[Bioc-devel] Preparing package release notes

[Zhu, Lihua (Julie)]

Martin,

It works perfectly now. Many thanks for your help!

Best regards,

Julie


On 11/2/11 2:28 PM, "Martin Morgan" <mtmorgan at fhcrc.org> wrote:

> 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.
>> 
>> 
>