[R] Should I wrap more package examples in \dontrun{} ?

[Terry Therneau]

To give a specific example, the simple code for my test suite is given at the bottom of 
this message.  A simpler (simple-minded maybe) approach than creating a new packge for 
testing.  I now run this on the survival package every time that I submit a new version to 
CRAN.  It takes a while, since there are over 200 dependencies.  It creates a file 
"progress" containing each package name as it is run folllowed by either "Ok" or "Failed" 
along with a directory "tests" containing the results.  Almost every run generates 1-3 hits.
   I have not automated this further because many runs also lead to exceptions, often 
packages that won't load because I don't have some ancillary piece of software installed 
that they depend on.  (I can't seem to get JAVA set up sufficient to satisfy everyone, for 
example, and have very low motivation to work harder at the task.)  And a small number 
have made it to the bad actors "I give up don't even bother to test" list.

Note that any package I want to fully test was installed on this local machine using
     install.packages("xxx", dependencies=TRUE, INSTALL_opts="--install-tests")
where "xxx" is the name of the package.

Terry T.


On 09/04/2013 05:00 AM, r-help-request at r-project.org wrote:
> n 03/09/2013 1:53 PM, Hadley Wickham wrote:
>>> >  >  As a user of your package, I would find it irritating if example(foo) didn't
>>> >  >  run anything.   It would be more irritating (and would indicate sloppiness
>>> >  >  on your part) if the examples failed when I cut and pasted them.  These both
>>> >  >  suggest leaving the examples running.
>>> >  >
>>> >  >  As the author of your package, it sounds as though you find it quite
>>> >  >  irritating when other authors break your code.
>>> >  >
>>> >  >  Isn't the right solution to this to work with the other package authors to
>>> >  >  come up with code that is unlikely to break?  If that's not possible, then
>>> >  >  maybe don't use those packages that cause you trouble.
>> >
>> >  It was my understanding that package authors are responsible for not
>> >  breaking other CRAN packages without warning.  For example, before I
>> >  release a new version of plyr or ggplot2, I run R CMD check on every
>> >  package that depends on my package. I then let the maintainers know if
>> >  something is broken - sometimes it's because I introduced a bug, and
>> >  other times it's because I'm enforcing a stricter check than I did
>> >  previously
> It sounds as though you're doing the right thing.   Can you describe how
> you determine the set of packages to check, and how you do your checks?
> It would be great if we could convince everyone to follow those steps.
>
> Duncan Murdoch
tmt% cat checkdeps.R
require("tools")

# First set a repository to look at
#chooseCRANmirror()     # do it graphically
#chooseBioCmirror()
options(repos=c(CRAN="http://streaming.stat.iastate.edu/CRAN/",
                 BioC="http://bioconductor.org/packages/2.11/bioc/"))

# This function is provided by Uwe Wigges
reverse <-
function(packages, which = c("Depends", "Imports", "LinkingTo"),
          recursive = FALSE)
{
     description <- sprintf("%s/web/packages/packages.rds",
                            getOption("repos")["CRAN"])
     con <- if(substring(description, 1L, 7L) == "file://")
         file(description, "rb")
     else
         url(description, "rb")
     on.exit(close(con))
     db <- readRDS(gzcon(con))
     rownames(db) <- NULL

     rdepends <- package_dependencies(packages, db, which,
                                      recursive = recursive,
                                      reverse = TRUE)
     rdepends <- sort(unique(unlist(rdepends)))
     pos <- match(rdepends, db[, "Package"], nomatch = 0L)

     db[pos, c("Package", "Version", "Maintainer")]
}

survdep <- reverse("survival")[,1]

# I don't want to check coxme (since I maintain a more up to date
# local copy), and there are a few known bad actors
avoid <- c("coxme", "STAR", "compareGroups")
survdep <- survdep[is.na(match(survdep, avoid))]

# Some packages may have failed to install, don't test those
inplace <- installed.packages()[,"Package"]  #ones we already have
missed <-  is.na(match(survdep, inplace))
if (any(missed)) {
     message("Unable to load packages ",
             paste(survdep[missed], collapse=", "), "\n")
     survdep <- survdep[!missed]
}

# Do the long list of tests
unlink("progress")
unlink("tests", recursive=TRUE)
system("mkdir tests")
pfile <- file("progress", open="write")
for (testpkg in survdep) {
     z <- testInstalledPackage(testpkg, outDir="tests")
     cat(testpkg, c("Ok", "Failed")[z+1], "\n", file=pfile)
}