bumped package version numbers prior to creating 2.9 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
version bump for start of 2.10 development cycle

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
remove backward compatibility

introduced in version 0.99.2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@61993 bc3139a8-67e5-0310-9ffc-ced21a209358
vignette: rtracklayer export disabled

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@61994 bc3139a8-67e5-0310-9ffc-ced21a209358
correct removal of backward compatibility

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@62135 bc3139a8-67e5-0310-9ffc-ced21a209358
man/plot-methods: add aliases for 'plot,*,ANY' methods

missing aliases caused warning during 'R CMD check':
"
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'plot' and siglist 'TssData,ANY'
  generic 'plot' and siglist 'TssNorm,ANY'
  generic 'plot' and siglist 'TssResult,ANY'
"

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@63659 bc3139a8-67e5-0310-9ffc-ced21a209358
vignettes: move vignette files from 'inst/doc/' to 'vignettes/'

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@63660 bc3139a8-67e5-0310-9ffc-ced21a209358
first version bump prior to creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
bumped version numbers after creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
man: correct 'mc.cores' argument

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@65731 bc3139a8-67e5-0310-9ffc-ced21a209358
replace 'multicore' with 'parallel' package
DESCRIPTION: correct version number for commit '17a12a3af8'

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@65732 bc3139a8-67e5-0310-9ffc-ced21a209358
man/normalize-methods.Rd: fix 'cores' argument for multicore

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@65733 bc3139a8-67e5-0310-9ffc-ced21a209358
The 'annotation' and 'annotation<-' generics have been moved from Biobase
(2.17.8) to BiocGenerics (0.3.2). All packages that 'setMethods' on these
generics import them from BiocGenerics.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@69535 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump all packages before creating 2.11 branch.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
bump package versions after creating 2.11 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
bump y of x.y.z version number for BioC 2.12 release

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
Bump y in version x.y.z to odd number in devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
switch from 'multicore' to 'parallel'

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@78712 bc3139a8-67e5-0310-9ffc-ced21a209358
bump version number for last commit

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/TSSi@78713 bc3139a8-67e5-0310-9ffc-ced21a209358