[Bioc-devel] Preparing package release notes

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?

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.