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Created with Raphaël 2.2.09Dec229Nov18117Oct30Sep12May10311Apr28Mar220Feb1815121110985328Jan222120191815118619Dec181716149127Nov22Oct1413520Sep172129Aug24428Jul2423212019171614Jun4218May1716Apr31Mar24181Feb28Jan2721201919Dec18131285425Nov2413111023Oct222113715Sep822Jul720Jun1626May830Apr2927242322117627Mar262411107418Feb1711106527Jan14916Dec425Nov211328Oct242317144223Sep1916131211954229Aug282730Jul2419181512653227Jun1828May722Apr19171311109854326Mar212019151484127Feb26211823Jan141Oct7Sep328AugPubchem switch to httpsMerge branch 'master' into s4powerfix in xcms workflow (the "standard" case 1 file for each cpdID was incorrect)fixed empty molfile issue (#165), was stray line in createMolfilefixed empty molfile issue (#165), was stray line in createMolfileadded filter for annotation and alternative accession number generationUpdate webAccess.R - PubChem has moved to httpsFixes in leMsMs.RAW: enforce polarity for switching-mode files; fixed precursor filling bug that failed for MS2 before first MS1 scanAdapted Erik's parseMassBank to parse into RmbSpectrum2 objects (retaining all information from the record)Adding option to treat unknown (level 5) masses as "charged" (default) or "neutral", as per #42.bump x.y.z versions to odd 'y' after creation of 3_4 branchbump x.y.z versions to even 'y' prior to creation of 3_4 branchMerge branch 'master' into s4powerMerge pull request #164 from sneumann/masterCopied code from splashR-0.0.3bump version after creating 3.3 branchBump versions prior to creation of 3.3 branchPush current fixed versionCactus changed their interface to https-onlyReworked isotopic annotationFixed SPLASH appearing in PKIsotopic annotation a bit betterRemoved global variable and modularized isotopic annotation furtherfix bugFixed bug in Recalibration if more than 1 MS1-peak falls withing the specified m/z ppm boundariesEliminated the _FORMULATAG workaround. Also, time for a version bump :)Thanks to https://github.com/lgatto/MSnbase/commit/3746a473aa0cdcc1eb7088812534efeb276fda53 polarity is now in Spectrum2 objects. Update to feed the data into there from the acquisition mode (note: even where present, data from mzR is unreliable and often -1)* Fixes in mb record generationMerge remote-tracking branch 'origin/master' into s4powerSupport for SMILES in RmbSpectraSetMore NULL-tolerance and independence during mbWorkflow. Fix for doublepeaks.Another selectPeaks fixremoved retrieval argument from findMsMsHRFixed fillback and additionalPeaks readditionRevamped mbWorkflow completely, cf #153:Fix selectPeaks methods again... (proper treatment of ... arguments)* Added fillback functionality: write results from reanalysis and peak filtering back into the spectrafixes #157Fixed bug that occurs under special conditions in workflow step 2Fixed some minor bugs