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

2018-01-31 Thread Duncan Murdoch
On 31/01/2018 8:59 AM, Mark van der Loo wrote: I fully agree with Joris and Hadley on roxygen2. Additionally: I wrote and published my first package before roxygen (or roxygen2) was available. I found editing .Rd extremely terse (especially when code is updated). For example, the fact that t

Re: [Rd] CRAN indices out of whack (for at least macOS)

2018-01-31 Thread Uwe Ligges
Thanks, Uwe On 31.01.2018 20:08, Simon Urbanek wrote: Dirk, yes, thanks, the edge server that serves the Mac binaries to CRAN has run out of disk space (due to size of CRAN itself) so the sync was incomplete. It is fixed now -- you can try by using the macos master server as mirror: https://

Re: [Rd] bug [methods]: double execution of `insertSource` within the same session does not work

2018-01-31 Thread Michael Lawrence
The issue should be resolved in R-devel. It was actually deeper and more important than this obscure insertSource() function. names() was not doing the right thing on S4 objects derived from "environment". On Mon, Jan 29, 2018 at 11:02 AM, Michael Lawrence wrote: > Thanks, I will fix this. > > O

Re: [Rd] CRAN indices out of whack (for at least macOS)

2018-01-31 Thread Simon Urbanek
Dirk, yes, thanks, the edge server that serves the Mac binaries to CRAN has run out of disk space (due to size of CRAN itself) so the sync was incomplete. It is fixed now -- you can try by using the macos master server as mirror: https://r.research.att.com/ and it will propagate through other mi

Re: [Rd] CRAN indices out of whack (for at least macOS)

2018-01-31 Thread Dirk Eddelbuettel
Bumping this as we now have two more issue tickets filed and a fresh SO question. Is anybody looking at this? Simon? Dirk On 30 January 2018 at 15:19, Dirk Eddelbuettel wrote: | | I have received three distinct (non-)bug reports where someone claimed a | recent package of mine was broken ... s

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

2018-01-31 Thread Gabriel Becker
Joris, With the large caveat that I am not Duncan, and thus am not speaking for him, I can see an argument for his claim that I think is, more or less, true. roxygen2 (as far as I know as someone who uses it at least some of the time) maps to only a subset of Rd. It is the most commonly used subs

Re: [Rd] Why R should never move to git

2018-01-31 Thread Suzen, Mehmet
On 31 January 2018 at 16:18, Barry Rowlingson wrote: >> > > Let the record also state that *gitlab* is an open source project and can be > downloaded and self-hosted, like gogs, but unlike github. Good to know. Nice one: https://github.com/gitlabhq/gitlabhq Best, -m > PS I've been running a g

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

2018-01-31 Thread Suzen, Mehmet
Dear Dr. Pfaff, Thank you for this, creating a package out of single file was my oriingal question, but not only creating and also maintaining it that way so R package is an artifact of the development process rather than "manually maintained" structure. I will have look at your sources. Best, M

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

2018-01-31 Thread Michael Lawrence
I pretty much agree. I tried using roxygen when it was first released but couldn't stand putting documentation in comments, especially for complex, S4-based software. Rd is easy to read and write and lets me focus on the task of writing documentation (focus is the hardest part of any task for me).

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

2018-01-31 Thread Yihui Xie
Similarly, I created this example a couple of years ago: https://github.com/yihui/rlp which shows that you can create a package from R Markdown documents (or any documents that knitr supports). Basically you can start with an R Markdown document, and after clicking a button in RStudio, you will get

Re: [Rd] Why R should never move to git

2018-01-31 Thread Barry Rowlingson
On Tue, Jan 30, 2018 at 11:07 PM, Suzen, Mehmet wrote: > This might be off topic, but if R-core development ever moves to git, > I think it would make sense to have its own git service hosted by a > university, rather than using > github or gitlab. It is possible via https://gogs.io/ project. > >

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

2018-01-31 Thread Pfaff, Bernhard Dr.
Dear All: stepping in late, but @Joris, if you would like to take 'from a single file' literally, have a look at: https://github.com/bpfaff/lp4rp (lp4rp: literate programming for R packages); Cheers, Bernhard ps: incidentally, within the noweb-file roxygen is employed. -Ursprün

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

2018-01-31 Thread Mark van der Loo
I fully agree with Joris and Hadley on roxygen2. Additionally: I wrote and published my first package before roxygen (or roxygen2) was available. I found editing .Rd extremely terse (especially when code is updated). For example, the fact that there are no spaces allowed between } and { in \para

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

2018-01-31 Thread Joris Meys
On Wed, Jan 31, 2018 at 1:41 PM, Duncan Murdoch wrote: > On 31/01/2018 6:33 AM, Joris Meys wrote: > > 3. given your criticism, I'd like your opinion on where I can improve the >> documentation of https://github.com/CenterForStatistics-UGent/pim. I'm >> currently busy updating the help files for a

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

2018-01-31 Thread Dirk Eddelbuettel
(Please do not quote without attribution) On 30 January 2018 at 20:44, Hadley Wickham wrote: | Personally, I think the biggest problem with package.skeleton() is | that it assumes that the source of truth is objects in an environment. | This seems the wrong way around to me. Basically irrelevant

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

2018-01-31 Thread Duncan Murdoch
On 31/01/2018 6:33 AM, Joris Meys wrote: 3. given your criticism, I'd like your opinion on where I can improve the documentation of https://github.com/CenterForStatistics-UGent/pim. I'm currently busy updating the help files for a next release on CRAN, so your input is more than welcome. Aft

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

2018-01-31 Thread Duncan Murdoch
On 31/01/2018 6:33 AM, Joris Meys wrote: Dear Duncan, With all respect, but I strongly disagree on your stance regarding roxygen2 for multiple reasons: 1. It is in my humble opinion not correct to evaluate a tool based on the abuse of some users. It's not because people write packages with b

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

2018-01-31 Thread Duncan Murdoch
On 30/01/2018 11:39 PM, Hadley Wickham wrote: On Tue, Jan 30, 2018 at 4:55 PM, Duncan Murdoch wrote: On 30/01/2018 4:30 PM, Kenny Bell wrote: In response to Duncan regarding the use of roxygen2 from the point of view of a current user, I believe the issue he brings up is one of correlation ra

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

2018-01-31 Thread Joris Meys
Dear Duncan, With all respect, but I strongly disagree on your stance regarding roxygen2 for multiple reasons: 1. It is in my humble opinion not correct to evaluate a tool based on the abuse of some users. It's not because people write packages with bad documentation, that roxygen2 is to blame. I