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>