[Bioc-devel] Preparing package release notes

Martin Morgan mtmorgan at fhcrc.org
Sat Oct 22 18:44:37 CEST 2011

On 10/22/2011 09:39 AM, Robert Castelo wrote:
> 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

Hi Robert --

The release is associated with a 'version bump' that takes x.y.z to 
x.y+1.0 in 'release' and x.y+2.0 in 'devel' so 1.9.9 becomes 1.10.0 in 
release, 1.11.0 in devel. See 
http://bioconductor.org/developers/version-numbering/ (I'll add your 
case shortly...)


> 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:
>> 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.
>> 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.

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