Removed vignettes/Makefile as it was not being used and caused problems
with R-alpha. Fixed problems preventing crlmmDownstream.tex from building.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@74237 bc3139a8-67e5-0310-9ffc-ced21a209358
Update crlmmDownstream vignette
merge with collab

* collab:
  Update crlmmDownstream vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@74572 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/VanillaICE@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/VanillaICE@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
bump versions prior to creating BioC 2.13 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
bump version after release branch has been created

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
bump version. put date tag in description

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/VanillaICE@83232 bc3139a8-67e5-0310-9ffc-ced21a209358
Need drop=FALSE in generatorViterbi when sex chromosomes present
Fix indentation
v. 1.25.3 remove tab-spacing on unit test files
created git-svn bridge
1.25.4 merged with collab