		CHANGES IN VERSION 1.40.0:

SIGNIFICANT USER-VISIBLE CHANGES

   o	The graphical user interface (TargetSearchGUI) is being deprecated.
	This is due to old source code, lack of time for maintenance, and
	lack of interest. The GUI it is still part of this release and it
	will be removed in the next release, ie, 1.42.0

BUG FIXES

   o	Fix NA handling in quantMass method.

		CHANGES IN VERSION 1.38.0:

NEW FEATURES

   o	New function `checkRimLim` to vizualise a retention index markers
	before the actual time correction. It can be useful to fix the search
	limits.

   o	Peak detection method (NetCDFPeakFinding) has the option to use a gaussian
	smoothing in addition to usual moving average.

   o	Detects if CDF files are not found during sample description import. In
	addition, search for column names matching a pattern if the expected names
	are not found.

   o	Add support for a custom CDF file for faster data retrieval.

SIGNIFICANT USER-VISIBLE CHANGES

   o	The parameter `massRange` (m/z mass range) which used to be needed in
	some functions is deprected. It was used mostly as a hint and usually
	detected automatically. If it is passed, there would be no effect.

BUG FIXES

   o	Big refactor of C code to eliminate duplicated code and to separate
	what is R-C code (ie, SEXP structs) out of the C code that actually does
	something.

   o	General R code refactoring and housekeeping.

		CHANGES IN VERSION 1.36.0:

NEW FEATURES

   o	New dataset object TSExample. This dataset contains data that used to
	be stored in package TargetSearchData.

   o	New low-level function to search peaks (FindAllPeaks). This allows advanced
	users to refine peak-searches.

   o	New function to plot peaks across samples (plotPeakRI). Used for quality
	checks of peak annotation and fine-tunning search parameters.

SIGNIFICANT USER-VISIBLE CHANGES

   o	Add extra checks when manipulating tsLib objects. Extra care needs to
	be taken if changes to the quant/selective/top masses are done.

   o	Sample IDs (names) must be unique. These might generate errors when
	loading old TargetSearch workspaces.

BUG FIXES

   o	tsLib: ensure that every slot in the object contain a library ID.

   o	Fix warnings during R CMD check.

   o	Refactor C code for finding peaks. It is possible to return all peaks
	instead of only the most abundant. No visibles changes for the end user.

   o	Refactor C code for NetCDF manipulation and peak finding to reduce
	code duplication. No visible changes for the end user.

   o	General R code houskeeping: Removal of mixed tabs and spaces, fix
	tabulation, add Rbuildignore.

		CHANGES IN VERSION 1.26.0:

SIGNIFICANT USER-VISIBLE CHANGES

   o	TargetSearch now depends on "ncdf" rather than mzR.

BUG FIXES

   o	Fix potential potencial pearson correlation errors that occur when the
	standard is deviation zero. If that is the case, replace the resulting
	NA/NaN by zero.

   o	Fix R check warnings.

		CHANGES IN VERSION 1.24.0:

BUG FIXES

   o	Add clarification note for "Window" parameter in "RIcorrect" function.

		CHANGES IN VERSION 1.22.0:

BUG FIXES

   o	Fix bug in quantMatrix. make sure that selection mass IDs match
	the library IDs. Add an attribute to indicate that the quantification
	mass is also a correlation mass.

		CHANGES IN VERSION 1.20.0:

BUG FIXES

    o	Write the actual retention index value instead of the work 'RI' in
	`ProfileCleanUp`.

		CHANGES IN VERSION 1.18.0:

NEW FEATURES

    o	New options for function 'ProfileCleanUp' that allow fine tuning of the
	suggested metabolite in case of redundancy. This problem occurs when the
	reference library contains two or more metabolites in the same
	retention time window.

    o	The function 'Write.Results' can create a quantification matrix based
	in one quantification mass. This mass can be selected automatically or
	specified by the user.

    o	The above options have been incorporated in the GUI as well.

		CHANGES IN VERSION 1.16.0:

SIGNIFICANT USER-VISIBLE CHANGES

    o	Function 'fixRIcorrection' is now defunct (previously was deprecated).
	Use 'fixRI'.

BUG FIXES

    o	Removed references to deprecated R functions.

    o	Fixed bug in 'ImportLibrary.msp' that occurs if there is only one
	metabolite.

		CHANGES IN VERSION 1.14.0:

NEW FEATURES

    o	New function 'fixRI'. This function can be used to correct RI markers
	or to manually force their location to specific retention times if,
	for example, the RI markers were not co-injected with the biological
	samples. Replaces the now deprecated 'fixRIcorrection'.

    o	New function 'riMatrix'. This function searches RI markers in RI
	files instead of CDF files.

    o	Improvements in CDF import functions:
	 - Automatic detection of m/z range.
	 - Detection and correction of CDF files with non-integer m/z values.
	   These values are converted to nominal mass.

    o	ImportLibrary:
	 - New parameter 'file.opt'. A list containing arguments to
	   be passed to 'read.delim'.
	 - It can take a data frame instead of a file to create a library
	   object.

SIGNIFICANT USER-VISIBLE CHANGES

    o	Function 'fixRIcorrection' is deprecated. Use 'fixRI'.

BUG FIXES

    o	The .Call function in FindPeaks.R would incorrectly coerce RI limits
	to integers instead of double.

    o	ImportLibrary:
	 - Fixed bug when reading one-metabolite libraries.
	 - Check for unexpected quotation mark characters in input file or
	   input data.frame. They will be removed.

    o	Profile: check for at least three top masses to calculate spectra
	similarity scores.

    o	quantMatrix: use character indeces instead of numeric indeces.

		CHANGES IN VERSION 1.12.0:

SIGNIFICANT USER-VISIBLE CHANGES

    o	New binary file format for the peak-list files, a.k.a. RI files.
	This speeds up metabolite searches by 5-10 fold. The old TEXT format
	is kept for compatibility. See method 'fileFormat'. Also see
	'bin2text' and 'text2bin' funtions.

    o	New plot peak function 'plotPeak'. The old function was renamed as
	plotPeakSimple. The function show also the regions in which the
	searches were performed to provide better quality controls.

BUG FIXES

    o	Changed to check.names=TRUE in 'read.delim' call in functions
	TargetSearchGUI() and ImportLibrary(). This prevents empty column names
	that might produce errors in downstream functions.

		CHANGES IN VERSION 1.10.0:

NEW FEATURES

    o	New function "writeLibText" to save "tsLib" objects in a tab-delimited
	text file (which can consecuently be re-imported). It might be also used to
	convert a MSP file into a TEXT file.

BUG FIXES

    o   Added some 'drop=FALSE' in plotSpectra function.

    o	Calls to 'pdf' are now followed by 'on.exit(dev.off())' to make sure that
	the device is closed after unexpected errors or user interruption.

		CHANGES IN VERSION 1.8.2:

BUG FIXES

    o	bug fixed error due to changes in TargetSearch object definitions in
	function writeMSP.

		CHANGES IN VERSION 1.8.1:

BUG FIXES

    o	'sampleRI' and 'Profile' functions would return NA if the minPairCor
	parameter was greater than the number of samples.

    o	Change GUI message to a more suitable one.

    o	'FAMEoutliers' failed if only one sample was analyzed.

    o	'ProfileCleanUP' accepts a minPairObs parameter like 'Profile'

    o	The parameter minPairObs is now checked so that cannot take a value
	lower than 5 in 'sampleRI', 'Profile', and 'ProfileCleanUP' functions.

		CHANGES IN VERSION 1.6.0:

NEW FEATURES

    o	The Retention Time information is now imported from the RI files.
	This means that the RT slot of the "tsMSdata" object contains the R.T.
	values (formerly it was just an empty slot).

BUG FIXES

    o	Several fixes, improvements, and code cleaning.

		CHANGES IN VERSION 1.4.3:

NEW FEATURES

    o	Function NetCDFPeakFinding: 'ppc' is now the default peak picking
	method.

		CHANGES IN VERSION 1.4.2:

BUG FIXES

    o	Bug creating a new library in GUI. Fixed.

		CHANGES IN VERSION 1.4.1:

BUG FIXES

    o	Fixed bug in "[" method, "tsLib" object.

		CHANGES IN VERSION 1.3.7:

    o	Column Sample_Count of metabolite Profile renamed to
	Sample_Count_per_Mass.

		CHANGES IN VERSION 1.3.6:

NEW FEATURES

    o	ImportLibrary.tab() now have a new parameter 'libdata'.

BUG FIXES

    o	Fixed bug with corrupted CDF files. Now TS will try to process it
	and issue a warning to the user.

    o	Fixed bugs in the GUI:
	- Quantitative masses were not loaded into the tsLib object.
	- Fixed bug ExcludedMasses parameter.

		CHANGES IN VERSION 1.3.5:

NEW FEATURES

    o	New method 'sampleData<-' for 'tsSample' class.

    o	New method 'libData<-' for 'tsLib' class.

DOCUMENTATION

    o	Vignette corrections and rewriting.

BUG FIXES

    o	plotFAME(): plot title changed to 'RI marker' to be consistent
	with the manual.

    o	Fixed examples that did not pass R CMD check.
	
    o	Object validation bug fixes and new checks (all classes).

		CHANGES IN VERSION 1.3.4:

BUG FIXES

    o	Fixed GUI error that occurred when creating/editing a library.

    o	Fixed Write.Result() file format output: columns were missing and
	column names were wrong. The file format should be compatible with older
	versions.

		CHANGES IN VERSION 1.3.3:

NEW FEATURES

    o	New function ImportSamplesFromDir. It makes easier to create a
	tsSample object from CDF files in a directory.

    o	A new GUI layout and new features: Now it is not required to
	have all the files in the working directory. Basline, Peak detection,
	and RI correction options gray out when 'Apex data' is selected.

		CHANGES IN VERSION 1.3.2:

NEW FEATURES

    o	New 'tsProfile' and 'tsMSdata' definitions. Many functions were
	internaly changed to conform to the changes, however, the changes
	should be (more or less) transparent for the user.

    o	classes.R:
	- new 'quantMass' slot in class 'tsLib'
	- class 'tsMSdata': slots changed from matrix to list
	- class 'tsProfile': new slots profInt, profRI and ProfRT

    o	Function FindPeaks: Now the parameter refLib can be either a list
	or a 3-column matrix. If it is a list, the function will iterate for
	every component, given that the components are 3-column matrices.

    o	Function ImportLibrary: code changed to incorporate the 'quantMass'
	slot.

    o	methods-tsLib.R: new methods to access quantMass slot. Also, new
	methods profileInt, profileRI and profileRT to access slots profInt,
	profRI and ProfRT. New method as.list

    o	Write.Results: Same as before, but the parameter peakData was
	removed, since the raw data is now included in the 'tsProfile' object.

    o	The following files were changed to conform to the new definicions.
	No changes in terms of functionality: dayNorm.R, peakFind.R, plot.R,
	profile.R, profileCleanUp.R, and sampleRI.R.

    o	new function quantMatrix.

    o	Changes in the GUI. Now two new parameters are accepted: topMasses
	and ExcludedMasses.

		CHANGES IN VERSION 1.3.1:

BUG FIXES

    o	Fixed NetCDFPeakFinding and tsSample-class manpages because
	of an error caused by wrong regular expressions in the example
	section at check.

DOCUMENTATION

    o	CITATION file of TargetSearch paper at BMC bioinformatics.

