2025-06-10 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.69.2
    * unit test system no uses test_that() consistently (all test previously
      implemented in RUnit got converted to test_theat() equivalents and RUnit
      was removed from the Suggests section in file DESCRIPTION)

2025-05-27 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.69.1
    * parameter `elements` can now be specified using a character like 'CHNOPS' 
      similar to the parameters `minElements` and `maxElements`
    * fix for issue #5; implementing checks for parameters `minElements` and 
      `maxElements` (both have default settings including element 'C' which 
      caused an error when C was not included in the defined element list)
    * implementing checks for parameter `elements` using internal function
      `check_elements()`

2025-01-22 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.67.5
    * fix for issue #22; implementing atomic masses with higher precision
    * the new set of elemental definitions will be used as the default which can
      be considered a breaking change as it might lead to minor changes in 
      previous analyses; previous results can be obtained by setting `method = 'IUPAC'`
      in function initialize

2024-11-08 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.67.4
    * fix for issue #33; use R based random number calls in a CRAN approved way.

2024-11-08 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.67.3
    * fix for issue #20; a wrongly specified `maxisotopes` parameter will not 
      crash R but return an error instead
    * fix for issue #12 and issue #5; `decomposeIsotopes` help section now better 
      explains how to define elemental limits specified via `minElements` and 
      `maxElements`
    * `maxElements`does respect now an upper limit of zero (basically another way
      to exclude elements, which could be achieved before only by not defining the
      element in the first place, which caused trouble for CHNOPS elements which 
      are always expected by disop.cpp)
    * fix for issue #1; `getMolecule` and `addMolecules` do check the elements of
      the provided formulas now and use only the minimal required elemental set
      to process the result. This prevents crashes that happend when the full PSE
      was initialized due to problems with atoms having exatly 7 isotopes in their 
      definition.

2024-11-05 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.67.2
    * fix for issue #21; `decomposeIsotopes` modified the object provided as
      parameter `intensities`

2024-10-18 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.67.1
    * !changed `getIsotope` function to return a list of matrices to be 
      consistent with the other getter functions
    * new exported function `getMonoisotopic()` which will return the mono-isotopic mass
      for a molecule object (also when a list of molecules as for decomposeMass)
      or alternatively for a vector of chemical formulas
    * modified documentation to clarify the difference of exactmass and mono-
      isotopic mass
    * `testthat` tests for `getMonoisotopic` were set up 
    * `getMolecule` is now testing the provided formula parameter to avoid crashes
      on the C++ level (addressing issue #3)
    * new internal function to count chemical elements (imported/copied from the
      CorMID package) to be utilized in `getMonoisotopic` and `getMolecule`
    * two data sets included in package and appropriately documented
    * `isotopes` (a data.frame version of the PSE info) 
    * `mono_masses` (a named vector containing only the most abundant isotope per 
      element)
    
2024-10-10 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.65.3
    * getMolecule now respects the charge parameter z
    * exact masses will be corrected by z times the electron mass
    * isotope masses will be additionally devided in case of abs(z)>=2
    * a `testthat` function for getMolecule was set up 
    * the documentation for getMolecule was updated
    * previous users will be informed by a message when calling getMolecule with z!=0

2024-10-10 Jan Lisec <jan.lisec@bam.de>

    * Rdisop-1.65.2
    * all R functions grouped to separate individual files
    * all R functions documented using roxygen2
    * `testthat` based testing environment set up
    * Rdisop.dll bound to R using R_useDynamicSymbols()
    * Vignette converted to Rmd format
    * GitHub actions included

2024-09-16  Miao Yu

	* fix C++-17 issue on recent compilers reported by Prof. Ripley

2024-05-16  Miao Yu

	* fix cpp Rferror issues with help of @vjcitn

2023-02-12  Steffen Neumann  <sneumann@msbi-corei>

	* search&replace deprecated auto_ptr with unique_ptr
	* use labda functions instead of e.g. bind2nd()

2019-05-02  Steffen Neumann  <sneumann@msbi-corei>

	* Rdisop-1.45.1: Merge fix by Max Helf for improved
	decomposeMass: element filter handling.

2019-04-01  Steffen Neumann  <sneumann@msbi-corei>

	* Rdisop-1.43.2: David Rasp helped to remove dependency
	to RcppClassic, which might not be supported at some time
	in the future

2015-12-08  Steffen Neumann  <sneumann@ipb-halle.de>

	* Added unit test for charge=0 and charge=1

2012-10-26  Steffen Neumann  <sneumann@ipb-halle.de>

	* /inst/doc -> /vignettes: to please lates R devel
	* src/ims/distributionprobabilityscorer.cpp: remove stdout messages

2012-10-26  Steffen Neumann  <sneumann@ipb-halle.de>

	* src/disop.cpp (decomposeIsotopes): Add support for element count filtering

2012-04-21  Steffen Neumann  <sneumann@ipb-halle.de>

	* R/elements.R (initializeCharges): Fixed electron mass

2012-03-28  Steffen Neumann  <sneumann@ipb-halle.de>
	* Added citations in package and documentation

2012-03-26  Steffen Neumann  <sneumann@ipb-halle.de>
	* src/disop.cpp: fixed missing UNPROTECT(), avoids warning
	and possibly memory corruprtion and crashes

2012-03-11  Steffen Neumann  <sneumann@ipb-halle.de>
	* Reverted Windows build hack

2012-03-10  Steffen Neumann  <sneumann@ipb-halle.de>
	* Windows build hack

2012-03-06  Steffen Neumann  <sneumann@ipb-halle.de>
	* Windows build fixes, removed old configure.in

2012-02-23  Steffen Neumann  <sneumann@ipb-halle.de>
	* Moved from the ancient embedded Rcpp to RcppClassic,
  	  thanks to the work of Dirk Eddelbuettel who did the porting

2010-11-04  Steffen Neumann  <sneumann@ipb-halle.de>
	* Corrected bug that leads to wrong monoisotopic masses for molecules
	  containing elements where the most abundant isotope is not the first one,
	  discovered by Ralf Tautenhahn

2010-10-22  Steffen Neumann  <sneumann@ipb-halle.de>
	* R/elements.R: Added remaining elements to PSE,
	  contributed by Canteri Roberto (http://m2b2.fbk.eu/en/people)

2010-05-18  Steffen Neumann  <sneumann@ipb-halle.de>
	* added Runit test infrastructure

2010-04-02  Steffen Neumann	<sneumann@ipb-halle.de>
	* added Selenium to list of elements
	* added Cobalt to list of elements
	* fixed Selenium abundances and masses

2010-02-08  Steffen Neumann	<sneumann@ipb-halle.de>
	* added parameter maxisotopes to getMolecule() and decompose*()

2008-09-02  ckuhl	<ckuhl@ipb-halle.de>
	* R/elements.R: added Deuterium

2008-08-11  sneumann  <sneumann@ipb-halle.de>

	* R/elements.R (initializeCharges): added initializeCharges, which
	can be useful for getMolecule("H3O+", elements=c(initializeCHNOPS(),initializeCharges()))
	* R/Rdisop.R: fixed important bug which always initialised the
	full PSE when supplying a special elements list

2008-04-23  sneumann  <sneumann@ipb-halle.de>

	* R/elements.R: fixed some masses/abundances,
	                added more elements

2008-02-15  sneumann  <sneumann@kons.ipb-sub.ipb-halle.de>

	* R/elements.R (initializePSE): Fixed Mass of Na isotope

2007-12-04  sneumann  <sneumann@ipb-halle.de>

	* configure.win, src/Makevars.win, src/win/*: Fix Windows build

2007-12-04  sneumann  <sneumann@ipb-halle.de>

	* R/Rdisop.R, man/decomposeMass.Rd: added absolute mass deviation

2007-10-29  begert  <begert@ipb-halle.de>

	* R/elements.R: Fixed O mass

2007-10-19  sneumann  <sneumann@ipb-halle.de>

	* NAMESPACE: Re-enabled useDynLib(libims) to fix Linux Build

2007-10-15  sneumann  <sneumann@ipb-halle.de>

	* configure.win, src/Makevars.win: Fix Windows build

2007-10-14  Steffen Neumann  <sneumann@ipb-halle.de>

	* man: fixed some manpages

2007-07-26  sneumann  <sneumann@ipb-halle.de>

	* removed several get*Masses in favour of getMass
	* polished vignette

2007-07-11  sneumann  <sneumann@ipb-halle.de>

	* R/elements.R, R/Rdisop.R: Formatting changes
	* configure.in: disabled autogen for imslib

2007-07-09  sneumann  <sneumann@ipb-halle.de>

	* DESCRIPTION (Version): bumped Version following BioC scheme

2007-07-03  sneumann  <sneumann@ipb-halle.de>

	* src/disop.cpp: Clear error Message before running

2007-06-14  sneumann  <sneumann@ipb-halle.de>

	* R/Rdisop.R: removed CHNOPS warning message
	* Windows: first Windows build

2007-06-07  sneumann  <sneumann@ipb-halle.de>

	* R/Rdisop.R (decomposeMass): fixed call

2007-06-05  sneumann  <sneumann@ipb-halle.de>

	* src/disop.cpp: Fixed stack imbalance for empty decompositions
	* src/disop.cpp: improved Error Handling

2007-05-25  sneumann  <sneumann@ipb-halle.de>

	* R/elements.R: Added na, k, cl, br, f, i, fe, mg, ca

	* R/Rdisop.R: moved isotope table to own file

2007-05-15  Steffen Neumann  <sneumann@ipb-halle.de>

	* Added addMolecule and subMolecule
	to do arithmetics with adducts / fragments

2007-05-04  Steffen Neumann  <sneumann@ipb-halle.de>

	* configure.in: Re-Added local copy of IMS as fallback

2007-04-30  Steffen Neumann  <sneumann@ipb-halle.de>

	* R/zzz.R: removed unnecesary library.dynam()
	which also caused problems on systems without libR.so
	* src/ims/*: moved imslib sources into src/ subfolder
	instead of using unchanged libims.a

2007-03-23  Steffen Neumann  <sneumann@ipb-halle.de>

	* src/disop.cpp: Removed decomposeMass(), this case is handled by
	the R code.

