan Murdoch wrote: > On 31/01/2018 6:59 AM, Duncan Murdoch wrote: >> >> On 30/01/2018 11:39 PM, Hadley Wickham wrote: > > [ lots deleted ] >>> >>> Personally, I don't find writing in comments any harder than writing >>> in .Rd files,

[Bioc-devel] Can't see updates from git repo in BioC package

Hello BioC group, I've recently moved my package repo from svn to github. Just noticed that the changes in the github repo aren't visible in either the release or devel version of BioC. e.g. I updated the Vignette and the new date on it should be 8 Dec 2017, but it's still at 27 Jan 2017. I've

Re: [Rd] Fwd: Re: Best practices in developing package:

Folding is a simple solution, but there are intrinsic problems, like the need to embed the documentation in comments. If the user already has to expand a fold to edit the docs, the IDE could instead just provide a link or shortcut that jumps to a separate documentation file, written in whatever

Re: [Rd] as.list method for by Objects

> Michael Lawrence > on Thu, 1 Feb 2018 06:12:20 -0800 writes: > On Thu, Feb 1, 2018 at 1:21 AM, Martin Maechler > wrote: >> > Michael Lawrence >> > on Tue, 30 Jan 2018

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

> Hervé Pagès > on Tue, 30 Jan 2018 13:30:18 -0800 writes: > Hi Martin, Henrik, > Thanks for the follow up. > @Martin: I vote for 2) without *any* hesitation :-) > (and uniformity could be restored at some point in the > future by having

Re: [Bioc-devel] updating Bioconductor package that is already on Github

Hi Simina, I think the missing information was your package name. There was also the fact that your initial google sheet submission was wrong. You were supposed to give your SVN ID “s.boca” to the google sheet, which would have automatically linked all your packages and your Github ID’s SSH

Re: [Rd] Best practices in developing package: From a single file

On 01/02/2018 7:44 AM, Joris Meys wrote: On Thu, Feb 1, 2018 at 1:29 PM, Duncan Murdoch > wrote: On 31/01/2018 6:59 AM, Duncan Murdoch wrote: On 30/01/2018 11:39 PM, Hadley Wickham wrote:  [ lots deleted ]

Re: [Rd] Fwd: Re: Best practices in developing package:

> On 1 févr. 2018, at 06:51, Therneau, Terry M., Ph.D. > wrote: > > A second is that I care a lot about documentation so my help files are > fairly long, so much so that the advantage of having the documentation of an > argument > "close" to the declaration of said argument

[Rd] Fwd: Re: Best practices in developing package:

I'm not going to force anyone to use roxygen2. But I personally find it easier to have the function right below the documentation, so that any change to the function can immediately be documented as well. You prefer to do this by keeping that strictly separated, which is absolutely fine. It's

Re: [Rd] Best practices in developing package: From a single file

On 01/02/2018 8:17 AM, Georgi Boshnakov wrote: It is indeed a matter of what the developer is comfortable with and the one-stop solution provided by devtools is difficult to beat. This may also vary across projects. I use EMACS/ESS with and without roxygen2. In some cases EMACS/ESS+Org mode

Re: [Rd] as.list method for by Objects

On Thu, Feb 1, 2018 at 1:21 AM, Martin Maechler wrote: > > Michael Lawrence > > on Tue, 30 Jan 2018 10:37:38 -0800 writes: > > > I agree that it would make sense for the object to have c("by", > "list") as > > its class

Re: [Rd] Best practices in developing package: From a single file

On 31 janv. 2018, at 09:08, Gabriel Becker wrote: > it *actively discourages* the bits it doesn't directly support. It may be discouraging to include Rd syntax in roxygen docs but only because the LaTeX-like syntax of Rd is burdensome, not because of roxygen. It is still

Re: [Rd] Best practices in developing package: From a single file

It is indeed a matter of what the developer is comfortable with and the one-stop solution provided by devtools is difficult to beat. This may also vary across projects. I use EMACS/ESS with and without roxygen2. In some cases EMACS/ESS+Org mode provides stunning benefits. Updating "usage"

Re: [Rd] Best practices in developing package: From a single file

On Thu, Feb 1, 2018 at 1:29 PM, Duncan Murdoch wrote: > On 31/01/2018 6:59 AM, Duncan Murdoch wrote: > >> On 30/01/2018 11:39 PM, Hadley Wickham wrote: >> > [ lots deleted ] > >> Personally, I don't find writing in comments any harder than writing >>> in .Rd files,

Re: [Rd] Best practices in developing package: From a single file

On 31/01/2018 6:59 AM, Duncan Murdoch wrote: On 30/01/2018 11:39 PM, Hadley Wickham wrote: [ lots deleted ] Personally, I don't find writing in comments any harder than writing in .Rd files, especially now that you can write in markdown and have it automatically translated to Rd formatting

Re: [Rd] Error message: 'Rscript' should not be used without a path

Hi Michal, On 02/01/2018 09:23 AM, Michal Burda wrote: Dear R-devel members, recently, I ran into the following error message (R-devel 2018-01-31): 'Rscript' should not be used without a path -- see par. 1.6 of the manual I would like to know more about it, why is it required to run Rscript

[Rd] Error message: 'Rscript' should not be used without a path

Dear R-devel members, recently, I ran into the following error message (R-devel 2018-01-31): 'Rscript' should not be used without a path -- see par. 1.6 of the manual I would like to know more about it, why is it required to run Rscript with a path, and where is that par. 1.6 of the manual. I

Re: [Rd] as.list method for by Objects

> Michael Lawrence > on Tue, 30 Jan 2018 10:37:38 -0800 writes: > I agree that it would make sense for the object to have c("by", "list") as > its class attribute, since the object is known to behave as a list. Well, but that (list behavior)

Re: [Rd] as.list method for by Objects

> Michael Lawrence > on Tue, 30 Jan 2018 15:57:42 -0800 writes: > I just meant that the minimal contract for as.list() appears to be that it > returns a VECSXP. To the user, we might say that is.list() will always > return TRUE. Indeed. I