Changes in version 1.17.22 (2019-01-24)                 

    o   code cosmetics to eliminate ERRORS and WARNINGS in R CMD
	BiocCheck of version 3.9.

                Changes in version 1.13.02 (2017-11-20)                 

    o   Eliminated C++-11 and Rcpp linking. Passing unit tests.

    o   use lower_bound_ function exported by
	<https://cran.r-project.org/package=protViz>

                 Changes in version 1.9.15 (2017-04-21)                 

    o   added prozor (>= 0.2.2) to the Suggest list.

    o   added more specific R package version numbers in DESCRIPTION
	file.

    o   in plot.specLSet (normalized RT versus RT) use pch=16 and color
	with parameter alpha=0.1.

    o   fixed issue #22 by including the iRTs in the ionlibrary; LIB <-
	genSwathIonLib(data=peptideStd, data.fit=peptideStd.redundant);
	LIB@input.parameter$iRTpeptides.

    o   fixed issue #19.

    o   removed par command in specLset plot function.

    o   added vignettes/report.Rmd file, see also
	<http://bioconductor.org/packages/devel/bioc/vignettes/specL/inst/doc/report.html>.

                 Changes in version 1.7.4 (2016-05-19)                  

    o   USER VISIBLE CHANGES
	
	  • added to specLSet summary "which std peptides (iRTs) where
	    found in which raw files"
	
	  • one plot per raw file in plot methode of specLSet object

                 Changes in version 1.7.1 (2016-05-13)                  

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	  • replaced NEWS by NEWS.Rd file
	
	  • modified specL object /replace decoy by score attribute
	    #1,#4
	
	  • specL on BioC 3.3

                      Changes in version 1.5.10-13                      

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	  • added specLSet class support for cdsw methode
	
	  • changed Rmd5 vignette style
	
	  • added cdsw test case
	
	  • intro new vignette for cdsw method
	    <http://bioconductor.org/packages/release/bioc/vignettes/specL/inst/doc/cdsw.html>

                        Changes in version 1.5.9                        

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	  • added test case for read.biliospec

                        Changes in version 1.5.5                        

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	  • added RT prediction vignette file

                        Changes in version 1.5.4                        

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	  • changed NAMESPACES and read.bibliospec docu to avoid
	    warnings in 3.3 check

                        Changes in version 1.5.3                        

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	  • added sqlite files for peptideStd RData #13

                        Changes in version 1.5.2                        

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	  • find all signals having two or more in-silico fragment
	    ions. #8
	
	  • keep only the nearest fragment ion; if there are more take
	    the first in line

                        Changes in version 1.3.7                        

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	  • getProteinPeptideTable - added

                        Changes in version 1.3.5                        

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	  • read.bibliospec - bugfixes

                        Changes in version 1.3.4                        

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	  • added Witold Wolski as maintainer

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	  • read.bibliospec - replaced old code (for loop) by using
	    mcmapply
	
	  • added time meassurements to read.bibliospec

                        Changes in version 1.3.3                        

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	  • plot::specLSet draws alpha circles iff plot(..., art=TRUE)

    o   USER UNVISIBLE CHANGES
	
	  • .mascot2psmSet buxfix
	
	  • renamed column name in spectronaut outpu from irt to
	    irt_or_rt

                        Changes in version 1.3.2                        

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	  • added ssrc (Sequence Specific Retention Calculator)
	    function
	
	  • added a CITATION file

                        Changes in version 1.3.1                        

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	  • added fucntion cdsw

    o   USER UNVISIBLE CHANGES
	
	  • modified unit test for genSwathIonLib

                       Changes in version 1.1.17                        

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	  • removed file argument in genSwathIonLib function

                       Changes in version 1.1.16                        

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	  • added unit test for genSwathIonLib

                       Changes in version 1.1.15                        

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	  • added circle plots to specLSet plot method
	
	  • added breaks argument in genSwathIonLib methode

                       Changes in version 1.1.14                        

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	  • LinkedTo Rcpp; added C++ STL lower bound function which is
	    reqired for determining overlapping q1 and q3 SWATH windows

                       Changes in version 1.1.13                        

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	  • fixed man pages

                       Changes in version 1.1.12                        

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	  • impoved package vignette

                       Changes in version 1.1.11                        

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	  • modified default parameters of genSwathIonLib
	
	  • add content to vignette

                       Changes in version 1.1.10                        

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	  • added generate.consensus

                        Changes in version 1.1.9                        

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	  • new features in specLSet 'summary' plot

    o   USER UNVISIBLE CHANGES
	
	  • refactored merge.specLSet; merge by group_id
	
	  • added unit test for merge.specLSet

                        Changes in version 1.1.8                        

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	  • renamed annotateProteinID to annotate.protein_id
	
	  • added graphics on plot.specLSet method

    o   USER UNVISIBLE CHANGES
	
	  • refactored merge

                        Changes in version 1.1.7                        

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	  • introduce peakplot for bibliospec object
	
	  • introduce LCMS map for bibliospec object
	
	  • vignette cosmetics

                        Changes in version 1.1.6                        

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	  • introduce specL_bibliospec summary method

                        Changes in version 1.1.5                        

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	  • specLSet merge function
	
	  • work on specLSet summary method

                        Changes in version 1.1.4                        

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	  • summary method of specLSet class

    o   USER UNVISIBLE CHANGES
	
	  • unit test for data containing no iRT peptides

                        Changes in version 1.1.3                        

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	  • renamed write.Spectronaut to write.spectronaut
	
	  • write.spectronaut writes filename
	
	  • added benchmark section in package vignette

                        Changes in version 1.1.2                        

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	  • uses modSeq in group_id iff existing

                        Changes in version 1.1.1                        

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	  • streamline modsequence, e.g., AAAMASATTM[+16.0]LTTK for
	    compatibility with peakView V2.0

                       Changes in version 0.99.23                       

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	  • added methods for specLSet class: ionlibrary, rt.input,
	    rt.normalized
	
	  • fixed Sys.time() units in message.

    o   USER UNVISIBLE CHANGES
	
	  • genSwathIonLib using bpmapply

                       Changes in version 0.99.22                       

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	  • specLSet plot method

                       Changes in version 0.99.21                       

    o   USER VISIBLE CHANGES
	
	  • specLSet class
	
	  • replace print by show and write.Spectronaut method in specL
	    and specLSet classes