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)

CHANGES IN VERSION 1.29.2
-------------------------

BUG FIXES

    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

CHANGES IN VERSION 1.25.3
-------------------------
BUG FIXES

    o Fix parallel processing with SNOW

CHANGES IN VERSION 1.25.2
-------------------------

USER VISIBLE CHANGES:
+ 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

