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