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List:       bioc-devel
Subject:    [Bioc-devel] Preparing package release notes
From:       Dan Tenenbaum <dtenenba () fhcrc ! org>
Date:       2012-09-26 22:32:32
Message-ID: CAF42j21V2Nqq+CrsEEg0D1aepcap9JwhXYM1mjTNNdL80EFvuA () mail ! gmail ! com
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Package developers --

Each Bioconductor release is accompanied by release notes that mention
new packages and other significant project developments. For the
forthcoming release we would also like to include release notes for
individual packages, so that users have an easy way to survey changes
in their favorite packages.

To have your package release notes made available in the Bioconductor
release notes, please arrange for your package to include a NEWS.Rd or
NEWS file that can be parsed by the utils::news function. We'll run
this command over all packages, using a 'query' argument that captures
all updates more recent than the start of the current release cycle.
For instance, Rsamtools in the devel branch is at version "1.9.30", so
we'll get news with

> utils::news(Version >= "1.9.0", "Rsamtools")

resulting in

Changes in version 1.10.0:

NEW FEATURES

    o   BamFile and TabixFile accept argument yieldSize; repeated calls
      to scanBam and scanTabix return successive yieldSize chunks of
      the file. readBamGappedAlignments, VariantAnnotation::readVcf
      automatically gain support for yield'ing through files.

BUG FIXES

    o   close razip, bgzip files when done

    o   bamReverseComplement<- failed to return the updated object

    o   scanBcfHeader works on remote files

    o   scanBamFlag isValidVendorRead deprecated in favor of
      isNotPassingQualityControls

    o   allow asBam to work without warnings on header-only SAM files

See ?news for more detail. We will collate these files no later than Monday,
October 1.

Thanks,
Dan

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