Re: [Rd] Is using devtools::release no longer allowed?

2014-08-21 Thread Geoff Jentry
On Tue, 19 Aug 2014, Duncan Murdoch wrote: If you use this, make sure you test it well enough to get it perfect the very first time you use it. If I were a CRAN administrator and received a series of bad submissions from someone who was working out the bugs, I would not find it difficult eithe

Re: [Rd] Question: Publishing R/S objects with WebServices (SOAP/WSDL)

2014-07-22 Thread Geoff Jentry
So far I see many packages that allow R to consume WebServices, but I haven't seen anything that allows you to publish a package as a WebService. If you haven't already, look at the RWebServices package from Bioconductor. __ R-devel@r-project.org ma

Re: [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit

2014-04-16 Thread Geoff Jentry
On Tue, 15 Apr 2014, peter dalgaard wrote: I'd say that that cat is out of the bag. There are probably umpteen documents around suggesting "R CMD Sweave". As people use Sweave only sporadically, it could take years before the old usage got stamped out. And anyways, the command format is the obv

Re: [Rd] The case for freezing CRAN

2014-03-26 Thread Geoff Jentry
On Thu, 20 Mar 2014, Dirk Eddelbuettel wrote: o Roger correctly notes that R scripts and packages are just one issue. Compilers, libraries and the OS matter. To me, the natural approach these days would be to think of something based on Docker or Vagrant or (if you must, VirtualBox). The

Re: [Rd] [RFC] A case for freezing CRAN

2014-03-19 Thread Geoff Jentry
using the identical version of each CRAN package. The bioconductor project uses similar policies. While I agree that this can be an issue, I don't think it is fair to compare CRAN to BioC. Unless things have changed, the latter has a more rigorous barrier to entry which includes buy in of vari

Re: [Rd] libR.so: cannot open shared object file

2013-09-04 Thread Geoff Jentry
Can you add some details? Suppose i have the package Model.tar.gz and my writable are is in user/area, what i have to do next to install the package? What I was picturing was something like this (forgive me if syntax isn't 100%): mkdir user/area/myRLib R CMD INSTALL --library=user/area/myRLi

Re: [Rd] libR.so: cannot open shared object file

2013-09-03 Thread Geoff Jentry
One problem is that i have not the privileges to install a package. If you have a writable area you can install to there with the --library=LIB argument and then load the package using the lib.loc command. __ R-devel@r-project.org mailing list https

Re: [Rd] Minimum requirements for package submission

2013-08-28 Thread Geoff Jentry
On Wed, 28 Aug 2013, Ben Bolker wrote: It may be suboptimal/there may be better ways, but what I would do in your situation would be to save the real twitteR results to a .Rdata file (e.g. put it in inst/vignetteData) and then 'fake' the twitter call: add a non-eval'd but echo'd chunk that app

Re: [Rd] Minimum requirements for package submission

2013-08-28 Thread Geoff Jentry
On Wed, 28 Aug 2013, Dirk Eddelbuettel wrote: The change to preferring vignettes/ over inst/doc/ is just one of many; there is also an ongoing preference for vignettes that fully reproducible from source. Which may eventually put an end to non-Rnw / non-(la)tex vignettes. I'm currently stymied

Re: [Rd] Extending suggestion for stopifnot

2013-08-21 Thread Geoff Jentry
first, I think it would be more useful if it had an optional character string, so users could write stopifnot( is.matrix(m), "m is not a matrix" ) stop() allows for arbitrary strings __ R-devel@r-project.org mailing list https://stat.ethz.ch/mai

Re: [Rd] [BioC] enabling reproducible research & R package management & install.package.version & BiocLite

2013-03-05 Thread Geoff Jentry
On Tue, 5 Mar 2013, Cook, Malcolm wrote: Thus, I might rather consider an approach that at 'publish' time tarzips up a copy of the R package dependencies based on a config file defined from sessionInfo and caches it in the project directory. If you had a separate environment for every project,

Re: [Rd] RFC: 'igraph' package update and backward compatibility

2011-10-20 Thread Geoff Jentry
On Thu, 20 Oct 2011, Hadley Wickham wrote: The optimal solution would be if R packages could depend on a specific version of a package, and a user could have multiple packages You used to be able to have a versioned install of a package, and then load a particular version. Not sure when it wa

Re: [Rd] readRDS and saveRDS

2011-10-18 Thread Geoff Jentry
On Tue, 18 Oct 2011, Hadley Wickham wrote: * read.csv and write.csv * load and save * readRDS and saveRDS Even loadRDS/saveRDS or readRDS/writeRDS would be better than the current combo. You could change the CSV functions to readCSV and writeCSV :)

Re: [Rd] Reference Classes: Accessing methods via [[...]], bug?

2011-05-03 Thread Geoff Jentry
On Sun, 1 May 2011, Martin Morgan wrote: On 05/01/2011 03:09 PM, John Chambers wrote: It would be interesting to get some experience and opinions on whether this is a good idea or not. It breaks encapsulation, in that the behavior of the class can no longer be inferred from the class definition

Re: [Rd] Conditional "Suggests"

2011-04-12 Thread Geoff Jentry
On Tue, 12 Apr 2011, Friedrich Leisch wrote: That is not the case, the checks will only get a NOTE that PkgB doesn't exist. E.g., my package flexclust suggests multicore, which is not available for windows. Still both live happily on CRAN, and of course there is a windows version of flexclust a

Re: [Rd] Conditional "Suggests"

2011-04-11 Thread Geoff Jentry
On Mon, 11 Apr 2011, Hadley Wickham wrote: To me this reads as being in the wheelhouse of what 'Suggests' is supposed to imply, as per the R Extensions manual.  The problem here is that if PkgB is put down as 'Suggests', it is required for R CMD check to pass which seems to defeat the purpose of

[Rd] Conditional "Suggests"

2011-04-11 Thread Geoff Jentry
Hi ... I came across an old post on R-devel that describes a situation very similar to one I find myself in: https://stat.ethz.ch/pipermail/r-devel/2006-December/043917.html As you can see in Gregor's example, the situation is that if I am writing Pkg A, I want to detect if Pkg B exists - if

Re: [Rd] Request: Suggestions for "good teaching" packages, esp. with C code

2011-02-15 Thread Geoff Jentry
f1 <- function(){ a=5 } The primary difference is that function 1 uses an incorrect assignment operator in an attempt to cause confusion ;) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Request: Suggestions for "good teaching" packages, esp. with C code

2011-02-15 Thread Geoff Jentry
On Wed, 16 Feb 2011, David Scott wrote: 4. We don't want gratuitous use of "return" at the end of functions. Why do people still do that? Well I for one (and Jeff as well it seems) think it is good programming practice. It makes explicit what is being returned eliminating the possibility of mis