[Bioc-devel] IRanges: 'extractROWS' fails for 'RangedData'

2013-09-15 Thread Julian Gehring
Hi, calling 'head' or 'tail' on a 'RangedData' objects fail with the lastest builds (R: 2013-09-14 r63932, IRanges: 1.19.35). The cause seems to be that there is no 'extractROWS' method that can be found for the signature 'RangedData'. As an example, see: ''' library(IRanges) ## generate

Re: [Rd] declaring package dependencies

2013-09-15 Thread Matthew Dowle
I'm a little surprised by this thread. I subscribe to the RSS feeds of changes to NEWS (as Dirk mentioned) and that's been pretty informative in the past : http://developer.r-project.org/RSSfeeds.html Mainly though, I submit to winbuilder before submitting to CRAN, as the CRAN policies

Re: [Rd] declaring package dependencies

2013-09-15 Thread Michael Friendly
On 9/13/2013 12:15 PM, John Fox wrote: If I understand this thread, Michael's package doesn't use loglm() -- it provides methods for objects produced by loglm() and hence Enhances the package. Well, here's the rub: vcdExtra uses MASS::loglm() in examples, and also in R code, where it provides

Re: [Rd] declaring package dependencies

2013-09-15 Thread Duncan Murdoch
On 13-09-15 12:52 PM, Michael Friendly wrote: On 9/13/2013 12:15 PM, John Fox wrote: If I understand this thread, Michael's package doesn't use loglm() -- it provides methods for objects produced by loglm() and hence Enhances the package. Well, here's the rub: vcdExtra uses MASS::loglm() in

Re: [Rd] declaring package dependencies

2013-09-15 Thread Paul Gilbert
On 13-09-14 07:20 PM, Duncan Murdoch wrote: On 13-09-14 12:19 PM, Paul Gilbert wrote: On 13-09-14 09:04 AM, Duncan Murdoch wrote: On 13-09-13 12:00 PM, Dirk Eddelbuettel wrote: On 13 September 2013 at 11:42, Paul Gilbert wrote: | On 13-09-13 11:02 AM, Dirk Eddelbuettel wrote: | It's not

[Rd] R-Forge SVN commit hook to email appears to be broken

2013-09-15 Thread Dirk Eddelbuettel
It would appear that commits no longer trigger emails; for Rcpp at least we are two commits (made earlier today) ahead of what was emailed. Maybe the mail agent needs to be restarted? Many thanks for taking care of r-forge. It is appreciated. Dirk -- Dirk Eddelbuettel | e...@debian.org |

Re: [Rd] declaring package dependencies

2013-09-15 Thread Brian Rowe
Something that might be of use to you guys is crant (https://github.com/muxspace/crant), which is a set of scripts to make package development and testing simpler. With crant you can build out multiple R instances (release, patch, devel) and then run the build chain against each one. It's

[Rd] FOSS licence with BuildVignettes: false

2013-09-15 Thread Viechtbauer Wolfgang (STAT)
Dear All, I have been checking the metafor package against R-devel. R CMD check --as-cran metafor yields one note: FOSS licence with BuildVignettes: false Yes, I have 'BuildVignettes: FALSE' in my DESCRIPTION file. I see at http://developer.r-project.org/blosxom.cgi/R-devel/NEWS: Tue, 25

Re: [Rd] FOSS licence with BuildVignettes: false

2013-09-15 Thread Uwe Ligges
Setting BuildVignettes: false is fine if it is possible to build the vignettes, and the latter is checked in CRAN incoming checks (but not the daily checks). Uwe Ligges On 15.09.2013 22:13, Viechtbauer Wolfgang (STAT) wrote: Dear All, I have been checking the metafor package

Re: [Rd] FOSS licence with BuildVignettes: false

2013-09-15 Thread Ben Bolker
Uwe Ligges ligges at statistik.tu-dortmund.de writes: Setting BuildVignettes: false is fine if it is possible to build the vignettes, and the latter is checked in CRAN incoming checks (but not the daily checks). Uwe Ligges Hmmm. I was told by the CRAN maintainers on Aug 7 that

Re: [Rd] declaring package dependencies

2013-09-15 Thread Ben Bolker
Matthew Dowle mdowle at mdowle.plus.com writes: I'm a little surprised by this thread. I subscribe to the RSS feeds of changes to NEWS (as Dirk mentioned) and that's been pretty informative in the past : http://developer.r-project.org/RSSfeeds.html Mainly though, I submit to

Re: [Rd] declaring package dependencies

2013-09-15 Thread Yihui Xie
I've been watching this thread closely and trying not to chime in, because as Brian Rowe mentioned about CRAN's mysterious absence in a previous reply. CRAN is like a ghost in r-devel (or any other mailing lists) -- everybody is discussing about it, and nobody has ever seen it. Perhaps one day

Re: [Rd] declaring package dependencies

2013-09-15 Thread Brian Rowe
That reminds me: I once made a suggestion on how to automate some of the CRAN deployment process, but it was shot down as not being useful to them. I do recall a quote that was along the lines of as long as you don't need help, do whatever you want, so one thought is to just set up a build