[Bioc-devel] Preparing package release notes

Gordon K Smyth smyth at wehi.EDU.AU
Wed Nov 2 07:55:58 CET 2011

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:


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 

Have we made a mistake, or has the query run omitted the NEWS.Rd files?

Best wishes

[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:


      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.


      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.
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793

The information in this email is confidential and intend...{{dropped:4}}

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