2008-03-18  Patrick Aboyoun  <paboyoun@fhcrc.org>

	* man/externalVectorWithStorage-class.Rd man/indirectExternalMatrix-class.Rd man/indirectExternalVector-class.Rd
	* R/basicFuns.R src/allocator.c src/coerce.c
	Fixed some long-standing issues that were causing warnings when checking the package.

2008-03-17  Patrick Aboyoun  <paboyoun@fhcrc.org>

	* R/basicFuns.R R/Groups.R R/indirect.R R/init.R src/allocator.c
	Fixed some long-standing issues that were causing errors when building the package.

2003-10-14  Saikat DebRoy  <saikat@stat.wisc.edu>

	* src/character.h, R/externalVector.R, R/index.R, R/init.R, src/character.c, src/common.h, src/externalVector.c, src/slice.c, src/storage.c, src/subscript.c:
	Preliminary code to simplify subscripting added to
	sdr-experimental branch.

2003-10-13  Saikat DebRoy  <saikat@stat.wisc.edu>

	* R/coerce.R: Remove the is.xxx methods.

	* src/externalVector.c:
	Fix problem in asEach. Fix names subsetting with allIndex.

	* R/coerce.R, R/externalVector.R, R/indirect.R, R/matrixIndex.R:
	Coercion fixes. Better compatibility with R subsetting.

	* DESCRIPTION: Switch from x.y-z to x.y.z version format.

	* R/coerce.R: Fix wrong method function argument lists.

	* R/coerce.R: Remove as.logical method until a bug fix in methods.

	* DESCRIPTION: Add coerce.R to Collate

	* DESCRIPTION: Bump version number.

	* R/allocators.R, R/externalVector.R, R/init.R, R/simpleStorage.R, R/storage.R, R/zzz.R, man/gcAllocator-class.Rd, src/allocator.c, src/externalVector.c, src/slice.c, src/storage.c, src/subscript.c:
	Bug fixes and tidying up.

	* R/coerce.R: Add coercion and type testing routines

2003-10-09  Saikat DebRoy  <saikat@stat.wisc.edu>

	* man/allIndex-class.Rd, man/noneIndex-class.Rd:
	Add manual pages for allIndex and noneIndex

	* man/coerce-methods.Rd: Remove extra title.

	* R/index.R, src/slice.c: Add initializers for the index classes

	* R/externalVector.R:
	Use length(dim(x)) == 2 instead of  dim(x) == 2 as a test for
	matrices.

	* R/externalVector.R, R/indirect.R:
	Add is.finite and other similar methods.

	* TODO: Add is.finite to the TODO list.

	* man/coerce-methods.Rd: Add documentation for coerce methods.

2003-10-08  Saikat DebRoy  <saikat@stat.wisc.edu>

	* man/Subset.Rd: Add documentation for coerce methods

	* man/Subset.Rd: Add documentation for Subset and Subset2

	* man/SubscriptList.Rd: Add documentation for SubscriptList

	* src/subscript.c: Add some coercion of arguments to SubscriptList

	* R/index.R:
	Remove function StandardIndexList - its work is now done by
	SubscriptList.

	* ChangeLog: Update ChangeLog.

	* R/basicFuns.R, R/indirect.R, src/allocator.c, src/arraySummary.c, src/common.h, src/externalVector.c, src/groups.c, src/slice.c, src/storage.c, src/storageMethods.h, src/subscript.c:
	Bug fixes for math operations. Add group generics for indirect external objects. Add two argument log methods.

	* TODO: Remove finished items.

	* DESCRIPTION: Bump version number.

	* R/basicFuns.R, R/externalVector.R, R/index.R, R/indirect.R:
	Make some bug fixes.

2003-10-07  Saikat DebRoy  <saikat@stat.wisc.edu>

	* R/init.R, install.R:
	Change package names in library() calls to character strings.

	* R/index.R: Remove setAs from positiveIndex to integer.
	Fix typos.

	* ChangeLog: Update ChangeLog.

	* DESCRIPTION: Bump version number.

	* R/externalVector.R, R/index.R, R/indirect.R, R/matrixIndex.R, src/slice.c, src/subscript.c, src/subscript.h:
	Fixes for indexing bugs.

	* man/gcAllocator-class.Rd: Fix loading of wrong library.

	* src/storage.c: Was #undef-ing INNER_IF instead of INNER_SWITCH.

	* src/storageMethods.h, src/subscript.c, src/subscript.h, ChangeLog, DESCRIPTION, R/externalVector.R, R/index.R, R/indirect.R, R/init.R, R/matrixIndex.R, install.R, src/allocator.c, src/arraySummary.c, src/common.h, src/externalVector.c, src/externalVector.h, src/groups.c, src/slice.c, src/storage.c:
	Add support for various subscript types. Add indirect external matrix and vector classes.

2003-09-25  Saikat DebRoy  <saikat@stat.wisc.edu>

	* TODO: Lower the priority of BerkeleyDB.

2003-09-18  Saikat DebRoy  <saikat@stat.wisc.edu>

	* src/externalVector.c: Fix error checking.

	* src/storage.c: More modifications to subset and subassign code.

2003-09-17  Saikat DebRoy  <saikat@stat.wisc.edu>

	* ChangeLog: Update ChangeLog.

	* DESCRIPTION: Bump version number.

	* src/externalVector.c: No need to calculate subscripts here any more.

	* src/subscript.c, src/storage.c, src/storageMethods.h:
	Change GET_STORAGE_EXT_PTR_UNCHECK to GET_STORAGE_EXT_PTR_UNCHECKED.

	* ChangeLog: Update ChangeLog.

	* DESCRIPTION: Add index.R to Collate field. Make a version bump.

	* src/storage.c:
	Slightly improve the performance of subset and subassign methods.

	Change in initialization routines.

	* src/groups.c: Change in initialization routines.

	* src/externalVector.h: Add declaration of SubscriptList.

	* src/externalVector.c:
	We do not need the externalVectorDropDims function - just use DropDims
	from R.

	Fix warnings handling in externalVector_asEach.

	Change initializer routine.

	* src/slice.c: Initial commit for C routines for slice objects.

	* src/subscript.c: Reimplement the subscript operations of R.

	* src/arraySummary.c, src/allocator.c: Change in initializer routine.

	* R/index.R:
	Preliminary version of various types of index objects. Add the
	SubscriptList function.

	* R/externalVector.R:
	Fix the show method. Fix dimnames<- and dim<- methods. Allow
	externalVector objects as dimnames elements. Use SubscriptList to
	precalculate the subscripts.

	* R/allocators.R: Make a library(methods) call.

2003-09-15  Saikat DebRoy  <saikat@stat.wisc.edu>

	* R/externalVector.R: Fix a typo.

2003-09-12  Saikat DebRoy  <saikat@stat.wisc.edu>

	* ChangeLog: Update ChangeLog.

	* DESCRIPTION: Bump version number

	* src/storageMethods.h:
	Rename GET_EXT_STORAGE and SET_EXT_STORAGE to GET_STORAGE_EXT_PTR and
	SET_STORAGE_EXT_PTR. Make GET_STORAGE_EXT_PTR check if the pointer was
	loaded from a previously saved R image and if so, try to restore.

	Add GET_STORAGE_EXT_PTR_UNCHECK which does not do this checking.

	* src/storage.c:
	Simplify simpleStorage class - make the gcAllocator do most of the
	work.

	Add support for restoring the external pointer after a saved R image
	is loaded.

	* src/externalVector.c:
	Add more error messages to VectorSubassign and do some code
	reorganization.

	* src/allocator.c: Add support for allocaton of vector R objects.

	Add support for restoring allocated pointers after loading a saved R
	image.

	* R/storage.R: Rename getCStorageSize to getStorageSize.

	Change signature of internalType.

	* R/simpleStorage.R:
	Simplify the simpleStorage class operations - most of the work is now
	done by the allocator.

	* R/primitivevectors.R: Add error checking for type argument.

	* R/externalVector.R:
	Fix class definition of externalVectorWithStorage - was missing
	inheritence from externalVector.

	Add generic getExternalStorage -> returns externalStorage object
	associated with an externalVector object.

	In initialize method for externalVectorWithStorage set each of the
	elements with the default element.

	Fix show method for externalVector.

	Fix defaultElement method for exterVector.

	* R/allocators.R:
	Add support for allocation of R vector objects by gcAllocator.

	Add support for restoring allocated external pointer address after
	restoring a saved R image.

	* TODO: Update TODO.

	* DESCRIPTION:
	Remove exprExternal.R from Collate field (not checked in).

	* DESCRIPTION:
	Remove xseq.R from the Collate field for now (xseq.R is not checked in
	at present).

	* src/arraySummary.c, src/externalVector.c, src/groups.c, src/storage.c, src/storageMethods.h:
	rename SET_EXT_STORAGE and GET_EXT_STORAGE to SET_STORAGE_EXT_PTR and GET_STORAGE_EXT_PTR

2003-09-11  Saikat DebRoy  <saikat@stat.wisc.edu>

	* ChangeLog: Update ChangeLog

	* DESCRIPTION: Bump version number

	* ChangeLog: Automatically generate ChangeLog from CVS logs

	* TODO: Add a TODO file

	* README: Add a README file

	* R/primitivevectors.R: Add the externalMatrix function

	* R/externalVector.R:
	change the name of the generic "elementType" to "defaultElement"

2003-09-10  Saikat DebRoy  <saikat@stat.wisc.edu>

	* src/arraySummary.c: add arraySummary.c.

	* R/basicFuns.R: add basicFuns.R.

	* R/01allocators.R, R/02storage.R, R/03simpleStorage.R, R/Groups.R, R/allocators.R, R/externalVector.R, R/simpleStorage.R, R/storage.R, R/zGroups.R, R/zzz.R, src/externalVector.c, src/storage.c, src/storageMethods.h, DESCRIPTION:
	Add colSums, colMeans etc. Reorganize the .R files and use
	Collate in DESCRIPTION.

2003-09-09  Saikat DebRoy  <saikat@stat.wisc.edu>

	* R/externalVector.R, R/zzz.R, src/externalVector.c:
	Add initial support for simpleStorage objects storing character
	or list like vectors.

	* R/02storage.R, R/03simpleStorage.R, src/externalVector.c, src/storage.c, src/storageMethods.h:
	Some bug fixes.

	* src/externalVector.c, src/externalVector.h, src/storage.c:
	Finish matrix subset and subassign operation implementations.

	* R/externalVector.R: Some small changes in show.

	* R/externalVector.R, src/storage.c:
	fix a problem with matrix subsetting.

2003-09-08  Saikat DebRoy  <saikat@stat.wisc.edu>

	* R/externalVector.R, R/zGroups.R, src/externalVector.c, src/groups.c, src/storage.c, src/storageMethods.h:
	Add matrix indexing support.

	* DESCRIPTION, R/externalVector.R, R/zGroups.R, src/externalVector.c, src/groups.c, src/storage.c, src/storageMethods.h:
	Bug fixes.

	* ChangeLog, DESCRIPTION, R/01allocators.R, R/02storage.R, R/03simpleStorage.R, R/externalVector.R, R/primitivevectors.R, R/zGroups.R, R/zzz.R, install.R, man/allocate-methods.Rd, man/allocator-methods.Rd, man/deallocate-methods.Rd, man/externalAllocator-class.Rd, man/gcAllocator-class.Rd, man/getPointer-methods.Rd, man/summary-methods.Rd, src/allocator.c, src/externalVector.c, src/externalVector.h, src/groups.c, src/storage.c, src/storageMethods.h:
	Initial check-in for externalVector.

