Fixes if XCMS did not find any peaks

Use an empty peaklist if XCMS does not detect any peak to avoid an error message downstream in the workflow

Added recalibrate.mean and recalibrate.linear (untested)

Option to circumvent formula assignment; fixes for zero data point; more settings in default ini file; progress bar handling slightly changed (subject to more change to fit with Shiny)

* Changed handling of settings in leMsMs.R and leMsMsRaw.R such that parameters can be passed more readily to functions (i.e. settings are now only default arguments to functions) createMassBank.R still handles settings the old way.
* Added precursor scan filler to handle mzML files without precursor information.

Conflicts:
	R/createMassBank.R

Conflicts:
	DESCRIPTION
	NAMESPACE
	R/createMassBank.R
	R/leMsMs.r
	R/leMsmsRaw.R
	R/parseMassBank.R
	R/validateMassBank.R
	R/webAccess.R
	inst/unitTests/runit.MS2.test.R
	man/parseMassBank.Rd
	man/smiles2mass.Rd
	man/validate.Rd

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RMassBank@78125 bc3139a8-67e5-0310-9ffc-ced21a209358

to avoid overly long lines in PDF

Authors