[Bioc-devel] Preparing package release notes
robert.castelo at upf.edu
Sat Oct 22 19:16:44 CEST 2011
hi, thanks for the clarification, i do not completely understand one of
the "Example Changes" in the webpage of the link you give below,
concretely the one right before the last one.
how does one package within a 6-month devel period gets from 1.5.0 to
1.99.x? is it something that the developer is allowed to set
him(her)self in order to bump to a 2.0.0 release version later?
On 10/22/11 6:44 PM, Martin Morgan wrote:
> On 10/22/2011 09:39 AM, Robert Castelo wrote:
>> 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)
>> 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
>>> 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.
More information about the Bioc-devel