fix the error in .qaCheck caused by more strict operation on empty factors of new R

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/QUALIFIER@71791 bc3139a8-67e5-0310-9ffc-ced21a209358
merge from labkey branch and remove labkey-specific routines
restore the NAMESPACE and DESCRIPTION from ITN branch
move the ITN-specific logic (parsing TubeID from FCS name) from saveToDB to a hidden function .parseTubeID thus keep the main framework generic
1.change the logic to tell whether a node is a root node 2.deal with boolgate in getQAStats close #27
close #28
it now tries to merge the pData from GatingSet with external meta data. The pData of gatingSet has to contain at least one column:'name',which is FCS filename.close #29
bump version
Merge commit '6667a9c1192f2894735e29f4fc7f1e0a2a992ae6' into trunk
write .parseCond routine to recursively parse the conditional variables to handle the ` symbol in a more generic way. issue #30
Fixes #32
DESCRIPTION : version bump to 1.3.4

NAMESPACE : exporting of writeGStbl removed

AllFunctions.R :
 qaPreprocess : gsId needed to be included as a parameter and gs.name is no longer an input parameter (provided from the UI)

 saveToDB :
  -gsId needed to be included as a parameter, hence its generation is removed
  -gs.name is no longer an input parameter (provided from the UI)
  -id variable is no longer generated in the annoData (supposed to be present already in the gating set's pData)
  -reference to gstbl data frame removed

db.R :
  -writeGStbl() method removed, because there is not longer gstbl table
  -writeProjections() method removed
  -added fixed schemaName param's value: 'opencyto_quality_control'

qaCheck.R : setting of gsid removed in clearCheck() method

qaReport.R : disallowed NULL for gsid in qaWrite.summary() method, setting of gsid removed in the same method and qaWrite.task

utils.R : setting of gsid removed in .TubeNameMapping() method

zzz.R : creation of gstbl data frame removed

qaCheck.R : methods from db.R adjusted to reflect the new signatures

qaPreprocess.R : adjusted according to all of the previous changes
AllFunctions.R : matchNode() fix

Merge branch 'trunk' into labkey

Conflicts:
	DESCRIPTION
	NAMESPACE
	R/AllFunctions.R
	R/db.R
	R/utils.R
	examples/example.R
	labkey/qaCheck.R
	labkey/qaPreprocess.R
	labkey/qaReport.R
Minor fix to the NAMESPACE file: methods that are assignments must be enclosed in quote marks, otherwise R CMD INSTALL fails