CHANGES IN VERSION 1.12.1
-------------------------
 o updated readMSData test unit to ignore object@.__classVersion__
   that fails with latest R/Bioc versions [2014-04-18 Fri]

CHANGES IN VERSION 1.12.0
-------------------------
 o Version bump for Bio 2.14

CHANGES IN VERSION 1.11.14
--------------------------
 o update dependency to R >= 3.1 [2014-04-05 Sat] 

CHANGES IN VERSION 1.11.13
--------------------------
 o Document [get|grep]Ecols in io vignette [2014-03-31 Mon]
 o typo in readMSnSet man [2014-03-31 Mon]
 o updated affiliation in vignettes [2014-03-31 Mon]

CHANGES IN VERSION 1.11.12
--------------------------
 o Fixed a bug in readMzTabData reported by Hendrik Weisser [2014-03-26 Wed]

CHANGES IN VERSION 1.11.11
--------------------------
 o precomputed msx test data now has id data [2014-03-25 Tue]
 o quantitation unit tests [2014-03-25 Tue]
 o quantify method now accepts label-free methods [2014-03-25 Tue]

CHANGES IN VERSION 1.11.10
--------------------------
 o import mzID [2014-03-20 Thu]
 o dummyiTRAQ id extdata [2014-03-21 Fri]
 o add addIdentificationData method for MSnExp and MSnSet [2014-03-21 Fri]
 o using data from pRolocdata (was pRoloc) [2014-03-23 Sun]
 o added removeNoId,MSnExp,MSnSet methods [2014-03-23 Sun]
 o added idSummary,MSnExp,MSnSet methods [2014-03-24 Mon]
 o Not generating different sample per file when reading raw
   data. pData(.) now has systematically 1 row if not specifically
   provided by the user. A message is also reported by validity,pSet
   if row(pData(.)) > 1. [2014-03-24 Mon]
 o NAnnotatedDataFrame now has default multiplex 1 [2014-03-25 Tue]
 o NAnnotatedDataFrame unit tests [2014-03-25 Tue]

CHANGES IN VERSION 1.11.9
-------------------------
 o write.exprs can have fDataCol or fcol (for consistence) [2014-03-17 Mon]
 o Fixing bug in combineFeatures(..., is.character(groupBy)) [2014-03-19 Wed]
 o fixed combineFeatures [2014-03-20 Thu]
 o added example, test and doc for combineFeatures with list [2014-03-20 Thu]

CHANGES IN VERSION 1.11.8
-------------------------
 o adding redundancy handling to combineFeatures (by vladpetyuk, pull
   request #18) [2014-03-14 Fri]
 o updated combineFeatures signature to accomodate above changes
   [2014-03-14 Fri]
 o updated unit tests for new testhat 0.8 [2014-03-14 Fri]

CHANGES IN VERSION 1.11.7
-------------------------
 o NA

CHANGES IN VERSION 1.11.6
-------------------------
 o add corresponding xcms functions to the chromatogram and xic
   manual page [2014-02-21 Fri]
 o new bpca imputation methods [2014-02-27 Thu]
 o replacing stop_on_error with option in vignette [2014-02-27 Thu]

CHANGES IN VERSION 1.11.5
-------------------------
 o typo in MSnSet droplevels man [2014-01-27 Mon]
 o typo in MSnbase-demo vignette [2014-02-20 Thu]
 o fix BPI legend in chromatogram [2014-02-20 Thu]

CHANGES IN VERSION 1.11.4
-------------------------
 o passing ... to sweep when normalising [2013-12-08 Sun]
 o updated makeMTD to accomodate new MS ontology [2013-12-23 Mon]

CHANGES IN VERSION 1.11.3
-------------------------
 o updated mzTab example files to new url [2013-11-15 Fri]
 o warning about mzTab versions [2013-11-15 Fri]

CHANGES IN VERSION 1.11.2
-------------------------
 o move inst/doc to vignettes [2013-10-19 Sat]

CHANGES IN VERSION 1.11.1
-------------------------
 o document na.rm in combineFeatures Rd [2013-10-18 Fri]

CHANGES IN VERSION 1.11.0
-------------------------
 o New devel version for Bioc 2.14

CHANGES IN VERSION 1.9.12
-------------------------
 o fix MSnSet -] ExpressionSet [2013-10-13 Sun]
 o MSnSet -] ExpressionSet unit test [2013-10-13 Sun]

CHANGES IN VERSION 1.9.11
-------------------------
 o MIAPE to MIAME conversion [2013-10-11 Fri]
 o proper MIAME when MSnSet -] ExpressionSet [2013-10-11 Fri]

CHANGES IN VERSION 1.9.10
-------------------------
 o faster plotMzDelta [2013-09-28 Sat]
 o faster plotMzDelta for mzRramp instances [2013-09-29 Sun]
 o chromatogram method [2013-10-04 Fri]
 o plotMzDelta has subset arg [2013-10-04 Fri]
 o xic method [2013-10-04 Fri]
 o suggesting msdata for chromatogram example [2013-10-04 Fri]
 o renamed plotting arg 'centroided.' [2013-10-04 Fri]

CHANGES IN VERSION 1.9.9
------------------------
 o typo in filterNA Rd [2013-09-18 Wed]
 o writeMgfData now has a progress bar [2013-09-24 Tue]
 o centroided(MSnExp) <- TRUE now allowed [2013-09-24 Tue]

CHANGES IN VERSION 1.9.8
------------------------
 o using new.env(parent=emptyenv()) to get rid of enclosing env
   when creating new MSnExps [2013-09-17 Tue]
 o new (private) MSnExp.size function [2013-09-17 Tue]

CHANGES IN VERSION 1.9.7
------------------------
 o Passing ... to read.table in MSnbase:::readIspy[Silac|15N]Data [2013-09-16 Mon]
 o QualityControl biocView [2013-09-16 Mon]

CHANGES IN VERSION 1.9.6
------------------------
 o new as.data.frame.MSnSet method [2013-08-16 Fri]
 o new ms2df function [2013-08-16 Fri]
 o new getEcols and grepEcols helpers for readMSnSet2 [2013-08-16 Fri]

CHANGES IN VERSION 1.9.5
------------------------
 o typo in Author[s]@R [2013-05-15 Wed]

CHANGES IN VERSION 1.9.4
------------------------
 o new simple MSnSet constructor [2013-05-07 Tue]

CHANGES IN VERSION 1.9.3
------------------------
 o Using knitr as VignetteEngine [2013-04-29 Mon]
 o Remove LazyLoad from DESCRIPTION,
   which is default nowadays [2013-04-29 Mon]
 o knitr dependency ] 1.1.0 for VignetteBuilder [2013-04-29 Mon]
 o Adding MSnSet creating sections in io vignette [2013-04-29 Mon]
 o new readMSnSet2 function [2013-04-30 Tue]

CHANGES IN VERSION 1.9.2
------------------------
 o clean has now a all param (default FALSE is retain original behavious)
   to remove all 0 intensity values [2013-04-17 Wed]
 o using BiocGenerics::normalize [2013-04-25 Thu]

CHANGES IN VERSION 1.9.1
------------------------
 o new logging utility function to update an MSnSet's
   processingData(object)$processing [2013-03-29 Fri]
 o Proper logging in t.MSnSet [2013-03-29 Fri]

CHANGES IN VERSION 1.9.0
------------------------
 o new Bioc 2.13 devel version

CHANGES IN VERSION 1.8.0
------------------------
 o new Bioc 2.12 stable version

CHANGES IN VERSION 1.7.25
-------------------------
 o updated itraqdata to fix issue in vignette when
   combine(exp1, exp2) and different MIAPE versions
   [2013-03-22 Fri]

CHANGES IN VERSION 1.7.24
-------------------------
 o Mention scale in vignette [2013-03-02 Sat]
 o exprsToRatio matrix method [2013-03-20 Wed]

CHANGES IN VERSION 1.7.23
-------------------------
 o new private nologging function [2013-02-21 Thu]
 o adding total number of features on plotNA [2013-02-22 Fri]
 o updated msnbase.r [2013-02-26 Tue]

CHANGES IN VERSION 1.7.22
-------------------------
 o msnbase.r na.rm arg [2013-02-20 Wed]

CHANGES IN VERSION 1.7.21
-------------------------
 o Added impute method  [2013-02-19 Tue]

CHANGES IN VERSION 1.7.20
-------------------------
 o Explicitating that normalise and normalize are the same
   methods in the man. [2013-02-13 Wed]

CHANGES IN VERSION 1.7.19
-------------------------
 o adding MIAPE and pSet accessors: analyserDetails, analyzerDetails,
   ionSourceDetails, instrumentModel, instrumentManufacturer,
   instrumentCustomisations [2013-02-12 Tue]
 o switching back to analyserDetails slot [2013-02-12 Tue]

CHANGES IN VERSION 1.7.18
-------------------------
 o readMgfData now supports comments and
   PEPMASS with precursor mz and intensity,
   requested by Thomas Taus [2013-02-11 Mon]
 o improved and running read/writeMgfData
   example [2013-02-11 Mon]
 o new scanIndex accessor method [2013-02-11 Mon]

CHANGES IN VERSION 1.7.17
-------------------------
 o added a analyzer accessors/slot to accomodate new mzTab
   files with more meta-data  [2013-01-30 Wed]

CHANGES IN VERSION 1.7.16
-------------------------
 o fixing knitr 1.0 compatibility [2013-01-15 Tue]

CHANGES IN VERSION 1.7.15
-------------------------
 o new scale method [2013-01-11 Fri]
 o renaming scale.mean and scale.median normalisation
   methods to center.mean and centre.median [2013-01-11 Fri]

CHANGES IN VERSION 1.7.14
-------------------------
 o new unexported readIspy15NData [2013-01-09 Wed]
 o min.int readIspy[Silac|15N]Data arg [2013-01-11 Fri]

CHANGES IN VERSION 1.7.13
-------------------------
 o msnbase.r v0.1.1 with -h (help) arg [2013-01-08 Tue]
 o msnbase.r coerce -b arg to numeric [2013-01-08 Tue]
 o testing if any features left in readIspyData [2013-01-08 Tue]

CHANGES IN VERSION 1.7.12
-------------------------
 o updated makeImpuritiesMatrix to create matrix from
   csv file with correction factors [2012-12-23 Sun]
 o makeImpuritiesMatrix test [2012-12-23 Sun]
 o readIspyData: message instead of warning if NA in
   featureData [2012-12-24 Mon]
 o Added msnbase.r script [2012-12-24 Mon]

CHANGES IN VERSION 1.7.11
-------------------------
 o new 'pattern' argument to filterNA [2012-12-15 Sat]
 o vignette and man updates [2012-12-15 Sat]
 o filterNA(, pattern) tests [2012-12-15 Sat]

CHANGES IN VERSION 1.7.10
-------------------------
 o new droplevels.MSnSet S3 method [2012-12-14 Fri]
 o fixed errors in vignette and udpates [2012-12-14 Fri]
 o vignette build stops in case of error [2012-12-14 Fri]

CHANGES IN VERSION 1.7.9
------------------------
 o Updating processing data on readIspyData [2012-12-05 Wed]
 o filterNA has a droplevels arg [2012-12-05 Wed]
 o featureCV's default cv.norm is 'sum' now [2012-12-11 Tue]
 o fixed featureCV for 1 sample [2012-12-11 Tue]

CHANGES IN VERSION 1.7.8
------------------------
 o new featureCV function [2012-12-04 Tue]
 o more MSnSet combineFeatures tests [2012-12-04 Tue]
 o new TMT6 impurity matrix and fixed
   purityCorrect [2012-12-05 Wed]
 o combineFeatures now automatically computes
   feature CVs (using featureCV) and collates this
   in featureData [2012-12-05 Wed]
 o new exprsToRatios method (moved from pRoloc) [2012-12-05 Wed]
 o initial implementation of impurity correction using
   Cramer's rule (see MSnbase:::cramer4) [2012-12-05 Wed]

CHANGES IN VERSION 1.7.7
------------------------
 o added scale.mean and scale.median MSnSet normalisation
   method [2012-11-30 Fri]
 o improvements to readMSData [2012-11-30 Fri]
 o small updates to caching code, max level 2 [2012-11-30 Fri]
 o readMSdata test [2012-12-01 Sat]

CHANGES IN VERSION 1.7.6
------------------------
 o Fixed bug in readIspyData, reported by
   Claire Mulvey [2012-11-27 Tue]

CHANGES IN VERSION 1.7.5
------------------------
 o dropping levels in readIspySilacData [2012-11-06 Tue]
 o fixed plotNA [2012-11-09 Fri]

CHANGES IN VERSION 1.7.4
------------------------
 o exporting log method [2012-11-02 Fri]
 o private readIspySilacData function [2012-11-05 Mon]
 o updating '['-MSnSet to log intial/final dims [2012-11-05 Mon]

CHANGES IN VERSION 1.7.3
------------------------
 o updating readMzTabData to properly capture
   experiment description [2012-10-12 Fri]

CHANGES IN VERSION 1.7.2
------------------------
 o fixed readMSData for MS1 [2012-10-08 Mon]

CHANGES IN VERSION 1.7.1
------------------------
 o fixed vignettes [2012-10-02 Tue]

CHANGES IN VERSION 1.7.0
------------------------
 o Version bump for next devel release [2012-10-01 Mon]

CHANGES IN VERSION 1.5.25
-------------------------
 o fixed bug when quantifying exp of length 1 (reported
   by Colin Archer), added test [2012-09-26 Wed]
 o fixed parallel default to FALSE [2012-09-26 Wed]

CHANGES IN VERSION 1.5.24
-------------------------
 o updated clean, removePeaks, combineFeatures, purityCorrect,
   trimMz, plot, MSnSet-class examples to not use readMSData [2012-09-25 Tue]
 o fixed clean,MSnExp-method [2012-09-25 Tue]
 o space in log message in extractPrecSpectra [2012-09-25 Tue]

CHANGES IN VERSION 1.5.23
-------------------------
 o updated quantify documentation [2012-09-24 Mon]
 o changed all foo.class functions to foo_class [2012-09-24 Mon]

CHANGES IN VERSION 1.5.22
-------------------------
 o setting parallel default to FALSE [2012-09-22 Sat]
 o enhanced parallel in DESCRIPTION and detectCores()
   passed to registerDoMC [2012-09-23 Sun]

CHANGES IN VERSION 1.5.21
-------------------------
 o removed registerDoMC no visible global function NOTE [2012-09-21 Fri]
 o fixed NOTE about xvarname which was a bug [2012-09-21 Fri]

CHANGES IN VERSION 1.5.20
-------------------------
 o an immediate warning is thrown is any(centroided(object))
   in quantify.MSnExp [2012-09-15 Sat]
 o mzTab file and loading time is now recorded in
   processingData [2012-09-15 Sat]
 o temporarily dontrun'ing' the mzTab read/write examples
   as OLS is down (and breaks rols) (note: modifed Rd files,
   not roxygen template) [2012-09-15 Sat]

CHANGES IN VERSION 1.5.19
-------------------------
 o updated all ReporterIons rda data [2012-09-13 Thu]
 o Using && in testing parallel, require(foreach and doMC) [2012-09-14 Fri]

CHANGES IN VERSION 1.5.18
-------------------------
 o new log method for MSnSet instances [2012-09-13 Thu]
 o new MAplot methods using generic and ma.plot/mva.pairs
   from affy [2012-09-13 Thu]

CHANGES IN VERSION 1.5.17
-------------------------
 o changed TMT7[7] mass from 229.26 to 230.17 and
   ReporterIons descriptions [2012-09-12 Wed]

CHANGES IN VERSION 1.5.16
-------------------------
 o parallel quantify is now always set to
   FALSE on Windows, fixing example checking
   issues [2012-09-11 Tue]
 o fixed types in plotMzDelta man [2012-09-11 Tue]

CHANGES IN VERSION 1.5.15
-------------------------
 o updating code to ggplot2 v0.9.2 [2012-09-07 Fri]

CHANGES IN VERSION 1.5.14
-------------------------
 o added platform test to use doMC (d.tenenbaum) [2012-08-31 Fri]

CHANGES IN VERSION 1.5.13
-------------------------
 o updated fillUp function [2012-08-15 Wed]
 o added tikzDevice to suggests [2012-08-16 Thu]
 o tikzDevice no longer on CRAN - removing from Suggests
   and using pdf as device in vignette [2012-08-16 Thu]

CHANGES IN VERSION 1.5.12
-------------------------
 o using knitr instead of pgfSweave and misc
   vignette updated[2012-08-13 Mon]
 o spectrum2 reporter plotting params updates [2012-08-14 Tue]
 o added reporterNames to NAMESPACE [2012-08-14 Tue]

CHANGES IN VERSION 1.5.11
-------------------------
 o type in filterNA log messaging and also
   rounding pNA [2012-06-07 Thu]
 o typo in demo vignette - Gb instead of Mb [2012-07-15 Sun]

CHANGES IN VERSION 1.5.10
-------------------------
 o Fixed readMSData instrumentInfo handling
   (reported by Gopuraja Dharmalingam) [2012-06-05 Tue]
 o new multiple file loading test in test_io [2012-06-05 Tue]

CHANGES IN VERSION 1.5.9
-------------------------
 o topN now properly updates processingData [2012-06-01 Fri]
 o combineFeatures updates featureNames based on the
   groupBy argument - updated demo vignette and man
   accordinlgy [2012-06-01 Fri]
 o additional parameters were not passed when normalise
   using vsn [2012-06-01 Fri]

CHANGES IN VERSION 1.5.8
-------------------------
 o added aa data in environment data.frame [2012-05-22 Tue]
 o fixed MSnbase:::subsetBy (used by topN) when
   ncol(object) == 1 [2012-05-25 Fri]
 o new nQuants function [2012-05-31 Thu]
 o minor vignettes updates [2012-05-31 Thu]
 o nQuants now return a matrix with col names,
   taken form sampleNames(object) [2012-05-31 Thu]

CHANGES IN VERSION 1.5.7
-------------------------
 o changed title method to exptitle to avoid conflict/confusion
   with graphics::title and consitency with expinfo method [2012-05-15 Tue]
 o changed email to expemail [2012-05-15 Tue]
 o Added rols to Suggests [2012-05-15 Tue]

CHANGES IN VERSION 1.5.6
-------------------------
 o new ionSource, analyser, detectorType, title accessor methods
   for MIAPE, pSet and MSnSet classes [2012-05-06 Sun]
 o updated quantify example to use data(itraqdata) instead of
   reading dummyiTRAQ.mzXML [2012-05-09 Wed]
 o initial mzTab write support [2012-05-10 Thu]
 o mzTab read support [2012-05-10 Thu]
 o updated demo and io vignettes with mzTab info [2012-05-10 Thu]

CHANGES IN VERSION 1.5.5
-------------------------
 o added email slot in MIAPE and accessor [2012-05-04 Fri]
 o added expinfo methods to pSet and MSnSet [2012-05-04 Fri]
 o updated itraqdata [2012-05-04 Fri]
 o misc man typos fixed [2012-05-04 Fri]
 o quantify now properly propagates processingData [2012-05-04 Fri]

CHANGES IN VERSION 1.5.4
-------------------------
 o automatically populating experiment data instrument info
   while reading data [2012-04-30 Mon]
 o msInfo fixed and exported [2012-04-30 Mon]
 o update demo vignette with 14 fractions analysis paragraph [2012-05-01 Tue]

CHANGES IN VERSION 1.5.3
-------------------------
 o extractSpectra is now defunct [2012-04-20 Fri]
 o caching full header in level 1; this is required when and MSnExp
   instance with *many* spectra (created from many raw files) is
   quantified - calling header(object) is a too big overhead compared
   to actual reporter quantification. [2012-04-20 Fri]
 o The header() method now uses the cached dataframe if level ]= 1;
   the (unexported) .header function can be used to generate the
   dataframe using the assayData slot data. [2012-04-20 Fri]
 o Setting processingData in MSnSet initialisation. [2012-04-20 Fri]
 o Dropping index column from header. [2012-04-20 Fri]
 o new Spectrum class v0.2.0 has tic slot. [2012-04-21 Sat]
 o *tic* method (data stored as a Spectrum slot) now returns
   _total ion current_ (as commonly used) and _total ion count_ is
   obtain using *ionCount*. [2012-04-21 Sat]
 o fixed normalisation boxplot titles and other tic/ionCount
   changes in demo vignette. [2012-04-21 Sat]
 o removed qual subetting in MSnSet's "[" method [2012-04-24 Tue]

CHANGES IN VERSION 1.5.2
-------------------------
 o transposing and MSnSet does _silently_ drop the
   protocolData now [2012-04-03 Tue]
 o fixed MSnExp pData creation for multiple files, feature names
   have a .fileNumber extension now. [2012-04-19 Thu]
 o testing for uniqueness of files (filenames) in
   readMSData [2012-04-19 Thu]
 o updated itraqdata.RData [2012-04-19 Thu]
 o added a paralle argument to quantify and using
   paralle = FALSE in vignette, to avoid duplicated display
   of the command [2012-04-19 Thu]
 o defined "reporterNames<-" generics [2012-04-19 Thu]
 o fixed warning in readMSData where all not used for
   comparison of verctors of length ] 1 [2012-04-20 Fri]

CHANGES IN VERSION 1.5.1
-------------------------
 o updated NA warning message in readIspyData [2012-03-05 Mon]
 o fixed combineFeatures/combineMatrixFeatures for 1 sample [2012-03-20 Tue]
 o image method for MSnSet instances [2012-03-20 Tue]
 o fixed bug in plotNA (first t was wring) [2012-03-21 Wed]
 o import plot from stats4 [2012-03-21 Wed]
 o using reshape2 [2012-03-30 Fri]

CHANGES IN VERSION 1.5.0
-------------------------
 o new devel version bump

CHANGES IN VERSION 1.3.15
-------------------------
 o new updateFeatureNames function [2012-02-17 Fri]
 o updated vignettes to illustrate vertical/horizontal combine [2012-02-17 Fri]
 o typo in normalised.Rd [2012-02-19 Sun]
 o TODO combine unit tests

CHANGES IN VERSION 1.3.14
-------------------------
 o new is.na.MSnSet [2012-02-16 Thu]
 o updated vignette and NA related man pages with cross-links [2012-02-16 Thu]

CHANGES IN VERSION 1.3.13
-------------------------
 o new plotNA method + doc [2012-02-15 Wed]
 o new filterNA method + doc + tests [2012-02-15 Wed]
 o added a check on 'n' in topN [2012-02-16 Thu]
 o created a .Rinstignore [2012-02-16 Thu]
 o Update package Rd [2012-02-16 Thu]

CHANGES IN VERSION 1.3.12
-------------------------
 o new topN methods + doc + tests [2012-02-14 Tue]

CHANGES IN VERSION 1.3.11
-------------------------
 o changed explicit close(file) in writeMgf methods to
   on.exit(close(file)) [2012-02-12 Sun]
 o typo in vignette [2012-02-13 Mon]

CHANGES IN VERSION 1.3.10
-------------------------
 o type in writeMgfData man [2012-02-07 Tue]
 o updated TITLE in writeMgfData [2012-02-08 Wed]

CHANGES IN VERSION 1.3.9
-------------------------
 o updated demo vignette [2012-02-03 Fri]
 o sorting numeric subsets in "[" pSet, as unsorted
   numerical indexes fails  [2012-02-03 Fri]
 o Added match.arg in combineFeatures so that
   a unique default value (the first) is used when no
   fun is specified [2012-02-03 Fri]


CHANGES IN VERSION 1.3.8
-------------------------
 o Modified trimMz warning to report acquisition number [2012-02-01 Wed]
 o add 'experimentData(object, value) <- ' method for signature eSet
   and MIAPE [2012-02-02 Thu]
 o combine methods for MIAPE instances [2012-02-02 Thu]
 o combine methods for MSnProcess instances [2012-02-02 Thu]
 o changed qual drop warning into message in combineFeatures,
   updated test_MSnSet accordingly [2012-02-02 Thu]
 o new updateFvarLabels and updateSampleNames function [2012-02-03 Fri]
 o combine method for MSnSets [2012-02-03 Fri]
 o Updated demo vignette figure 8 [2012-02-03 Fri]

CHANGES IN VERSION 1.3.7
-------------------------
 o Speeded up writeMgfData [2012-01-28 Sat]
 o fixes for ggplot2 0.9.0
 o added import(grid) and import(reshape) [2012-01-30 Mon]
 o importFrom(plyr, ...) instead of only llply [2012-01-31 Tue]
 o loading reshape and grid in vignette [2012-01-31 Tue]
 o fixed chunk 21 (label = quantitation-plot) [2012-01-31 Tue]

CHANGES IN VERSION 1.3.6
-------------------------
 o Updated NoteAboutSpeedAndMemory since parallel processing
   has been added. [2011-12-18 Sun]
 o Added CITATION [2012-01-27 Fri]
 o Added information to header output: acquisition number
   and precursor intensity [2012-01-27 Fri]
 o Added a test in plot.Spectrum2 for empty dataframe [2012-01-27 Fri]
 o moved foreach, doMC to enhances [2012-01-27 Fri]

CHANGES IN VERSION 1.3.5
-------------------------
 o added a gc() before mzR::close(msdata)... seems to help
   with Rcpp and ref classes issue. [2011-12-09 Fri]
 o added a show parameter to getCacheEnv to define .cache
   should be printed out before being returned. [2011-12-09 Fri]
 o added cache unit test [2011-12-09 Fri]
 o readMzXMLData is now defunct and remove xcms from Imports [2011-12-16 Fri]

CHANGES IN VERSION 1.3.4
-------------------------
 o fixed bug in show MSnExp method for MS1 experiments.
   When loading MS1 spectra, cache is set to 0.
   Bug reported by Jesse Meyer. [2011-12-06 Tue]
 o fixed another bug/typo in readMSData [2011-12-06 Tue]
 o now running extractSprectum example again [2011-12-06 Tue]
 o setting default cache to 0, as cache=1 introduces
   unstabel behavious... will investigate that [2011-12-06 Tue]

CHANGES IN VERSION 1.3.3
-------------------------
 o added parallel computation for MSnExp quantitation using
   foreach with llply(..., .parallel=TRUE) [2011-12-03 Sat]
 o TODO document above in quantify-methods.Rd
 o added foreach and doMC in Suggests [2011-12-03 Sat]
 o added Spectrum removePeaks and clean'ing in
   readMSData [2011-12-05 Mon]

CHANGES IN VERSION 1.3.2
-------------------------
 o \dontrun{} extractSpectrum example, as this seems to be
   a major offender producing the intermittent check
   'Error in function (x)  : attempt to apply non-function'
   error [2011-11-07 Mon]
 o typo in Author@R [2011-11-14 Mon]
 o modified utils.removePeaks and utils.clean to call sapply
   instead of IRanges:sapply [2011-12-01 Thu]

CHANGES IN VERSION 1.3.1
-------------------------
 o Herve added BioGenerics as a dependency and import
   statement in NAMESPACE  [2011-11-29 Tue]

CHANGES IN VERSION 1.3.0
-------------------------
 o Version bump for Bioc 2.10 devel

CHANGES IN VERSION 1.2.0
-------------------------
 o Version bump for Bioc 2.9 release

CHANGES IN VERSION 1.1.28
-------------------------
 o added pgfSweave to Suggests [2011-10-23 Sun]

CHANGES IN VERSION 1.1.27
-------------------------
 o fixed bug in readIspyData [2011-10-07 Fri]
 o removed (unexported) ratio code [2011-10-12 Wed]
 o added processing description when MSnSet['ing [2011-10-12 Wed]
 o man typos corrected [2011-10-14 Fri]
 o changed readMzXMLData to readMSData in tests [2011-10-14 Fri]
 o expecting warning for readMzXMLData in test_io [2011-10-14 Fri]

CHANGES IN VERSION 1.1.26
-------------------------
 o extractSpectra deprecated [2011-10-05 Wed]
 o small changes in cache.R functions [2011-10-05 Wed]
 o changed [, extractSpectra and extractPrecSpectra
   to update the .cache slot [2011-10-05 Wed]
 o MSnExp show method uses .cache when level==1. [2011-10-05 Wed]
 o Finished level 1 cache implementation: leads to an
   average 11.8 times faster MSnExp show method. [2011-10-05 Wed]

CHANGES IN VERSION 1.1.25
-------------------------
 o added .cache slot to pSet class [2011-10-03 Mon]
 o added pSet initialize method to set .cache and
   .cache$level as '0'. [2011-10-03 Mon]
 o Check that level is defined in .cache and env is locked
   in pSet validity method. [2011-10-03 Mon]
 o updated itraqdata.RData  [2011-10-03 Mon]
 o Deprecated readMzXMLData, added defunct.Rd [2011-10-03 Mon]
 o changed readMzXMLData to readMSData in man [2011-10-03 Mon]
 o updated show MSnExp for speed [2011-10-03 Mon]
 o updated read*Data is support cache = [0|1]. [2011-10-03 Mon]
 o updated precScanNum to use sapply(spectra(...), precScanNum)
   instead of unlist(eapply(assayData(...), precScanNum)) to
   preserve splectra order. [2011-10-03 Mon]
 o new cache.R file with @.cache related code [2011-10-03 Mon]

CHANGES IN VERSION 1.1.24
-------------------------
 o in readMgfData, SCANS is not used to populate
   acquisitionNum anymore, as several scans might
   have been combined upstreams [2011-09-26 Mon]
 o added fillUp function in utils.R and exported [2011-09-27 Tue]
 o new MSnbase-io vignette [2011-09-28 Wed]

CHANGES IN VERSION 1.1.23
-------------------------
 o fixed writeMgfData("MSnExp") [2011-09-21 Wed]
 o readMgfData now works when mz and intensty are separated
   by a '\t' (as exported by PRIDE Inspector) [2011-09-21 Wed]
 o show("MSnExp") now works without retention time [2011-09-21 Wed]
 o updated mgf2Spectrum2 to make it faster [2011-09-21 Wed]
 o fixed missing fromFile slot in data created from readMgfData
   that prevented calling header [2011-09-21 Wed]
 o readMgfData now creates a fData based on the peak header [2011-09-21 Wed]
 o modified getCurveWidth to work with centroided data [2011-09-21 Wed]
 o fixed bug getCurveWidth [2011-09-21 Wed]

CHANGES IN VERSION 1.1.22
-------------------------
 o removed (internal) Mascot query link column in readIspyData
   to work with latest ouput version [2011-09-12 Mon]
 o removed the fillUp part in readIspyData [2011-09-14 Wed]
 o exported readIspyData [2011-09-20 Tue]
 o removed link to proteomics sig list [2011-09-20 Tue]
 o removed url in DESCRIPTION [2011-09-20 Tue]
 o Spectrum2 slot ms1scan renamed to precScanNum and populated using
   mzR::header()$precursorScanNum. Updated affected methods/functions
   and manual pages. New accessor method precScanNum is exported.
   THIS CHANGE IS NOT COMPATIBLE WITH PREVIOUSLY CREATED
   MSnSet OBJECTS! [2011-09-20 Tue]


CHANGES IN VERSION 1.1.21
-------------------------
 o updated write.exprs to add fData columns [2011-09-08 Thu]
 o added write.exprs and readMSnSet unit test [2011-09-08 Thu]

CHANGES IN VERSION 1.1.20
-------------------------
 o added a readMSnSet function [2011-09-08 Thu]
 o added a write.MSnSet("MSnSet") method  [2011-09-08 Thu]
 o vignette/man updates - mainly data import section documenting
   readMSData and readMgfData [2011-09-08 Thu]

-------------------------
 o incorporating mzR io frame work [2011-09-05 Mon]
 o use mzR's peaksCount and header generics [2011-09-05 Mon]
 o added test to check that readMzXMLData and readMSData give same output [2011-09-05 Mon]
 o added readMSData.Rd doc file [2011-09-05 Mon]
 o added Author@R field in DESCRIPTION [2011-09-07 Wed]
 o compressed/resaved (using resaveRdaFiles) itraqdata.RData file to  [2011-09-07 Wed]

CHANGES IN VERSION 1.1.18
-------------------------
 o read support for mgf files contributed by Guangchuang Yu [2011-07-06 Wed]
 o added as.ExpressionSet.MSnSet and setAs methods and updated MSnSet doc [2011-07-09 Sat]
 o fixed read/write mgf compatibility [2011-09-01 Thu]
 o added mgf io test [2011-09-01 Thu]
 o exported and document mfg read/write support [2011-09-01 Thu]
 o added centroided parameter to rawToSpectrum[1|2] to set this directly
   at object creation in readMzXmlData [2011-09-01 Thu]
 o other minor changes in Rd files [2011-09-01 Thu]
 o added warning checks for combineFeatures when verbose=TRUE in test_MSnSet.R [2011-09-02 Fri]

CHANGES IN VERSION 1.1.17
-------------------------
 o updated itraqdata manual [2011-06-27 Mon]
 o fixed bug in MSnSet validity method - msg was initialised
   to NULL when testing Biobase:::isValidVersion and
   Biobase::assayDataValidMembers [2011-07-02 Sat]
 o added t.MSnSet method [2011-07-02 Sat]
 o document t.MSnSet method [2011-07-05 Tue]
 o test for t-MSnSet [2011-07-05 Tue]
 o new "["-MSnSet method to properly subset qual slot [2011-07-06 Wed]
 o updated MSnSet validity method to check qual dims [2011-07-06 Wed]
 o combineFeatures now drops the spectrum-specific qual slot [2011-07-06 Wed]
 o test for "["-MSnSet [2011-07-06 Wed]

CHANGES IN VERSION 1.1.16
-------------------------
 o added addVigs2WinMenu call in .onAttach [2011-06-26 Sun]
 o added plotMzDelta paragraph in vignette [2011-06-26 Sun]

CHANGES IN VERSION 1.1.15
-------------------------
 o new names and description methods for ReporterIons [2011-06-16 Thu]
 o added validObject() checks [2011-06-16 Thu]
 o new removeReporters method [2011-06-16 Thu]
 o plotMzDelta is exported and documented [2011-06-17 Fri]

CHANGES IN VERSION 1.1.14
-------------------------
 o Adding plotMzDelta QC plot (not yet exported), contributed by Guangchuang Yu [2011-06-14 Tue]
 o created a locked environment to store amino.acids dataframe [2011-06-14 Tue]
 o TODO plotMzDelta documentation and vignette section - man DONE in v 1.1.15 , vignette DONE in v 1.1.16

CHANGES IN VERSION 1.1.13
-------------------------
 o changed pSet [[ method [2011-06-13 Mon]
 o additional updates pSet [[ method [2011-06-13 Mon]
 o added MSnExp subsetting error tests [2011-06-13 Mon]
 o created new plotting-dataframe.R file with former plotting
   utils functions, now renamed plot*.header [2011-06-13 Mon]

CHANGES IN VERSION 1.1.12
-------------------------
 o added invisible(NULL) to all show methods [2011-06-08 Wed]
 o added centroided argument to plot.MSnExp [2011-06-09 Thu]

CHANGES IN VERSION 1.1.11
-------------------------
 o harmonised MSnExp and Spectrum plot axes labels [2011-05-18 Wed]
 o Added plotting customisation section in vignette [2011-05-18 Wed]
 o updated signature of plot2d method to "MSnExp" only [2011-05-18 Wed]
 o added/exported plotDensity methods [2011-05-18 Wed]
 o started QC vignette section [2011-05-18 Wed]
 o added preprocSelection and preprocSelectionTable functions [2011-05-18 Wed]
 o TODO document preprocSelection[Table] in vignette
 o reduces plot2d-figure and plotDensity-figure sizes using png [2011-05-19 Thu]
 o added plotDensity doc [2011-05-19 Thu]
 o added round param to preprocSelection[Table] [2011-05-19 Thu]
 o preprocSelection[Table] documented and exported [2011-05-19 Thu]
 o fixed bug in plot.Spectrum1 [2011-05-24 Tue]
 o changed removePeaks setGeneric explicit signature [2011-05-26 Thu]
 o added MassSpectrometry biocView [2011-05-27 Fri]

CHANGES IN VERSION 1.1.10
-------------------------
 o minor updates in demo vignette [2011-05-13 Fri]
 o added plot argument to plot methods [2011-05-16 Mon]
 o fix in makeImpuritiesMatrix [2011-05-16 Mon]
 o added meanSdPlot MSnSet method [2011-05-17 Tue]
 o minor cosmetic fix in purityCorrect error message [2011-05-17 Tue]
 o added method="sum" to Spectrum/MSnExp normalisation [2011-05-17 Tue]
 o typo in MSnSet-class.Rd corrected [2011-05-17 Tue]

CHANGES IN VERSION 1.1.9
-------------------------
 o exporting normali[s|z]e methods for MSnSet, Spectrum and MSnExp [2011-05-12 Thu]
 o added quantile normalisation [2011-05-12 Thu]
 o added quantile.robust normalisation [2011-05-12 Thu]
 o added vsn2 normalisation [2011-05-12 Thu]
 o added normalise manual  [2011-05-12 Thu]
 o included normalisation section in vignette [2011-05-13 Fri]
 o more vignette updates [2011-05-13 Fri]
 o updated plotting methods to round MZ in title [2011-05-13 Fri]

CHANGES IN VERSION 1.1.8
-------------------------
 o added writeMgfData method from spectra and experiment [2011-05-09 Mon]
 o added writeMgfData manual [2011-05-09 Mon]
 o added itraqdata data set and updated vignette to use it [2011-05-11 Wed]
 o updated man pages to use tiny dummyiTRAQ.mzXML [2011-05-11 Wed]
 o added makeImpuritiesMatrix function [2011-05-11 Wed]

CHANGES IN VERSION 1.1.7
-------------------------
 o reporter ions purity correction method, man and test [2011-05-09 Mon]
 o updated vignette [2011-05-09 Mon]

CHANGES IN VERSION 1.1.6
-------------------------
 o added incomplete dissociation and spectral counting sections
   to demo vignette [2011-05-06 Fri]
 o added bioc-sig-proteomics link to foreword [2011-05-06 Fri]
 o type in foreword [2011-05-06 Fri]

CHANGES IN VERSION 1.1.5
-------------------------
 o added combineFeatures example in demo vignette [2011-05-05 Thu]

CHANGES IN VERSION 1.1.4
-------------------------
 o readIspyData updated to return updated factors [2011-05-03 Tue]
 o added unexported/undocumented combineFeatures function for MSnSets [2011-05-03 Tue]
 o added basic tests for combineFeatures [2011-05-03 Tue]
 o added combineFeatures manual [2011-05-04 Wed]
 o exportig combineFeatures  [2011-05-04 Wed]

CHANGES IN VERSION 1.1.3
-------------------------
 o as.data.frame.Spectrum columns now are (first) mz and (second) intensity [2011-04-27 Wed]
 o exporting as.data.frame.Spectrum and coerce [2011-04-27 Wed]

CHANGES IN VERSION 1.1.2
-------------------------
 o Simplified quantify generic signature - now only object argument [2011-04-19 Tue]
 o Added strict parameter to quantify method, man updated, added relevant test
 o Added illustrative plot for quantitation methods in MSnbase-demo vignette [2011-04-19 Tue]
 o Added illustrative plot for data pre-processing (removePeaks and clean)
   in MSnbase-demo vignette [2011-04-20 Wed]
 o No warnings are issued anymore when peaks expands outside of mz(reporters) +/- width(reporters).
   See ?quantify on how to check this manually. [2011-04-19 Tue]
 o No warnings are issued anymore when reporter peaks are missing.
   See ?quantify on how to check this manually. [2011-04-20 Wed]
 o pSet validity warns if length(unique(msLevel(object))) ] 1, rather than != 1.
   The latter triggered a warning for a new("MSnExp"). [2011-04-20 Wed]

CHANGES IN VERSION 1.1.1
-------------------------
 o added setAs data.frame and as.data.frame methods for
   Spectrum objects [2011-03-29 Tue]
 o support for uncentroided MS2 spectra plots [2011-03-31 Thu] [2011-04-02 Sat]
 o support for uncentroided MS1 spectra plots [2011-04-02 Sat]
 o minor modification to readIspyData [2011-04-04 Mon]
 o removed centroided slot from MSnProcess and added to
   individial Spectrum instances. Relevant for Velos
   HCD (profile)/CID (uncentroided) data [2011-04-04 Mon]
 o modified readMzXmlData accordingly [2011-04-04 Mon]
 o added validObject(new(...)) tests for each class [2011-04-04 Mon]
 o added centroided[<-] methods to Spectrum and pSet [2011-04-04 Mon]
 o added 'keepAll' parameter to readIspyData [2011-04-11 Mon]

CHANGES IN VERSION 0.99.4
-------------------------
 o removed pgfSweave from Suggests field [2011-04-04 Mon]

CHANGES IN VERSION 0.99.3
-------------------------
 o Using Sweave rather than pgfSweave to build on lamb1. [2011-03-28 Mon]

CHANGES IN VERSION 0.99.2
-------------------------
 o updated references in package Rd [2011-03-24 Thu]
 o added readIspyData.Rd  [2011-03-24 Thu]
 o removed old readMzXMLData function [2011-03-24 Thu]
 o cleaning up code [2011-03-24 Thu]
 o fixed MSnSet initialize: setting experimentData as MIAPE [2011-03-25 Fri]
 o fixed MSnSet initialize: identical featureNames in assayData and
   featureData for empty MSnExp istances [2011-03-25 Fri]
 o better test organisation and added object validity tests [2011-03-25 Fri]
 o updated readIspyData function [2011-03-25 Fri]

CHANGES IN VERSION 0.99.1
-------------------------
 o fake vignettes are copied back in inst/doc/. to
   make sur tar tarball can be extracted and build
   again [2011-03-24 Thu]
 o Making clean after make all [2011-03-24 Thu]

CHANGES IN VERSION 0.99.0
-------------------------
 o MSnProcess@process get's one line when subsetting and MSnExp object [2011-03-21 Mon]
 o Updated vignette Makefile [2011-03-22 Tue]
 o Added fake vignettes [2011-03-22 Tue]
 o Version set to 0.99.0 [2011-03-22 Tue]
 o Minor changes in quantify-method.Rd [2011-03-22 Tue]
 o added .Rbuildignore to ignore 'sweave-cache.*' [2011-03-22 Tue]
 o added R/zzz.R with start-up message [2011-03-23 Wed]
 o Added width generic [2011-03-23 Wed]
 o IRanges in now imported [2011-03-23 Wed]

CHANGES IN VERSION 0.2.0 [2011-03-17 Thu]
------------------------
 o MSnSet now extends eSet, reimplementing the ExpressionSet class
   with exception of the experimentData slot, that must now be a MIAPE
   instance.
 o updated MIAPE substantially and added accessor methods.
 o updated docs and vignettes to reflect above changes.

CHANGES IN VERSION 0.1.5
------------------------
 o added zoo to Suggest, as zoo::rollapply is used in vignette.
 o changes rollapply call to zoo:::rollapply.zoo, to make it
   work with zoo_1.6-4, rather that depending on zoo_1.7-0, which
   is not yet on CRAN (only r-forge).
 o added vns to Suggests, as it is used in the demo vignette.

CHANGES IN VERSION 0.1.4
------------------------
 o added pgfSweave to Suggests, as is called in vignette Makefile

CHANGES IN VERSION 0.1.3
------------------------
 o Updates to ReporterIons man page
 o Moved some Depends to Imports and updated NAMESPACE
 o corrected a IRanges:::sapply ot IRanges::sapply in utils.R
 o added inst/tests/test_MSnProcess.R

CHANGES IN VERSION 0.1.2
------------------------
 o MSnProcess@MSnbaseVersion is not set in the initialize method instead to the prototype
 o changed R CMD to $(R_HOME)/bin/R CMD in inst/doc/Makefile
 o removed first and last (was 5th) MS1 spectra and associated MS2 spectra
   from dummy file to reduce size below 2MB.
 o Updated tests to reflect new dummy data set
 o Edition of dummy brakes readMzXMLData with msLevel=1 -- comment related tests
 o Updated MSnbase-demo vignette and man to use good spectra un plots (i.e "X43" instead of "X64")

CHANGES IN VERSION 0.1.1
------------------------
 o Added LazyLoad: yes in DESCRIPTION and modified docs accordingly
 o Added NEWS file

CHANGES IN VERSION 0.1.0
------------------------
 o Added MSnbase-demo vignette
 o Added MSnbase-development vignette
