[Bioc-devel] Preparing package release notes

[Zhu, Lihua (Julie)]

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?
> 
> 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.