timings for examples in R CMD check

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
<mailto: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
    <http://cran.r-project.org/doc/manuals/R-exts.pdf>