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