[Bioc-devel] Nightly builds

[Martin Morgan]

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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