[R-pkg-devel] Warning Message on Vignettes

2019-07-02 Thread Charith Karunarathna
(Reposting..) Hi everyone, I am getting following two warnings when I submit my R package (perfectphyloR) to CRAN. Warning 1: * checking files in 'vignettes' ... WARNING Files in the 'vignettes' directory but no files in 'inst/doc': 'perfectphyloR.html',

Re: [R-pkg-devel] CRAN pre-test failed on NOTE "no visible binding for global variable"

2019-07-02 Thread Duncan Murdoch
On 02/07/2019 11:00 a.m., Georgi Boshnakov wrote: ... if(getRversion() >= "2.15.1") utils::globalVariables(c(".")) Using such a general pattern eventually and inevitably will prevent the check from reporting legitimate bugs. I believe globalVariables() takes a vector of names, not a

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Rolf Turner
On 2/07/19 11:13 PM, Ivan Krylov wrote: Could R CMD check be using valgrind to run the examples? Valgrind has to interpret CPU instructions manually to be able to warn about results of code execution depending on memory values it considers undefined, so it is much slower than execution on a

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Duncan Murdoch
On 02/07/2019 5:31 a.m., Rolf Turner wrote: Many thanks to Henrik Bengtsson and Martin Maechler for pointing out that I can monitor progress by looking at the file "mypkg.Rcheck/mypkg-Ex.Rout" e.g. by using "tail -f". This strategy indeed revealed where the hangup was happening. I

Re: [R-pkg-devel] CRAN pre-test failed on NOTE "no visible binding for global variable"

2019-07-02 Thread Georgi Boshnakov
> ... > if(getRversion() >= "2.15.1") utils::globalVariables(c(".")) Using such a general pattern eventually and inevitably will prevent the check from reporting legitimate bugs. One alternative is to list explicitly the variables in question and make sure that they are not commonly used

Re: [R-pkg-devel] CRAN pre-test failed on NOTE "no visible binding for global variable"

2019-07-02 Thread Iñaki Ucar
raúl On Tue, 2 Jul 2019 at 14:18, Berlanga, Antonio J wrote: > > Hi r-package-devel, > > I've submitted my first package but it failed the CRAN pre-tests on > NOTES. I got: > > - my email > > - an extra non-standard file (which I have now added to .Rbuildignore) > > - NOTEs on "no visible global

[R-pkg-devel] CRAN pre-test failed on NOTE "no visible binding for global variable"

2019-07-02 Thread Berlanga, Antonio J
Hi r-package-devel, I've submitted my first package but it failed the CRAN pre-tests on NOTES. I got: - my email - an extra non-standard file (which I have now added to .Rbuildignore) - NOTEs on "no visible global function definition" The first two I assume are harmless. The third I do not

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Ivan Krylov
Could R CMD check be using valgrind to run the examples? Valgrind has to interpret CPU instructions manually to be able to warn about results of code execution depending on memory values it considers undefined, so it is much slower than execution on a real CPU. One way to verify that on a

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Rolf Turner
On 2/07/19 9:45 PM, Iñaki Ucar wrote: Which line of code is it? Dunno that it's very enlightening, without having access to the package, but the two lines involved are: fit <- ldFit(inLogs,predictor="logDose",link="logit") x3 <- cvCompare(fit,nrep=5) The first line runs

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Ben Bolker
It's a pain in the neck, but even more basic than inserting browser() calls all over the place (but possibly useful in this situation) would be inserting appropriate cat() statements all over the place ... (and maybe using cat() with proc.time() to report on elapsed time as you go?) (As for

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Iñaki Ucar
Which line of code is it? Iñaki On Tue, 2 Jul 2019 at 11:32, Rolf Turner wrote: > > > Many thanks to Henrik Bengtsson and Martin Maechler for pointing out > that I can monitor progress by looking at the file > > "mypkg.Rcheck/mypkg-Ex.Rout" > > e.g. by using "tail -f". This strategy

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Rolf Turner
Many thanks to Henrik Bengtsson and Martin Maechler for pointing out that I can monitor progress by looking at the file "mypkg.Rcheck/mypkg-Ex.Rout" e.g. by using "tail -f". This strategy indeed revealed where the hangup was happening. I wrapped a line of the examples in \dontrun{}

Re: [R-pkg-devel] The correct way to put additional DLLs on windows?

2019-07-02 Thread Jialin Ma
Sorry, it was a mistake. CC the list. 于 2019年7月2日 GMT-07:00 上午12:17:01, Jeff Newmiller 写到: >I recommend that you "reply-all" to keep the mailing list included. > > >On July 1, 2019 11:30:23 PM PDT, Jialin Ma wrote: >>Hi Jeff, >> >>Thanks for your reply. I would like to clarify a little bit: >>

Re: [R-pkg-devel] "Progress reports" for examples in packages.

2019-07-02 Thread Martin Maechler
> Henrik Bengtsson > on Mon, 1 Jul 2019 20:36:26 -0700 writes: > FWIW, when running R CMD check mypkg_1.0.tar.gz > the example output is captured to the file > 'mypkg.Rcheck/mypkg-Ex.Rout', so you could monitor that > one for what's going on. > /Henrik Yes,