Merge branch 'master' (v0.99.5) into local-hedgehog (V0.99.4)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72180 bc3139a8-67e5-0310-9ffc-ced21a209358
removing old Rd files and Deprecating renamed functions

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72279 bc3139a8-67e5-0310-9ffc-ced21a209358
removed updateClass.Rd and deprecated function test

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72280 bc3139a8-67e5-0310-9ffc-ced21a209358
vignette changes for compatibility with knitr 1.0

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72560 bc3139a8-67e5-0310-9ffc-ced21a209358
local installation description

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72562 bc3139a8-67e5-0310-9ffc-ced21a209358
README.md udpate

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72563 bc3139a8-67e5-0310-9ffc-ced21a209358
fixed installation instructions

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72564 bc3139a8-67e5-0310-9ffc-ced21a209358
fixed deps and pRolocdata install

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72565 bc3139a8-67e5-0310-9ffc-ced21a209358
knitr 1.0 compatibility

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72566 bc3139a8-67e5-0310-9ffc-ced21a209358
fixing conflicts

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72567 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@72570 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@73388 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@73557 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@73571 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@73606 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@73751 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@73852 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@74580 bc3139a8-67e5-0310-9ffc-ced21a209358
Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@74670 bc3139a8-67e5-0310-9ffc-ced21a209358
new addMarkers function

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pRoloc@74694 bc3139a8-67e5-0310-9ffc-ced21a209358