Gavin, You were correct. Operator error.
My tests/Examples directory contained both a ‘PerformanceAnalytics-Ex.Rout’ and a ‘PerformanceAnalytics-Ex.Rout.save’ file. Corrected now, and check shows * checking examples ... OK Thanks for the help. Brian On 09/03/2014 03:36 PM, Gavin Simpson wrote:
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 <br...@braverock.com <mailto:br...@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>
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