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

2019-07-06 Thread Jeff Newmiller
This is why I only put localization variables in .Rprofile and am always putting such options into my project-specific scripts. This may sound like I am a masochist, but I hate sharing my scripts with someone else contaminated with compatibility bombs like that. On July 6, 2019 8:19:27 PM PDT,

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

2019-07-06 Thread Rolf Turner
Just thought it might be of interest were I to give a progress report ( :-) ) on this problem. I managed to track down and fix what was going wrong. It turns out that the issue was "stringsAsFactors". I *hate* stringsAsFactors being TRUE so I have a call to options() setting it to FALSE

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] "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] "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,

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

2019-07-01 Thread Henrik Bengtsson
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 On Mon, Jul 1, 2019 at 7:00 PM Rolf Turner wrote: > > > I am currently working on a package such that when "R CMD

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

2019-07-01 Thread Rolf Turner
I am currently working on a package such that when "R CMD check" is run the procedure seems to disappear into a black hole when it gets to the "* checking examples ..." stage. Strangely, when I run the examples individually, although they take a rather long time, they do not take an