Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
On Aug 27, 2014 5:24 PM, "Hadley Wickham" > I'd say: Depends is a historical artefact from ye old days before > package namespaces. Apart from depending on a specific version of R, > you should basically never use depends. (The one exception is, as > mentioned in R-exts, if you're writing somethi

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Hadley Wickham
On Wed, Aug 27, 2014 at 5:01 PM, Gavin Simpson wrote: > > On 27 August 2014 15:24, Hadley Wickham wrote: >> >> > Is that the cause of these NOTEs? Is the expectation that if I am using >> > a >> > function from a package, even a package that I have in Depends:, that I >> > have to explicitly decl

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
On 27 August 2014 16:25, Uwe Ligges wrote: > Again, I am happy to be re-educated on this though :-) >> > > If you like, you can fill the search path with lots of packages (and make > masking of functions more likely), but you shoudl really import into your > namesoace so that unanticipated order

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Uwe Ligges
On 28.08.2014 00:19, Gavin Simpson wrote: On 27 August 2014 16:09, Dan Tenenbaum wrote: - Original Message - From: "Gavin Simpson" To: "Hadley Wickham" Cc: r-devel@r-project.org Sent: Wednesday, August 27, 2014 3:01:53 PM Subject: Re: [Rd] Re R CMD check checking in development ve

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
On 27 August 2014 16:09, Dan Tenenbaum wrote: > - Original Message - > > From: "Gavin Simpson" > > To: "Hadley Wickham" > > Cc: r-devel@r-project.org > > Sent: Wednesday, August 27, 2014 3:01:53 PM > > Subject: Re: [Rd] Re R CMD check checking in development version of R > > > > On 27 A

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Dan Tenenbaum
- Original Message - > From: "Gavin Simpson" > To: "Hadley Wickham" > Cc: r-devel@r-project.org > Sent: Wednesday, August 27, 2014 3:01:53 PM > Subject: Re: [Rd] Re R CMD check checking in development version of R > > On 27 August 2014 15:24, Hadley Wickham wrote: > > > > Is that the

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
On 27 August 2014 15:24, Hadley Wickham wrote: > > Is that the cause of these NOTEs? Is the expectation that if I am using a > > function from a package, even a package that I have in Depends:, that I > > have to explicitly declare these imports in NAMESPACE? > > Yes. > > (Otherwise your package

Re: [Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Hadley Wickham
> Is that the cause of these NOTEs? Is the expectation that if I am using a > function from a package, even a package that I have in Depends:, that I > have to explicitly declare these imports in NAMESPACE? Yes. (Otherwise your package won't work if it's only attached and not loaded. i.e. if some

[Rd] Re R CMD check checking in development version of R

2014-08-27 Thread Gavin Simpson
Dear list, This is related to the change discussed in the thread "no visible binding for global variables for data sets in a package". I went to look at the Check results for one of my packages (analogue) on CRAN: http://cran.r-project.org/web/checks/check_results_analogue.html Under the r-devel

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread peter dalgaard
On 27 Aug 2014, at 16:48 , Hadley Wickham wrote: >> I think the right answer _is_ to export the lazy data; the question is how >> to do it. There's nothing particularly strange about exporting non-functions >> ("letters" would be an example, save for the special status of >> package:base). If

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread peter dalgaard
On 27 Aug 2014, at 19:51 , Michael Friendly wrote: > - Peter Dalgaard noted the change in R-devel, and nobody so far has suggested > a working remedy, so a clean solution > seems warranted. Actually, both Peter Dalgaard and Brian Ripley suggested Lahman:battingLabels, and, with the current s

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Hadley Wickham
On Wed, Aug 27, 2014 at 12:51 PM, Michael Friendly wrote: > On 8/27/2014 10:41 AM, peter dalgaard wrote: >> >> Using data() in a package with lazyloaded data seems like asking for >> trouble to me. But you're making me curious (and I'm too lazy[*] to set up >> for rebuilding the package myself): >

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Michael Friendly
On 8/27/2014 10:41 AM, peter dalgaard wrote: Using data() in a package with lazyloaded data seems like asking for trouble to me. But you're making me curious (and I'm too lazy[*] to set up for rebuilding the package myself): Did you actually try putting battingLabels & friends in the namespace

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Prof Brian Ripley
http://cran.r-project.org/doc/manuals/r-patched/R-exts.html#Suggested-packages suggests e.g. Lahman::battingLabels, and that does work for lazy-loaded datasets (which is what these appear to be). We have seen a couple of other instances in which this was needed for code within the package. Ho

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Hadley Wickham
> I think the right answer _is_ to export the lazy data; the question is how to > do it. There's nothing particularly strange about exporting non-functions > ("letters" would be an example, save for the special status of package:base). > If you attach the package, the lazyloaded data appear in t

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread peter dalgaard
Using data() in a package with lazyloaded data seems like asking for trouble to me. But you're making me curious (and I'm too lazy[*] to set up for rebuilding the package myself): Did you actually try putting battingLabels & friends in the namespace? What happened? A workaround could be to use

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Michael Friendly
On 8/27/2014 9:29 AM, Michael Friendly wrote: It works in the sense that Lahman::Label("yearID") will work even when Lahman is not in the search path, but R-devel CMD check will still give the same NOTE, though you can argue that that note is actally a "false positive". So, this would be v

Re: [Rd] working with huge memory: single precision?

2014-08-27 Thread Prof Brian Ripley
On 27/08/2014 14:43, Simon Urbanek wrote: Mario, On Aug 27, 2014, at 4:03 AM, Mario Emmenlauer wrote: Hello, I'm very new to R and don't know much about it yet. I would like to develop R-programs that work with data of sizes of 10^10 - 10^11 data points. We have very-high-memory machines wi

Re: [Rd] R, OSX, should creating SVGs request XQuartz

2014-08-27 Thread Simon Urbanek
On Aug 27, 2014, at 5:45 AM, Jonathon Love wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA512 > > hi, > > on OS X, when you try and use something which depends on X11, and you > don't have XQuartz installed, you receive an error message, it directs > you to download XQuartz, and then it

Re: [Rd] working with huge memory: single precision?

2014-08-27 Thread Simon Urbanek
Mario, On Aug 27, 2014, at 4:03 AM, Mario Emmenlauer wrote: > > Hello, > > I'm very new to R and don't know much about it yet. I would like > to develop R-programs that work with data of sizes of 10^10 - 10^11 > data points. We have very-high-memory machines with ~256 GB, but it > would signif

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Michael Friendly
On 8/27/2014 5:24 AM, Martin Maechler wrote: Michael Friendly on Tue, 26 Aug 2014 17:58:34 -0400 writes: > I'm updating the Lahman package of baseball statistics to the 2013 > release. In addition to > the main data sets, the package also contains several convenience >

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread John Maindonald
Re solution 2, the following is in the function tabFarsDead() the latest (0.55) version of gamclass: data('FARS', package='gamclass', envir=environment()) FARS <- get("FARS", envir=environment()) The second statement is, strictly, redundant, but it makes the syntax checker happy. Another pos

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Joshua Wiley
I have had similar notes, but in cases where the dataset was created internally by a function: * checking R code for possible problems ... NOTE vm_diagnostics: no visible binding for global variable 'Median' vm_diagnostics: no visible binding for global variable 'Index' vm_diagnostics: no visible

[Rd] R, OSX, should creating SVGs request XQuartz

2014-08-27 Thread Jonathon Love
-BEGIN PGP SIGNED MESSAGE- Hash: SHA512 hi, on OS X, when you try and use something which depends on X11, and you don't have XQuartz installed, you receive an error message, it directs you to download XQuartz, and then it euthanizes your process. (my guess is that there is a skeleton X11

[Rd] working with huge memory: single precision?

2014-08-27 Thread Mario Emmenlauer
Hello, I'm very new to R and don't know much about it yet. I would like to develop R-programs that work with data of sizes of 10^10 - 10^11 data points. We have very-high-memory machines with ~256 GB, but it would significantly help if I could store the data points in single precision in RAM inst

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread peter dalgaard
The change would seem to be this \item \command{R CMD check} now by default checks code usage directly on the package namespace without loading and attaching the package and its suggests and enhances. and perhaps the remedies could be stated more clearly? Putting the data objec

Re: [Rd] no visible binding for global variable for data sets in a package

2014-08-27 Thread Martin Maechler
> Michael Friendly > on Tue, 26 Aug 2014 17:58:34 -0400 writes: > I'm updating the Lahman package of baseball statistics to the 2013 > release. In addition to > the main data sets, the package also contains several convenience > functions that make use > of these