Changes in version 1.65.1                        

BUG FIXES

    o   Fix a few more logic expressions causing "the condition has length > 1" type issues

                       Changes in version 1.59.1                        

BUG FIXES

    o   Add multtest to dependencies to fix testing on daily build

                       Changes in version 1.51.1                        

USER VISIBLE CHANGES

    o   Move to mzML for example data and vignette following the removal of mzData support in mzR

                       Changes in version 1.47.1                        

BUG FIXES

    o   Thanks to Lain (INRAe) and Team W4M for this PR, fixing argument passing 
	to annotatedDiffreport()

                       Changes in version 1.45.2                        

BUG FIXES

    o   Thanks to Sebastien Hutinet @shutinet for fixing the adduct mass of CF3COOH. 
	Includes a corresponding change in unit tests. Closes #61 

                       Changes in version 1.43.2                        

BUG FIXES

    o   Change several && causing failure
	with _R_CHECK_LENGTH_1_CONDITION_ and _R_CHECK_LENGTH_1_CONDITION_

                       Changes in version 1.43.1                        

BUG FIXES

    o   Improve vignette layout and fix typos, thanks to Anton Nikolas Waniek

                       Changes in version 1.41.1                        

NEW FEATURES

    o   allow findAdducts alternative intval (thanks to Sunil Dhakad)

                       Changes in version 1.39.2                        

BUG FIXES

    o   Fix duplicate vignette name

                       Changes in version 1.33.3                        

BUG FIXES

    o   Fix getPeaklist not pulling rownames correctly, closing #22, thanks to Jan Stanstrup

                       Changes in version 1.33.2                        

BUG FIXES

    o   Fix getPeaklist, updated getReducedPeaklist(), Thanks to Kristian Peters

                       Changes in version 1.33.1                        

NEW FEATURES

    o   allow matchedfilter alternative intval in getPeaklist (J. Stanstrup)

    o   pass intval from Groupcorr to calcCaS (J. Stanstrup)

    o   getReducedPeaklist returns just one intensity per pspec (K. Peters) 

                       Changes in version 1.29.2                        

BUG FIXES

    o   Fix build issues and Vignette encoding (again)

    o   Fix build issues and Vignette encoding

                       Changes in version 1.29.1                        

NEW FEATURES

    o   Added function findIsotopesWithValidation 

                       Changes in version 1.27.2                        

BUG FIXES

    o   Fix imports in DESCRIPTION to avoid igraph overwriting xcms::group()

                       Changes in version 1.25.3                        

BUG FIXES

    o   Disabled Rmpi support and usage in the unit tests, 
	which lead to timeouts on BioC build farm

    o   Fix parallel processing with SNOW

                       Changes in version 1.25.2                        

USER VISIBLE CHANGES

    o   Disabled Rmpi support and usage on Windows

                       Changes in version 1.25.1                        

BUG FIXES

    o   Fix the import of the igraph methods, because it also exported a groups function. Solves the error "Error in x$membership : $ operator not defined for this S4 class"

                       Changes in version 1.23.2                        

BUG FIXES

    o   Fix bug in generateRules() if no ions matching the polarity are provided explicitly

                       Changes in version 1.23.1                        

BUG FIXES

    o   Fix bug in generateRules() with empty neutraladditions

                       Changes in version 1.20.1                        

NEW FEATURES

    o   Added possibility to pass cor_exp_th from annotateDiffreport to groupCorr()

                       Changes in version 1.20.0                        

SIGNIFICANT USER-VISIBLE CHANGES

    o   Version bump for BioC release

                       Changes in version 1.19.1                        

BUG FIXES

    o   Fixed bug in the generateRules function, where in the negative mode
	rules with polycharged positve ions are not created

                       Changes in version 1.15.5                        

SIGNIFICANT USER-VISIBLE CHANGES

    o   MPI Version of findAdducts() should now consume a lot less memory then before

                       Changes in version 1.15.4                        

NEW FEATURES

    o   findKendrickMass() now allows negative retention time windows,
	essentially allowing homologous series of losses

                       Changes in version 1.15.1                        

BUG FIXES

    o   Fix in findIsotopes, where sometime peak with huge m/z differences where annotated as isotopes

                       Changes in version 1.13.9                        

SIGNIFICANT USER-VISIBLE CHANGES

    o   findNeutralLossSpecs and findNeutral now accepts multiple masses and use correctly the ppm error

BUG FIXES

    o   Memory fix in groupCorr if all peaks are contained in one group.

                       Changes in version 1.13.8                        

SIGNIFICANT USER-VISIBLE CHANGES

    o   Add igraph package to the dependencies

BUG FIXES

    o   Fix for groupCorr with graphMethod="lpc", with a igraph library > 0.6

                       Changes in version 1.13.7                        

BUG FIXES

    o   Fixed problem in findIsotopes with a previous grouped single sample xcmsSet

                       Changes in version 1.13.6                        

BUG FIXES

    o   Fixed problem in findAdducts where higher nM+x annotations were erroneous deleted

    o   Fixed problem in combinexsAnnos, which produces a "subscript out of bounds " error

                       Changes in version 1.13.5                        

BUG FIXES

    o   Fixed problem "Error in data.frame(...)" in findAdducts when using polarity = negative