dimnames(), notably names(dimnames()) -- primarily in connection with symmpart(), skewpart() and forceSymmetric()

thinko

Fix remaining parts of R-(3.2.0) compatible behavior of matrix products (%*%, [t]crossprod) -- including previous bug of wrong m %*% v in one case

fix crossprod(<vec>, <dsyMatrix>) bug, sent from David Ruegamer, LMU.
Keep dimnames in (some more of) such products

new rsparsematrix() {with 'encoding trick'} for random sparse matrices;  
m_encodeInd[2]?() gains new argument 'orig_1'

.set.factors(x, *) now also works when 'x' has no 'factors' slot

A few things at once:
1) all.equal(*,..): "tolerance" instead of "tol";  "check.attributes"
2) All matrix products (%*%, [t]crossprod) in one new *.Rd file: man/matrix-products.Rd
3) R/products.R : Extend matrix products (and consistency tests) 
   a. to work with sparseVectors, 
   b. to correctly work in some cases they did not
   c. to be faster in other cases

all0() and any0() now via .Call(R_all0,..)

Version 1.1-0: as have C API change; class union "numIndex" is unused (and can harm, as it is not exported

3 new C-->R utilities; notably R_set_factors() -> .set.factors() for caching also from R, not just in C

 as(<csr>, "dgCMatrix") works again; Matrix now *runs* in older R even if installed in R >= 2.15.2

cannot use R_SVN_REVISION (inside #if ..) yet

use R_SVN_REVISION (instead of less precise R_VERSION)

declare La_norm_type / La_rcond_type

update (before release)

using .External(Mmatrix, ...) instead of .Internal(matrix(...))

denseMatrix methods for  'diag<-' which preserve (uni)triangularity, symmetry,
etc and are fast via C *_setDiag() functions.
Further, more Ops, e.g. preserving symmetry for  <symmetric> o <diagonal>

remove "old" R_VERSION dependencies

Matrix_check_class_etc() has been in R-devel for a while now;
NAMESPACE imports for border line situation

doxygen "fixes"

ready for 1.0-0

get rid of "set but unused" warnings from gcc 4.6.0

use "(static) const char*" for the valid[] strings in Matrix_check_class_*()

R >= 2.10.0: ==> no longer needing Matrix_make_named(); R >= 2.13.0 will have R_check_class_and_super()

m_encodeInd(ij, ..): thinko from rev. 2614

m_encodeInd(ij, ..): better error message for non-matrix 'ij'

move Matrix/ directory "down"

M[ij] indexing now works with non-integer numeric ij and checks better; other changes, see ChangeLog

cosmetic

some cleanup; notably the exported M_R_cholmod_error()

more PROTECT() {from Andrew Runnalls}; doxy

make use of Rf_mkNamed() [as from the very latest R-devel] when in R >= 2.10.0

Change value of set_factor to be the cached factor

fix up internationalization of (error/warning) messages

Matrix_check_*() slightly more logical  PROTECT() / UNPROTECT() .. 
does not solve the problems (completely).

PROTECT()  "every SEXP in sight" inside the two  Matrix_check_class*(),
but this is still not quite sufficient

Add const in declaration (-Wall)

Remove unnecessary call to strdup whose result was not being freed

"fix" for the problem that .M.classEnv is not found when Matrix is only loaded but not attached

more robust MatrixClass(); in C, use methods:::classEnv() via wrapper

use C-level Matrix_check_class_and_super() ... forgot one

Matrix_check_class_and_super() [+ 'const' for Matrix_make_named()]

first step at dealing with NA in indices

get rid of superfluous 'return .. /* -Wall */' lines, producing warnings on Sunstudio cc

C based encodeInd() -> faster indexing; any()/all() for nsparse; printSpMatrix2(); show(<diag>)

slight change in class-definition of [d]diMatrix; better pos.definite checks for dpo* and dpp*

need  La_(norm|rcond)_type  definitions also for R-devel  {for now}

use diagU2N in more places; also new Tsparse_diagU2N()

s/norm_type/La_norm_type/ in order to move to R-devel

+ forceSymmetric(); generalize ddense_to_symmetric to dense_to_s.. and ddense_band to dense_band allowing simplified methods;  Matrix() and many man/*Rd : replace many as(*, <specific>) by as(*, <virtual superclass>)

-Wall additions

miscellaneous cleanup; typically indexing and coercion

Documentation errors caught by doxygen

merge 'branches/Matrix-APIchange' back into the trunk

Remove warnings after change to const char* CHAR

Consistency of bounds

many more coercions for diag(), "!", etc; see ChangeLog

accomplished quite a few small FIXMEs; see ChangeLog

miscellaneous "fixes" mostly in ChangeLog and/or related to diagonalMatrix

comments only

Move checks on column sorting of CsparseMatrix objects to Csparse_validate

Move the alloc_d**Matrix utility functions from the Matrix package to the lme4 package

Cleanup

Merging changes from Matrix-nolmer branch

Define and use class_P and mMatrix_as_dgeMatrix

Remove sections of code that are no longer used

use setAs("ddenseMatrix", "dgeMatrix", *) instead of older specific ones

Add ddiMatrix,dtpMatrix, dspMatrix and dppMatrix conversions. Remove no-longer-used functions.

Use dup_mMatrix_as_dgeMatrix

eliminate classed argument from dup_mM*() and dependencies

comments; cosmetic

Misunderstood effect of make_d_matrix_triangular and make_d_matrix_symmetric.  Now fixed.  Use _NOT_A_CLASS_ instead of dmatrix for the name of the class that should not occur.

updated for general types of classed Matrices, matrices or numeric or logical vectors.

Added dup_mMatrix_as_dgeMatrix utility

make*_(triangular|symmetric) : now for ldense* as well

new dMatrix_validate and dense_nonpacked_validate

Move glmer reweighting to internal_update_ZXy; rearrange the deck chairs

Modifications to mer2

packed_to_full_(double|int) and full_to_packed_*

use uplo_P() and diag_P() macros instead of *_value() functions

+ uplo_value(), diag_value()

comments

Coercion method for graphNEL to sparseMatrix class

Isolating and cleaning up the mer, lmer, and glmer functions

Keep -Wall quiet

Added Matrix_expand_pointers (callable from R) and moved utility for duplicating slots

Release 0.95-6

do not Calloc()/Free() in "good" case of check_scalar_string()

Methods and coercions for the dtpMatrix class

Clean up *_validate functions

shorten csc_components_transpose to csc_compTr

Internationalization and localization

rearranging utility functions in the C code

use mkString(); "uplo" and "diag" must be uppercase

Move the make_named function to Mutils as Matrix_make_named

renaming and rearranging classes

Renaming and reorganizing classes

Change name of slot from factorization to factors

Updates for factorization name and default value

Add registration of .Call functions

Bug fixes in 0.8-14

Add cscBlocked, tweak lmeRep

extending lmeRep to multiple nested grouping factors

Add the lmeRep class

Remove pdMat classes

Moving utilities to Matrix package

Remove storage of L-inverse

Permutations and update_mm

Adding coercions - fixing bugs

Move triplet_to_col from umfpack

Initial import