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
I did not really try it, but perhaps setting _R_CHECK_TIMINGS_=false in your ~/.Renviron works? http://cran.rstudio.com/doc/manuals/r-release/R-ints.html#Tools Regards, Yihui -- Yihui Xie <xieyihui at gmail.com> Web: http://yihui.name On Wed, Sep 3, 2014 at 2:58 PM, 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
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 [[alternative HTML version deleted]]