export(
	rows,
	columns,
	"rows<-",
	"columns<-",
	"dimnames<-.biom",
	merge.biom,
	"[.biom",

	biomRequest,
	biom.environment,

	metadata.character,
	search.MGRAST,
	dir.MGRAST,

	t_NA2Zero,
	t_Threshold,
	t_Log,
	t_ColCenter,
	t_ColScale,
	transform.biom,

	boxplot.biom,
	princomp.biom,
  	image.biom,

	rowstats,
	rowstats.matrix,
	rowstats.biom,

	distx,
	distx.matrix,
	distx.biom,

	getMetRows,
	getMetColumns,
	subRow,
	subColumn,
	parMap,
	parAuto,

	readSet,
	scrubSet,
	scrapeSet,
	expandSet,

	demoSets,
	buildDemoSets,
	hazPackages,
	dependencies,
	stepper,
	step.through,
	collapse,
	
	.Last.lib)

S3method ("dimnames<-", biom)
S3method (merge, biom)
S3method ("[", biom)

S3method (biom, environment)

S3method (metadata, character)

S3method (transform, biom)

S3method (boxplot, biom)
S3method (princomp, biom)
S3method (image, biom)

S3method (rowstats, matrix)
S3method (rowstats, biom)

S3method (distx, matrix)
S3method (distx, biom)

#-----------------------------------------------------------------------------------------
#  package BIOM.utils is a strict dependency, declared in "Depends:"
#  also (this is a separate point) methods for class "biom" are used throughout,
#  so it makes sense to import the entire package namespace.
#-----------------------------------------------------------------------------------------
import (BIOM.utils)

#-----------------------------------------------------------------------------------------
#  package MGRASTer ought not to be considered a dependency, perhaps, yet is declared in "Depends:"
#  because its environment seems to fail if not loaded this way.  nonetheless, the
#  following namespace import might reasonably be removed, in favor of explicit references.
#-----------------------------------------------------------------------------------------
import (MGRASTer)

#-----------------------------------------------------------------------------------------
#  all other packages are optional, each providing specific and limited analysis functionality.
#  we adopt the approach described in this remark from the (forthcoming) R-ext manual:
#    "If the intention is to give an error 
#    if the suggested package is not available, 
#    simply use e.g. rgl::plot3d."
#  the following are exceptions, because the matR package namespace depends on them:
#-----------------------------------------------------------------------------------------
importFrom (graphics, boxplot)
importFrom (graphics, image)
importFrom (stats, princomp)
