Re: [Rd] advise on Depends

2013-10-25 Thread Hervé Pagès
On 10/25/2013 11:26 AM, Michael Lawrence wrote: On Wed, Oct 23, 2013 at 8:33 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’ ‘b

Re: [Rd] advise on Depends

2013-10-25 Thread John Chambers
Software generated in methods for user classes calls functions in the methods package, as I said. I don't know the circumstances (if any) when such calls fail to find functions if the whole package is imported. Perhaps someone on this list may have examples. But for sure just importing th

Re: [Rd] advise on Depends

2013-10-25 Thread Paul Gilbert
On 13-10-25 05:21 PM, Henrik Bengtsson wrote: On Fri, Oct 25, 2013 at 1:39 PM, John Chambers wrote: One additional point to Michael's summary: The "methods" package itself should stay in Depends:, to be safe. It would be nice to have more detail about when this is necessary, rather than s

Re: [Rd] advise on Depends

2013-10-25 Thread Henrik Bengtsson
On Fri, Oct 25, 2013 at 1:39 PM, John Chambers wrote: > One additional point to Michael's summary: > > The "methods" package itself should stay in Depends:, to be safe. > > There are a number of function calls to the methods package that may be > included in generated methods for user classes. T

Re: [Rd] advise on Depends

2013-10-25 Thread Dirk Eddelbuettel
On 25 October 2013 at 13:39, John Chambers wrote: | One additional point to Michael's summary: | | The "methods" package itself should stay in Depends:, to be safe. | | There are a number of function calls to the methods package that may be included in generated methods for user classes. These

Re: [Rd] advise on Depends

2013-10-25 Thread John Chambers
One additional point to Michael's summary: The "methods" package itself should stay in Depends:, to be safe. There are a number of function calls to the methods package that may be included in generated methods for user classes. These have not been revised to work when the methods package is n

Re: [Rd] Multivariate time series in R 3 vs R 2

2013-10-25 Thread Martyn Plummer
This has nothing to do with changes in base R. It is due to changes in the dependent packages. These changes mean that when you call lapply it does not dispatch the right as.list method. The method you want (as.list.ts) is provided by the zoo package. It splits a multivariate time series into a li

Re: [Rd] advise on Depends

2013-10-25 Thread Michael Lawrence
On Wed, Oct 23, 2013 at 8:33 PM, Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > This is about the new note > > Depends: includes the non-default packages: > ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ > ‘Biostrings’ ‘bumphunter’ > Adding so many packages to the

Re: [Rd] R CMD check problem with R 3.0.2

2013-10-25 Thread Duncan Murdoch
On 25/10/2013 11:37 AM, Sanford Weisberg wrote: Using SUSE Linux, Windows 32 bit and Windows 64 bit R 3.0.2 , I am unable to use R CMD check successfully. Here is the Windows 64 bit report: Both checking and installing code are really designed to work on tarballs, as John said. Some parts of

Re: [Rd] appropriate work-around for problems with a specific plot device (Rstudio)?

2013-10-25 Thread Yihui Xie
You can see how R sets up the device option in grDevices:::.onLoad, but unfortunately the code there is not easily usable. I think you can treat the NOTE in R CMD check as a false warning and explain the situation to CRAN maintainers in the email. Code analysis using codetools in R CMD check is no

Re: [Rd] R CMD check problem with R 3.0.2

2013-10-25 Thread Yihui Xie
This has been asked s many times that I think it may be a good idea for R CMD check to just stop when the user passes a directory instead of a tar ball to it, or automatically run R CMD build before moving on. In my opinion, sometimes an FAQ and a bug are not entirely different. Regards, Yihui

[Rd] R CMD check problem with R 3.0.2

2013-10-25 Thread Sanford Weisberg
Using SUSE Linux, Windows 32 bit and Windows 64 bit R 3.0.2 , I am unable to use R CMD check successfully. Here is the Windows 64 bit report: Z:\R\source\effects>R CMD check pkg * using log directory 'Z:/R/source/effects/pkg.Rcheck' * using R version 3.0.2 (2013-09-25) * using platform: x86_64-w

Re: [Rd] appropriate work-around for problems with a specific plot device (Rstudio)?

2013-10-25 Thread Lorenz, David
Skye, I ran into a similar problem with RStudio. My solution was just to check if "windows" exists and if it does, open windows, then check "quartz" and so forth. You can restrict the exists function to look only in grDevices. Dave On Fri, Oct 25, 2013 at 4:19 AM, Milan Bouchet-Valat wrote: >

Re: [Rd] appropriate work-around for problems with a specific plot device (Rstudio)?

2013-10-25 Thread Milan Bouchet-Valat
Le jeudi 24 octobre 2013 à 17:13 -0700, Skye Bender-deMoll a écrit : > Dear r-devel-opers, > > I'm working on a package that does some plot-intensive work using the > animation library. It turns out that this performs very badly in the > RStudio plot device, which is the preferred IDE for our t