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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1833, Tue May 8 12:25:57 2007 UTC
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1    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
4            entries.
5            * tests/indexing.R(out): add regression test for it
6    
7    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
10            name for "!" method definitions.
11    
12    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Tsparse.R (intI): new utility, used for "[" :
15                    Cleanup up there, and fixes for duplicated indices - more TODO!
16    
17            * tests/indexing.R(out): more tests
18    
19    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
20    
21            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
22            code that is now part of the R Lapack library.
23    
24            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
25            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
26    
27    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
30    
31    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
34            up with extraneous names '0'...'<n-1>'
35    
36    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgTMatrix.R (mat2dgT): care about NAs
39    
40    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/kronecker.R: triangularity preserving methods
43    
44    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/kronecker.R: new file collecting kronecker() methods in one
47                    place.  Goal: become much faster!
48    
49    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
52            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
53            can be much faster.
54    
55            * tests/matprod.R: add regression tests for these (upper & lower).
56    
57    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/Matrix.R (diff): method for our Matrices.
60    
61            * R/sparseMatrix.R (isDiagonal): check dim()!
62    
63    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (dim<-): new method for "reshape()" built on a
66            proposal from Tamas Papp.
67    
68    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
71    
72            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
73            rather define and export  cBind() and rBind() only.
74            --> useRs *must* change code that used to have cbind()/rbind() !!
75    
76            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
77            * R/bind.Rout.save: ditto
78    
79    2007-02-16  Douglas Bates  <bates@r-project.org>
80    
81            * DESCRIPTION (Date, Version): 0.9975-11 with new date
82            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
83            const modifier on declaration of the array 'valid'
84    
85    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
88    
89    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
92    
93            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
94            * tests/simple.R: test the above and some of these coercions:
95    
96            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
97                    be careful to avoid infinite recursion, using new coercions in
98            * R/ngCMatrix.R and nsC... and ntC...
99            * R/lsparseMatrix.R: ditto
100    
101            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
102    
103            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
104            * R/Rsparse.R: reactivate .Call()s
105    
106            * tests/Class+Meth.R: a bit more on actual classes
107    
108    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
111    
112    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.9975-10 to upload
115    
116            * tests/Class+Meth.R (tstMatrixClass): require coercions to
117            specific classes less unconditionally.
118    
119            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
120    
121            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
122    
123            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
124            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
125            R_to_CMatrix segfaults on one platform.
126            Eliminate most coercion method to *specific* classes, and replace
127            with virtual classes coercions.
128    
129    
130    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
131    
132            * src/init.c: export the CHM...._validate() placeholders, since
133            they *are* called.
134    
135            * tests/Class+Meth.R (classCanCoerce): and starting to test
136            all as(<from>, <to>)
137    
138    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
141            * tests/indexing.R: tested now
142            * tests/indexing.Rout.save: updated
143    
144            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
145            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
146            appropriate.
147    
148            * NAMESPACE: export a trivial
149            * R/Matrix.R: drop() Matrix-method
150    
151            * R/AllClass.R: moved all prototypes to virtual super classes.
152    
153            * R/Rsparse.R: many more coercions to have less exceptions in
154            * tests/Class+Meth.R:
155    
156            * R/Ops.R (Compare): tweak for case with NA
157            * tests/simpl.R: hence another 'FIXME' eliminated
158    
159    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
162            objects.
163    
164            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
165              and more of "!", "&", "|", all, any; coercions
166    
167            * R/Rsparse.R: many coercions (which enable quite a few other
168            methods), thanks to enhancements in
169            * src/dgCMatrix.c (R_to_CMatrix): new, and
170            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
171            symmetric & triangular and ..RMatrix objects.
172    
173            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
174            renamed file from src/dsTMatrix.c;
175            now dealing with symmetric and triangular Tsparse coercions, both
176            to dense and general.
177    
178    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
181    
182            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
183            where sensible when the <numeric> is of length > 1.
184    
185    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Matrix.R ([<-): for M[] <- value: fix length
188    
189    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
192            * R/ndenseMatrix.R: new coercions n* -> l*
193    
194    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
197    
198            * R/Ops.R ("Logic"): and other "Ops", many updates
199    
200    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * src/Mutils.h (SET_DimNames): new utility
203    
204            * R/Auxiliaries.R (nnzero): improved and now exported via
205    
206            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
207    
208    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/diagMatrix.R (!): fix typo.
211    
212    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/Auxiliaries.R (as_Csparse): and quite a few others:
215                    allow to pass class definition --> speedup
216            * R/sparseMatrix.R: apply the above
217    
218            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
219    
220            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
221            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
222            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
223    
224            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
225    
226            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
227            and use it for "sparse*" as well, since it's faster than the
228            as_Csparse(.) way.
229    
230    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
233    
234    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
237            as method for   M[ ij ] <- v
238            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
239    
240            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
241            FALSE answer
242    
243            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
244            * tests/indexing.R: test it, and some of the above
245    
246    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Auxiliaries.R (is_duplicatedT): new utility
249    
250    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * src/init.c (R_init_Matrix): export cholmod_scale
253    
254    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
257            base::as.matrix to (x, ...)
258    
259    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
262            file; start using "Logic", hence
263    
264            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
265            * NAMESPACE: import and export "Logic"
266    
267    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
270            only needed previously to R version 2.5.0.
271    
272    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
275    
276            * R/Tsparse.R (replTmat): fix subassignment of triangular
277            * R/Csparse.R (replCmat): ditto
278            * tests/indexing.R: more tests, incl the above fix
279    
280    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/Auxiliaries.R (drop0): extend for non CSparse
283            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
284    
285            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
286                    use uplo correctly (!); other places: use uplo_P() macro
287    
288            * R/Csparse.R (replCmat): call diagU2N() when needed
289            * R/Tsparse.R (replTmat): ditto
290    
291            * src/dtCMatrix.c (tCMatrix_validate): new
292            * src/dtTMatrix.c (tTMatrix_validate): new, used in
293            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
294    
295            * R/diagMatrix.R (replDiag): to use in [<-
296    
297    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
300                    also more general diagU2N().
301    
302    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
305            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
306    
307    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * tests/bind.R: a few more cases
310            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
311    
312            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
313            * R/ddenseMatrix.R (cbind2/rbind2)
314            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
315            * tests/indexing.R
316            * tests/indexing.Rout.save: updated
317    
318    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
321            * tests/indexing.R
322    
323    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
326            align with proper position of "0", i.e., right for integers.
327            argument 'align' by default is "fancy".
328    
329    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
332            * R/Csparse.R: and fix "Compare" for more cases.
333            * tests/Class+Meth.R: test some of these (m == m, m != m)
334    
335    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/lsparseMatrix.R: all() and any() methods
338            * R/ldenseMatrix.R:      ditto
339            * NAMESPACE, R/Matrix.R: ditto
340    
341            * man/all-methods.Rd: document them minimally
342    
343            * tests/simple.R: add a few examples for these
344    
345    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Tsparse.R ([): fix long standing typo in symmetric case
348            * man/dsCMatrix-class.Rd: add example exhibiting the above case
349    
350    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
353            to LL before converting to a sparse matrix. (The LDL form can be
354            converted to a sparse matrix but it is implicitly a unit
355            triangular matrix and a diagonal matrix overwritten on the diagonal.)
356    
357    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
358    
359            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
360    
361    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * DESCRIPTION (Version): updated -> release 0.9975-7
364            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
365    
366    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
369    
370    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
371    
372            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
373            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
374            is exactly singular.
375    
376    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * DESCRIPTION (Date): updated -> release 0.9975-6
379    
380    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
383            now returns symmetric.
384    
385            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
386    
387            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
388            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
389    
390            * R/Auxiliaries.R (.type.kind): added
391    
392    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
395            running src/CSparse_install.sh
396    
397            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
398    
399    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
402            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
403    
404            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
405    
406            * tests/Class+Meth.R (tstMatrixClass): now assure
407            the (important in method programming) property :
408    
409                    ###>>  Every "Matrix" is either
410                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
411    
412                    (where "*" stands for "Matrix")
413    
414            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
415    
416            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
417            * tests/validObj.R: checks for "comparison"
418    
419            * R/sparseMatrix.R ([): improved indexing for sparse;
420                    trying to keep <symmetric>[ n, n] symmmetric
421    
422            * tests/indexing.R: indexing for logical sparse now ok
423    
424    
425    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * src/Tsparse.c: use xTsparse_validate() , and hence remove
428    
429            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
430    
431    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
434    
435            * tests/simple.R: validObject() checking the above.
436    
437            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
438            replacing both dgCMatrix_validate and lgCM*.
439    
440            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
441            fix dimnames setting in other places.
442            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
443    
444    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
447    
448            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
449            symmetry test, via
450            * R/Auxiliaries.R (.as.dgC.0.factors):
451    
452    2006-11-01  Douglas Bates  <bates@r-project.org>
453    
454            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
455            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
456            <CsparseMatrix>) added
457    
458    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * tests/matprod.R: add a variation of Harri's example
461    
462            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
463            recursive infinitely.
464    
465            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
466    
467            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
468    
469    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
472            matrix if possible; test m+m == 2*m; now test dgRMatrix.
473            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
474            satisfy the above test.
475    
476    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
479    
480            * R/dgCMatrix.R: solve(a, b="missing") based on
481            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
482            RHS = NULL.
483    
484            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
485            add more (needed) [t]crossprod() methods.
486    
487            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
488    
489            * R/Auxiliaries.R (as_CspClass): cleanup
490            (drop0): internal utility for "Csparse_drop(*, 0)"
491            (.bail.out.2): encourage active feedback
492    
493    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
494    
495            * R/dMatrix.R(Compare): new(), then slots [no validity check]
496    
497            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
498            non-valid or 'sorted' case).
499    
500            * R/dsparseMatrix.R: add "chol" method.
501            * R/ddenseMatrix.R: ditto
502    
503            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
504            * NAMESPACE (Ops)
505            * R/diagMatrix.R (diag2T): simple utility used "higher level"
506            coercion; deprecating direct lower level coercions.
507    
508            * R/*.R (seq): use seq_len() and seq_along() where possible.
509    
510    
511    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * DESCRIPTION (Version): 0.9975-5 ready for release
514    
515    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
516    
517            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
518    
519    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/AllClass.R (corMatrix): add 'validity' check;
522                    comment out unused "LDL" class definition
523            * NAMESPACE: mention, but do not export "LDL" class
524            * R/corMatrix.R: new (simple), needed for R-devel with
525            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
526              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
527    
528    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
531            use Rprintf and R's error handling.
532    
533    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
536            * tests/matprod.R: add tests for the bug fixed.
537    
538    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
539    
540            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
541            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
542    
543    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
546    
547    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * DESCRIPTION (Version): 0.9975-3
550    
551            * R/diagMatrix.R (bdiag): new function constructing block diagonal
552            (sparse) matrices.
553            * man/bdiag.Rd: docu + examples
554    
555            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
556    
557            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
558            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
559    
560            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
561            that result is sparse or diagonal (and not dense).
562    
563            * man/Subassign-methods.Rd: fix examples
564    
565            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
566            should always return a sparse (and not sometimes a diagonal) matrix.
567    
568    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
571    
572    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
573    
574            * DESCRIPTION (Version): 0.9975-2
575    
576            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
577    
578    2006-10-02  Douglas Bates  <bates@R-project.org>
579    
580            * tests/dg_Matrix.R: Simplify test taking into account new code.
581    
582    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
585    
586            * R/lsTMatrix.R: new files w/ missing methods
587            * R/nsTMatrix.R:  "  'for completeness'
588    
589            * tests/Class+Meth.R: a bit less 'not.ok.classes'
590    
591            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
592    
593    
594    2006-09-28  Douglas Bates  <bates@R-project.org>
595    
596            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
597            included.
598    
599            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
600            Export C-callable functions used in Zt_create in lme4.
601    
602    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * DESCRIPTION (Version): 0.9975-1
605    
606            * tests/simple.R: less checks fail; using NA, found that our
607                    kronecker() is not base-compatible with NA's.
608    
609            * R/dMatrix.R: "Compare" method now implemented for all cases
610    
611            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
612    
613            * man/dtpMatrix-class.Rd: mention length of 'x' slot
614    
615            * src/dtpMatrix.c (dtpMatrix_validate): fix check
616            * src/dspMatrix.c (dspMatrix_validate): ditto
617    
618            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
619              including coercion to [nl]tTMatrix.
620    
621            * R/diagMatrix.R (show): print a header line as for other classes.
622    
623    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * src/Makefile.win (SUBDIRS): fix typo
626    
627    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
630    
631    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
632    
633            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
634            symmetric and y missing in R code using %*% (cholmod_aat doesn't
635            accept a symmetric matrix).
636            * tests/group-methods.R: Uncomment test of crossprod applied to
637            lsCMatrix objects.
638    
639    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/AllClass.R (symmetricMatrix): add validity method (available
642            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
643    
644            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
645    
646            * tests/indexing.Rout.save:
647            * tests/indexing.R: additions, mainly for 'lsparse'
648    
649            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
650            case.
651    
652            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
653    
654    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
657                    as 'N' (1-letter - Ok?)
658    
659            * tests/group-methods.R: add test for logical + NAs
660    
661            * R/dMatrix.R ("Compare"): fix to work with NA's
662    
663            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
664    
665            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
666                    which is implemented.
667    
668    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * src/chm_common.c: coerce logical <-> double instead of
671            typecasting;  needed for "l" matrix handling in cholmod.
672    
673            * tests/other-pkgs.R (graph): small extension in "graph" checks.
674    
675            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
676            (Tsp2grNEL): other fixes needed
677    
678    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
681                    Matrices, since "lMatrix", also "lsparseM" can have NA
682            * R/ndenseMatrix.R, etc: new source files
683            * man/nsparseMatrix-classes.Rd, etc: new help files
684            * tests/: adaptions
685            * src/chm_common.c (chm_dense_to_SEXP): and others:
686                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
687            * src/Csparse.c, etc: ditto
688    
689    2006-09-11  Douglas Bates  <bates@R-project.org>
690    
691            * src/Mutils.[ch],init.c inst/include/*.h: Move the
692            alloc_d**Matrix functions to the lme4 package.
693    
694    2006-09-09  Douglas Bates  <bates@R-project.org>
695    
696            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
697            fixed
698    
699    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/lMatrix.R: new
702    
703            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
704    
705            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
706            * man/tcrossprod.Rd: ditto
707    
708    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
709    
710            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
711            for exported functions
712            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
713            Remove partitioning algorithms for sparse matrix reordering.  The
714            copyright on the Metis code was problematic and the methods were
715            rarely used.
716            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
717            operations are now done entirely in CHOLMOD code.
718    
719    2006-09-06  Douglas Bates  <bates@R-project.org>
720    
721            * src/Mutils.h: Remove functions that are no longer used.
722    
723    2006-09-04  Douglas Bates  <bates@R-project.org>
724    
725            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
726            * src/DEPS.mkf: update
727    
728    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * created branches/Matrix-for-R-2.3.x;  on trunk: do
731            * DESCRIPTION (Version): 0.9975-0
732            (Depends): R (>= 2.4.0)
733    
734    2006-09-01  Douglas Bates  <bates@R-project.org>
735    
736            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
737    
738    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
741            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
742    
743            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
744    
745    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
748            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
749            * R/dsparseMatrix.R: ditto
750            * R/Csparse.R: ditto
751    
752    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/dMatrix.R (Compare): improve availability of "<", etc
755            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
756    
757    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
760            of a 0-index which was used as 1-index (..hmm)
761    
762            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
763    
764            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
765            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
766            (.is.diagonal): ditto
767    
768            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
769    
770            * R/Matrix.R (Matrix): also work for NA data
771    
772  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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