On Fri, May 13, 2016 at 05:37:35PM +0200, Gordon Ball wrote: > I don't have permissions for debian-med, nor am I a DM/DD, so I'm afraid > I haven't committed any patches or uploaded them, but a couple should be > attached here.
In any case I've added you to the Debian Med team to enable you commiting next time. > > A suggested patch (commited to SVN + team upload) would be great. > > My suggested patch for this is just to rm debian/tests/control (so the > test is still installed for manual running, but won't be autopkgtested). > CI will have to make do with the autodep8 load test (which should > hopefully appear before too long - the relevant version of autodep8 (>= > 0.5) is now in jessie-backports and will presumably make it to the CI > installation at some point. Done since last week in version 2.28.0-1. > >> r-bioc-cummerbund > >> ----------------- > >> > >> Both vignettes are patched (suppress_test_writing_to_usr.patch) removing > >> attempts to write to a readonly dir, but leaving subsequent code which > >> consequently fails (data hasn't been loaded). > >> > >> Possibly changing the patch to copy extdata from the installed package > >> and replace the `system.file` call with a local dir would let these run. > > > > A suggested patch (commited to SVN + team upload) would be great. > > Patch (git format-patch for the repository) is attached. It > suppress_test_writing_to_usr.patch, which removed some of the pre-amble > to each vignette with one which modifies the paths the vignettes check > for their data files. They should now build, but the example data has to > be copied to the pwd (run-unit-test has been updated to do this). I'll check the patch soon. Upgrade of the package is pending anyway but there are some missing preconditions for the new version. > >> r-bioc-genefilter > >> ----------------- > >> > >> Two vignettes (independent_filtering{,_plots}.Rnw) require knitr > >> (unpackaged), not Stangle for compilation. > > > > knitr is ITPed (#808155) but needs some dependencies itself. Its available now. > >> r-bioc-genomicalignments > >> ------------------------ > >> > >> I think this is a bug with the test from upstream. > >> test_readGAlignments.R :: test_read_GAlignments_BamViews creates a > >> temporary file, doesn't hold onto the file handle and then tries to read > >> it. Hence a race condition depending on whether R has yet > >> garbage-collected the reference and the file has consequently been > >> deleted first. > > > > Hoping for upstream to respond to my first mail. I might ping at > > end of the week with these more detailed information. > > I'm now less certain this is exactly the cause - it's still somehow > related to a tempfile/tempdir race, but I misunderstood the semantics of > tempfile() so the above is probably not exactly correct. > > > >> r-bioc-limma > >> ------------ > >> > >> Compared stdout of the test script to a saved copy. It's probably > >> sufficient to just run the script and test the exit code, since this > >> seems to fail on trivial differences. > > > > I might have a look. Needs to be updated anyway. > > Attached a replacement run-unit-test script which does this. I'll check this out. > >> r-bioc-shortread > >> ---------------- > >> > >> A bug somehow related to the package's class system, but I haven't > >> managed to identify a cause. > > > > I might ping upstream. > > Error disappeared in 1.30.0 Yep. > >> r-cran-doparallel > >> ----------------- > >> > >> Uses R CMD BATCH instead of R --no-save < filename to run tests, so all > >> the output is hidden in the CI output. Doesn't copy the test files to a > >> temporary dir so when they try and create output it fails due to read-only. > > > > (Hopefully) fixed in upload of new upstream version. > > > > Still appears present in 1.0.10. I think the test script needs to be > patched since it hardcodes an attempt to write a report to the directory > in which the package is installed. I'll try and write a patch for this. Fine. As I said you should be able to commit now. > In addition, a re-do of the r-bioc-snpstats run-unit-test is attached > (three vignettes should be blacklisted, but the current script only gets > two of them). I'll check soon. Thanks a lot for your input Andreas. -- http://fam-tille.de