[Bioc-devel] spring cleaning -- errors, warnings and NEWS

Martin Morgan mtmorgan at fhcrc.org
Mon Mar 1 17:35:00 CET 2010


Hi Bioc Developers and Maintainers --

Now is a good time to address the various errors and warnings showing up
on the daily build reports

  http://bioconductor.org/checkResults/2.6/bioc-LATEST/

Many are documentation inconsistencies, and the error or warning
messages point toward possible solutions. Feel free to post here with
any hard-to-resolve issues.

Many packages contain a NEWS file, either in the package base directory
(e.g., Biobase/NEWS) or in the inst/ directory. These are viewable in R,
once the package is installed, using news(), e.g.,

> news(Version > 1.4, "ShortRead")
Changes in version 1.5:

SIGNIFICANT USER-VISIBLE CHANGES

    o   levels(strand(aln)) is c("+", "-", "*") (was c("-", "+", "*"))

NEW FEATURES

    o   Optionally retrieve multiplex bar code, paired read number, and
    id from SolexaExport (contribution from Nicolas Delhomme)

    o   renew() and renewable() provide an interface to updating
    ShortRead instances

    o   srapply checks for and uses multicore

    o   readIntensities supports Illumina RTA '.cif' / '.cnf' files

BUG FIXES

    o   readIntensities type="IparIntensity" correctly handles multiple
    tiles

NEWS files can be a very useful way of letting users know about changes
to your package. I encourage you to add a NEWS file if one does not
already exist. And if you have added a NEWS file, you might be surprised
to find that news() doesn't print out as nicely as you might hope,
instead displaying a data.frame with a very wide fourth column. The
correct format is described in ?news, and the main stumbling blocks I've
encountered include

* No lines like

CHANGES IN VERSION 1.5

to indicate which version the NEWS applies to. I'm numbering my versions
to be consistent with ShortRead's DESCRIPTION file.

* Heading with no content, e.g., in

NEW FEATURES

BUG FIXES

    o fixed a bug

The 'NEW FEATURES' heading has no items, and this confuses the parser.

* Unfortunate use of white space. For instance, tab characters may not
be expanded correctly, and in individual items spanning several lines
the continuation line should be indented to the bullet (the lower case 'o')

    o this is an item entry that spans several
    lines

Martin
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



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