Hi, I try to follow all the best practices but sometimes I end up relying on the Bioc nightly build.
Anyhow, I personally use r-travis** for quick checks to detect broken commits instead of running R CMD check/build on my laptop. This way I can submit a new commit that fixes a broken commit before the Bioc nightly build in about the same time as using my laptop. r-travis doesn't always work as Bioc might have newer versions of dependencies or other issues (cache, timing, installation of deps), but it helps most of the time. A scenario where I definitely rely on the Bioc nightly build is when I can't reproduce the error/warning on my machine (with the latest setup). For example, Windows issues***. Note that I do run a quick local test of whatever bug I'm solving, but I might miss how my changes affected another unit test. Best, Leonardo ** Example setup https://github.com/leekgroup/derfinderPlot/blob/master/.travis.yml *** You can also use r-hub for testing in other OS including Windows but maybe not with the R version that bioc-devel needs and/or without being able to set useDevel(). Example https://github.com/LieberInstitute/jaffelab/blob/master/.travis.yml#L17-L18 I've only used it for that non-bioc package. On Wed, Feb 7, 2018 at 9:51 AM, Martin Morgan <martin.mor...@roswellpark.org> wrote: > > > Bioc developers! > > I've been exploring the Bioconductor nightly builds > > http://bioconductor.org/checkResults/ > > a bit using this in-development package. > > https://github.com/mtmorgan/BiocBuildReports > > This > > rpt <- report() > filter_recent(rpt) %>% print(n = n()) > > summarizes the packages changed in the 24 hours before the current build > snapshot, and their fate on the nightly builds > > > filter_recent(rpt) %>% print(n=nrow(.)) > # A tibble: 18 x 5 > package buildsrc checksrc push txt > <chr> <fct> <fct> <fct> <chr> > 1 AllelicImbalance ERROR skipped skipped skipped > 2 ChIPpeakAnno ERROR skipped skipped skipped > 3 GenomicScores ERROR skipped skipped skipped > 4 genphen ERROR skipped skipped skipped > 5 metavizr ERROR skipped skipped skipped > 6 QUBIC ERROR skipped skipped skipped > 7 Repitools OK ERROR skipped skipped > 8 rtracklayer OK WARNINGS UNNEEDED same version exists in > interna… > 9 genoset OK WARNINGS YES new version is higher than in > … > 10 IRanges OK WARNINGS YES new version is higher than in > … > 11 LOLA OK WARNINGS YES new version is higher than in > … > 12 DAPAR OK OK UNNEEDED same version exists in > interna… > 13 AnnotationHubData OK OK YES new version is higher than in > … > 14 BEARscc OK OK YES new version is higher than in > … > 15 ChemmineR OK OK YES new version is higher than in > … > 16 DESeq2 OK OK YES new version is higher than in > … > 17 Onassis OK OK YES new version is higher than in > … > 18 synergyfinder OK OK YES new version is higher than in > … > > A couple of things strike me about this. > > - All the packages with 'ERROR' in the buildsrc or checksrc column failed > to propagate because the commit, or a previous version, does not build or > check. It is not a very productive development model to push broken commits > to git.bioconductor.org, especially if the developer doesn't realize that the > commits are broken. The best practice is to build and check packages locally, > and then commit. > > R CMD build <YourPackage> > R CMD check <YourPackage_<version>.tar.gz > > An even more robust approach is to clone the repository locally, so that the > build and check are against only the committed changes and not miscellaneous > files or versions hanging out in your source directory > > cd /tmp > git clone /path/to/<YourPackage git> > R CMD build <YourPackage> > ... > > I would not suggest using devtools during this final stage; the build system > doesn't use devtools, as devtools has its own ideas about options etc with > which to build packages. The very careful would also use the build and check > options found on the build report of each package, e.g., from > > > http://bioconductor.org/checkResults/3.7/bioc-LATEST/rtracklayer/malbec2-buildsrc.html > > one might > > R CMD build --keep-empty-dirs --no-resave-data rtracklayer > > A common problem is that packages are built and checked locally using the > wrong version of R and / or Bioconductor -- commits to the devel branch > should be against the devel version of Bioconductor and (for the current > release cycle) the devel version of R. > > http://bioconductor.org/developers/how-to/useDevel/ > > - two packages (rtracklayer, DAPAR) built and checked successfully, but did > not propagate to the public repository. This is because they did not bump > their version number according to policy > > http://bioconductor.org/developers/how-to/version-numbering/ > > While there might be reasons for pushing commits to Biocoductor without > version bumps, this usually seems to be an oversight on the developer's part. > Basically, every public version of a package should have a different version > -- there is no shortage of version numbers. > > Martin > > > This email message may contain legally privileged and/or... > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
