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
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