CHANGES IN VERSION 1.38.3
--------------------------

BUG FIXES

	- Updated Joseph N. Paulson's email address in Authors@R to
	  joseph.paulson@yale.edu.

	  R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.

CHANGES IN VERSION 1.38.2
--------------------------

BUG FIXES

	- Replaced deprecated Author:/Maintainer: DESCRIPTION fields with the
	  modern Authors@R: format using person() with role=c("aut","cre") for
	  the maintainer. BiocCheck >= 1.46 ERRORs on the old field format.
	  Updated maintainer email to joey711@gmail.com.
	  Added .BiocCheck to .Rbuildignore.

	  R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.

CHANGES IN VERSION 1.38.1
--------------------------

BUG FIXES

	- Removed plyr from Imports. plyr was archived on CRAN, causing
	  R CMD check to ERROR on dependency resolution. All plyr calls
	  (alply, laply, ldply, llply) replaced with base-R equivalents
	  (lapply, do.call(rbind, lapply(...))) — backported from devel branch.

	- Moved rhdf5 from Imports to Suggests. HDF5 functionality is now
	  guarded by requireNamespace("rhdf5") checks; the package loads and
	  all JSON BIOM functionality works without rhdf5 installed.

	- Fixed Maintainer email address to a reachable address.

	- Bumped R dependency from >= 3.2 to >= 4.1 and Matrix from >= 1.2
	  to >= 1.7-0, matching the current Bioconductor build environment.

	- Fixed deprecated expect_that(), is_identical_to(), is_a(), and
	  is_true() calls in tests/ that caused test ERROR under testthat >= 3.0.

	- Added write_hdf5_biom() exported function (backported from devel);
	  added write_hdf5_biom.Rd documentation; added test-hdf5-write.R.

	  R CMD check: 0 ERRORs, 0 NOTEs, 2 pre-existing vignette WARNINGs.

CHANGES IN VERSION 0.3.13
-------------------------

USER-VISIBLE CHANGES

	- Added make_biom function. Creates biom object from standard R data table(s).

CHANGES IN VERSION 0.3.12
-------------------------

USER-VISIBLE CHANGES

	- No user-visible changes. All future compatibility changes.

BUG FIXES

	- Unit test changes to work with upcoming R release and new testthat version. 

	- This solves Issue 4: https://github.com/joey711/biom/issues/4

CHANGES IN VERSION 0.3.11
-------------------------

USER-VISIBLE CHANGES

	- No user-visible changes. All future CRAN compatibility changes.

BUG FIXES

	- Clarified license and project in the README.md

	- Added TODO.html, README.html, and TODO.md to .Rbuildignore (requested by CRAN)

	- Moved `biom-demo.Rmd` to `vignettes/`

	- Updated `inst/NEWS` (this) file to official format

	- Removed pre-built vignette HTML so that it is re-built during package build.
 		  This updates things like the build-date in the vignette, but also ensures that 
		  the user sees in the vignette the results of code that just worked with their 
		  copy of the package.

CHANGES IN VERSION 0.3.10
-------------------------

USER-VISIBLE CHANGES

	- These changes should not affect any package behavior.

	- Some of the top-level documentation has been changed to reflect new development
 	  location on GitHub.

BUG FIXES

	- Minor fixes for CRAN compatibility

	- This addresses Issue 1: https://github.com/joey711/biom/issues/1

CHANGES IN VERSION 0.3.9
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

	- speed improvement for sparse matrices

NEW FEATURES

	- The `biom_data` parsing function now uses a vectorized (matrix-indexed) 
	  assignment while parsing sparse matrices.

	- Unofficial benchmarks estimate a few 100X speedup.

CHANGES IN VERSION 0.3.8
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

	- First release version released on CRAN