[Bioc-devel] Preparing package release notes

[Martin Morgan]

Hi Gordon, Julie, and others...

On 11/02/2011 07:18 AM, Zhu, Lihua (Julie) wrote:
> Martin,
>
> The inst/NEWS text file in the ChIPpeakAnno package is not included on the
> news page either. Thanks!
>
> Best regards,
>
> Julie
>
>
> On 11/2/11 2:55 AM, "Gordon K Smyth"<smyth at wehi.EDU.AU>  wrote:
>
>> Hi Martin,
>>
>> I prepared a file inst/NEWS.Rd in the limma package, but it isn't included
>> on the Bioc 2.9 NEWS page:
>>
>>     http://www.bioconductor.org/news/bioc_2_9_release/
>>
>> I notice that the same thing is true for other packages including cqn and
>> geneplotter, i.e., the packages contain valid NEWS.Rd files that include
>> the latest release but which haven't been captured on the release html
>> page.
>>
>> Have we made a mistake, or has the query run omitted the NEWS.Rd files?

Yes 'we' have made a mistake, but in this case it is me; should be 
updated now, but please let me know if there are remaining omissions / 
errors.

Thank you for your patience,

Martin

>>
>> Best wishes
>> Gordon
>>
>>
>>
>> [Bioc-devel] Preparing package release notes
>> Martin Morgan mtmorgan at fhcrc.org
>> Fri Oct 21 23:45:19 CEST 2011
>>
>> 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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