From ucfagls at gmail.com  Wed Sep  3 22:36:41 2014
From: ucfagls at gmail.com (Gavin Simpson)
Date: Wed, 3 Sep 2014 14:36:41 -0600
Subject: [Rd] timings for examples in R CMD check
In-Reply-To: <540772CC.3070108@braverock.com>
References: <540772CC.3070108@braverock.com>
Message-ID: <CAAHES9zN07jPXFGa2ezTEC=Vq0U_Vb+3d7_mqXa2fm4CGu3j0A@mail.gmail.com>

Brian,

What you are doing is how I have always checked my packages:

1. Run R CMD check pkg_tarball.tar.gz
2. mv pkg.Rcheck/pkg-Ex.Rout pkg_sources/tests/Examples/pkg-Ex.Rout.save
3. Next R CMD check pkg_tarball.tar.gz checks against the new Example output

Are you sure you are getting the newly created pkg-Ex.Rout file and placing
it in the correct part of the package and adjusting the name
to pkg-Ex.Rout.save?

The only time I ever had a problem with this was when I inadvertently used
a .Rout file from a check with --as-cran.

G


On 3 September 2014 13:58, Brian G. Peterson <brian at braverock.com> wrote:

> I'm having a very hard time making R CMD check produce a clean check on
> examples because of the timings inserted into examples by R CMD check.
>
> I am getting a difference on every example output caused by timing
> information being inserted by 'R CMD check'.
>
> The current 'Writing R Extensions' manual[1] states on p. 14:
>
>    If directory tests has a subdirectory Examples containing a
>    file pkg-Ex.Rout.save, this is  compared to the output file
>    for running the examples when the latter are checked.
>    Reference  output should be produced without having the
>    --timings option set (and note that --as-cran  sets it).
>
> As is suggested above, if I run
>
>    R CMD check --as-cran mypkg.tar.gz
>
> or
>
>    R CMD check --timings mypkg.tar.gz
>
> the my.pkg.Rcheck/mypkg-Ex.Rout file contains timing lines inserted by 'R
> CMD check'
>
> If, instead, I follow my reading of the manual, and run
>
> R CMD check mypkg.tar.gz
>
> the mypkg.Rcheck/mypkg-Ex.Rout file does not contain timings.  If I then
> copy the mypkg.Rcheck/mypkg-Ex.Rout file to
>
> mypkg/tests/Examples/mypkg-Ex.Rout.save
>
> as described by footnote 17 on the previously referenced p. 14, I would
> expect to now have no differences, as demonstrated by 'diff' or 'diff -bw'
> as used by 'R CMD check'.
>
> To my surprise, whether I copy a version of the mypkg-Ex.Rout file with or
> without timing rows, I get differences reported for every example by the
> (spurious?) insertion of timings by R CMD check.
>
> e.g.
> 8169a8549,8550
> > > base::assign(".dptime", (proc.time() - get(".ptime", pos =
> "CheckExEnv")), pos = "CheckExEnv")
> > > base::cat("textplot", base::get(".format_ptime", pos =
> 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n",
> file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> 8175a8557
>
>
>
> Is this expected?
>
> It is certainly not the behavior we had for many years, where a check of
> examples could actually be clean, producing differences only on the 'Time
> elapsed:' line, which has been present for many R versions.  I have tried
> testing against a package with both the timing lines includes and excluded
> in /mypkg-Ex.Rout.save, and with R CMD check run without additional
> options, with --timings, and with --as-cran.   They produce equivalent
> check files. on their example checks.
>
> This behavior is on R 3.1.0, 3.1.1, and R-devel.
>
> I would assume from the documentation that there should be a way to get a
> clean check, without the timing diffs.
>
> Advice appreciated,
>
> Brian
>
> Ref:
> [1] http://cran.r-project.org/doc/manuals/R-exts.pdf
>
> --
> Brian G. Peterson
> http://braverock.com/brian/
> Ph: 773-459-4973
> IM: bgpbraverock
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>



-- 
Gavin Simpson, PhD

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[Rd] timings for examples in R CMD check
Gavin Simpson