[Bioc-devel] Preparing package release notes

[Robert Castelo]

Martin,

i see in the example below that Rsamtools in its NEWS file is guessing 
that its next release version is going to be 1.6.0 which is pretty 
straightforward given that its current devel is 1.5.76. however, the 
package i maintain (qpgraph) has currently 1.9.x devel version and i was 
wondering whether the next release is going to be 1.10.0 or 2.0.0, is 
there any policy that allows one to know in advance when the first digit 
in the release version is also bumped ? (in order to put the proper 
version in the NEWS file)

thanks,
robert.

On 10/21/11 11:45 PM, Martin Morgan wrote:
> 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 "1.5.76", so we'll
> get news with
>
>  > utils::news(Version >= "1.5.0", "Rsamtools")
>
> resulting in
>
> Changes in version 1.6.0:
>
> NEW FEATURES
>
> o TabixFile, indexTabix, scanTabix, yieldTabix index (sorted,
> compressed) and parse tabix-indexed files
>
> o readBamGappedReads(), bamFlagAsBitMatrix(), bamFlagAND()
>
> o Add use.names and param args to readBamGappedAlignments();
> dropped which and ... args.
>
> o PileupFiles, PileupParam, applyPileup for visiting several BAM
> files and calculating pile-ups on each.
>
> o Provide a zlib for Windows, as R does not currently do this
>
> o BamFileList, BcfFileList, TabixFileList, FaFileList clases
> extend IRanges::SimpleList, for managings lists of file
> references
>
> o razfFa creates random access compressed fasta files.
>
> o count and scanBam support input of larger numbers of records;
> countBam nucleotide count is now numeric() and subject to
> rounding error when large.
>
> o Update to samtools 0.1.17
>
> o asBcf and indexBcf coerces VCF files to BCF, and indexes BCF
>
> o Update to samtools 0.1.18
>
> o scanVcf parses VCF files; use scanVcf,connection,missing-method
> to stream, scanVcf,TabixFile,*-method to select subsets. Use
> unpackVcf to expand INFO and GENO fields.
>
> BUG FIXES
>
> o scanBam (and readBamGappedAlignments) called with an invalid or
> character(0) index no longer segfaults.
>
> o scanBcfHeader parses values with embedded commas or =
>
> o scanFa fails, rather than returns incorrect sequences, when file
> is compressed and file positions are not accessed sequentially
>
> o scanBcf parses VCF files with no genotype information.
>
> o scanBam called with the first range having no reads returned
> invalid results for subsequent ranges; introduced in svn r57138
>
> o scanBamFlag isPrimaryRead changed to isNotPrimaryRead,
> correctly reflecting the meaning of the flag.
>
>
> See ?news for more detail. We will collate these files no later than
> Friday, October 21.