[Bioc-devel] Preparing package release notes

[Martin Morgan]

On 10/22/2011 10:16 AM, Robert Castelo wrote:
> 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?

yes, if the developer has made significant changes that merit a 'version 
2', then they would set the version number to 1.99.0, 1.99.1, etc. and 
at release it would become 2.0.0.

Martin

>
> robert.
>
> On 10/22/11 6:44 PM, Martin Morgan wrote:
>> 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...)
>>
>> Martin
>>
>>> 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.
>>>
>>
>>
>


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