On Thu, Apr 28, 2016 at 10:42:45AM +0200, Gordon Ball wrote: > > me. My only idea is to rather use > > > > pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'` > > > > and so I try this even if I think this is equivalent. > > Hmm, yes. I can't obviously see why this fails. (Aside - `tr A-Z a-z` > works just as well, but as far as I can see both are valid syntax).
Anyway - I think those packages I uploaded for other reasons (new upstream version) and added quotes are now passing the test so I'll fix this. > However, since the working dir for the test is the root of the extracted > source package, we should be able to extract the R and debian package > names directly rather than hardcoding or deriving them: > > rpkg=$(grep-dctrl -s Package -n '' DESCRIPTION) > dpkg=$(grep-dctrl -s Package -n '' debian/control) > > and in fact, skip finding tests and vignettes in the installed > filesystem and just find them in the source package: tests/*.R ; > vignettes/*.Rnw - in which case we don't need to know the package R or > debian names. I confirm that if you use the script for CI *only* this would work nicely. However, I consider it a good idea to provide the user with some test case / example use and thus I always put the script into /usr/share/doc/<pkgname> where grep-dctrl does not work. On the other hand I could check the directory name if all other means to calculate the package name might fail. > As discussed in the autodep8 thread, it would definitely be good to > extend the implicit test to running tests/*.R and vignettes/*.Rnw/md, > and clearly this would avoid duplication of a large number of similar > run-unit-test files (although I think we should wait a while and see > what happens with the simple autodep8 test already added and see how > that works out first). +1 > > That's even more strange. I like to just insert the original CRAN > > spelling and calculate the Debian package from mit but tr does not > > seem to do a reliable job and I wonder why. > > The version with quotes in r-bioc-cummerband now seems to work (or at > least, it gets further and finds a different error - > vignettes/cummeRbund-example-workflow.Rnw appears not to load the > library before using functions from it, which I suspect is a package bug). I need to check this ... > >> r-bioc-aroma.light: attempts install.packages > > > > I don't understand this one. > > The culprit appears to be R.utils::use(packagename) buried in various > functions. It attempts to install if the package isn't available. It > fails trying to load/install princurve (unpackaged, in the Suggests field). Just found this a couple of minutes ago and uploaded a fix (hack) stripping the test past the attempt to use princurve. > >> r-bioc-genomicalignments: min_overlap_score bug > >> r-bioc-genomicranges: min_overlap_score bug > > > > I don't understand this type. > > Not sure, but this has disappeared in today's resuults. I suspect some > of the bioconductor packages might need tighter dependencies on each other. Something remains wrong here. I'll upgrade to latest version and check again. > >> r-cran-dplyr: R version mismatch (built under 3.3.0) > > > > Huhu, what's that??? > > It looks like this is not the cause of failure, just a warning (the > immediate failure in this case is that the package doesn't depend on > r-cran-rcpp (necessary to load the namespace, not just run tests). > However, it also warns that it was built by R 3.3.0 - presumably a > binary upload by someone with an experimental R package on their system. > The package is loadable at least after r-cran-rcpp is installed. Fixed in recent upload. > >> r-cran-futile.logger: error in run-unit-test script > > > > What kind of error? Runs fine for me if I call it directly. > > > > The error in the CI run is "find: missing argument to -exec". Maybe > missing a trailing \; ? Grrrr, you are right. Fixed. > >> r-cran-lambda.r: error in run-unit-test script > > > > What kind of error? Runs fine for me if I call it directly. > > > Same as r-cran-futile.logger above it appears. Whether it errors is > maybe sensitive to the CWD it is run from since it does `find .`? Fixed cut-n-pasto. > >> r-cran-magrittr: error in run-unit-test script > > > > What kind of error? Runs fine for me if I call it directly. > > > > find -exec again. Fixed cut-n-pasto > >> r-cran-r.methodss3: bad subsitution in run-unit-test > > > > Waiting for confirmation that quotes in tr call are helpful. Fixed in new upstream version upload. > >> r-cran-r.utils: error in run-unit-test > > > > What kind of error? Runs fine for me if I call it directly. > > > > Looks like the delete at the end (rm -f $ADTTMP/*) fails since some of > the targets are directories (missing -r) Ahhh, stupid. Fixed in recent upload of new upstream version. > And thanks for fixing so many of these so quickly You are welcome. I'm keen on getting the tests really functional so its a pleasure to support your attempt. > - hopefully it'll look > in much better shape in a few days and we can see if CI is actually > doing its job and identifying some real errors. Yes. > I'll have a better look at the "?" ones. Thanks again Andreas. -- http://fam-tille.de