Changes in version 2.3-2 (2024-10-24)                  

    o   fix PROTECT stack imbalance caused if variable names are not
	provided (thanks to Nicholas Davies for identifying; github issue #1).

    o   update to use latest R API to eliminate CRAN NOTEs.

                 Changes in version 2.3-1 (2024-04-17)                  

    o   previously, the maxtau argument only constrained tau-leaping
	steps.  Now modified to also constrain exact steps and the jump to
	the final time that occurs if all transition rates are 0; these
	changes allow for rate functions that are strongly time-dependent.

    o   clarify description of maxtau argument in help page

    o   eliminate use of Rinternal #defines that strip the Rf_ prefix

                  Changes in version 2.3 (2023-11-28)                   

    o   add option to report executed transitions

    o   explicitly use format string with "error" and "warning" functions
	to pass cran automatic checks.

                 Changes in version 2.2-3 (2019-03-19)                  

    o   fix clang compiler error

                 Changes in version 2.2-2 (2019-03-12)                  

    o   add "Gillespie stochastic simulation algorithm" keyword phrase to
	DESCRIPTION to aid people searching for a package such as this
	one.

    o   fix two PROTECT errors (thanks to Tomas Kalibera's tool for identifying)

    o   refactor C++ convenience functions to avoid false warnings about
	PROTECT errors from above tool.

    o   update R/C interface code to use R's automatic registration of
	exported symbols

    o   remove from help pages the "see also" mention of GillespieSSA
	package, which has been orphaned for many years now.

                 Changes in version 2.2-1 (2016-10-25)                  

    o   rework to avoid usage of C99 features not included in C++98

    o   use title case for package title in DESCRIPTION

    o   update maintainer email address

                  Changes in version 2.2 (2014-11-19)                   

    o   Add check for infinite transition rate; if found, abort with a
	meaningful warning message and return results generated until this point.

    o   If abort due to user interrupt, now return results generated so far.

                  Changes in version 2.1 (2014-05-08)                   

    o   Remove automatic byte-code compilation of R rate functions handed
	to ssa.adaptivetau (previously had been using library(compile)).
	Previous behavior led to significant inefficiencies if
	ssa.adaptivetau was called multiple times with the same rate
	function; thanks to Sebastian Funk for raising this issue.
	Instead, modify documentation to recommend that users use
	enableJIT(1).

                  Changes in version 2.0 (2014-03-24)                   

    o   transition matrix ("nu") can now be specified with an
	alternative data structure to reduce memory usage for large sparse
	matrices

    o   new feature: transitions may be designated as "halting", which
	will cause simulation to stop after executing one of these
	transitions

    o   streamlined code for dealing with transition classification

    o   call PutRNGstate before calling user-supplied rate function.
	While the rate function itself must not be stochastic, if a
	unnecessary call to Get/PutRNGState were to occur (e.g., as done
	by Rcpp at entry/exit to all exported functions), the adaptivetau
	algorithm could get scrambled.  Adding this call covers this
	situation at relatively low cost.

    o   fix vignette typo

    o   bug fix: incorrect type allocation for R_NamesSymbol; thanks to
	Brian Ripley for catching.

    o   handle case where final time ("tf" parameter) is an integer data
	type; thanks to Sebastian Funk for sending a patch.

                 Changes in version 1.1-1 (2013-11-11)                  

    o   Remove #include <cmath>, which appears (?) to have been
	unnecessary and causes a conflict when using isnan with -std=c++11
	and "using namespace std".

    o   Replace "isnan" (from standard) with "ISNAN" (R macro to ensure
	portability)

    o   also remove stray files from vignette directory

                  Changes in version 1.1 (2013-07-28)                   

    o   Fix use of "eval" by using R_EmptyEnv instead of NULL.

    o   Revert memory leak prevention / error handling code due to not
	being part of the public R API (as pointed out by Brian Ripley,
	only public API is allowed in CRAN).  Unfortunately interrupting
	execution will now almost certainly lead to memory leaking.

                        Changes in version 1.0-1                        

    o   Fixed validity check that aborts on non-integer initial conditions
	(previously was being too permissive).

    o   removed .Rhistory file accidently left under /vignettes directory

                  Changes in version 1.0 (2012-04-10)                   

    o   Fixed memory bug which could, under some circumstances, have lead
	to segmentation fault from premature garbage collection.

    o   Fixed implementation of implicit tau-leaping algorithm (used when
	Jacobian supplied & specified by adaptive tau algorithm) and
	clarified corresponding documentation.

    o   Fixed error handling to free memory allocated in heap upon abort

    o   Added new entrypoint -- ssa.exact -- that directly runs the "exact"
	simulation C++ function rather than the tau-leaping algorithm.

    o   Made algorithm more robust for deterministic transitions.

    o   Improved error messages when passed invalid initial conditions or
	rate function.

    o   Byte-code compile user rate functions if compiler package is available.

    o   Allow ssa.maketrans to handle variable names in addition to indices.

    o   Wrote vignette with three examples.

                 Changes in version 0.902 (2011-01-03)                  

    o   Fix Solaris compiler errors.

                 Changes in version 0.901 (2010-11-13)                  

    o   Fix non-portable use of LAPACK_LIBS.  Thanks to Brian Ripley.

                  Changes in version 0.9 (2010-10-20)                   

    o   First version in CRAN