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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1878, Tue Jun 5 17:08:18 2007 UTC
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1    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4421] src/CSparse_install.sh: Modify for new organization of
4              CSparse package
5            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
6              SuiteSparse
7            * [r4426] src/Makefile: add ./UFconfig to the include path for
8              compilation
9            * [r4427] src/cs.c, src/cs.h: update to CSparse version 2.2.0
10            * [r4428] inst/doc/UFsparse/* src/AMD/* src/CHOLMOD/*
11              src/COLAMD/* src/UFconfig/UFconfig.h: Update to version 3.0.0 of
12              SuiteSparse
13    
14    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
17            * R/sparseMatrix.R (prSpMatrix): now gives a message about
18            suppressed column names.
19    
20    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
21    
22            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
23              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
24              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
25              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
26              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
27              Remove warnings after change to const char* CHAR
28    
29    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
30    
31            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
32              type of M_cholmod_ssmult
33    
34    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
35    
36            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
37              src/init.c: Yet another cholmod export - cholmod_ssmult
38    
39    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * NAMESPACE: exported drop0(), since
42            * man/drop0.Rd: I have seen several cases, I really wanted to use
43            it, so our users may want too.
44    
45    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * man/colSums.Rd: separately document colSums() etc, since these
48            have the extra argument 'sparseResult'.
49    
50    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
53            * man/spMatrix.Rd: docu., including examples
54    
55            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
56            in order to make colMeans() etc fast *and* correct.
57            * R/sparseVector.R (replSPvec): "[<-" functionality for
58            sparseVectors; tested in
59            * tests/simple.R:
60    
61    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
64            (very) sparse Matrices; output similar to Matlab's print().
65    
66    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
67    
68            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
69            0-based, indices (Jose Quesada <quesada@gmail.com>).
70    
71    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
72    
73            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
74    
75    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/Auxiliaries.R (sparsapply): new utility, much faster than
78            tapply1() for large sparse matrices.
79    
80    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/Matrix.R (dim<-): reshape now via sparseVector.
83    
84            * R/sparseVector.R: methods and function for
85            * R/AllClass.R: new "sparseVector" class and daughters.
86            * NAMESPACE: export new classes
87    
88    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * DESCRIPTION (Version): 0.99875-1
91            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
92    
93    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
96            indexing
97            * tests/indexing.R: test set for that.
98    
99    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
102            entries.
103            * tests/indexing.R(out): add regression test for it
104    
105    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
108            name for "!" method definitions.
109    
110    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Tsparse.R (intI): new utility, used for "[" :
113                    Cleanup up there, and fixes for duplicated indices - more TODO!
114    
115            * tests/indexing.R(out): more tests
116    
117    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
118    
119            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
120            code that is now part of the R Lapack library.
121    
122            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
123            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
124    
125    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
128    
129    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
132            up with extraneous names '0'...'<n-1>'
133    
134    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/dgTMatrix.R (mat2dgT): care about NAs
137    
138    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/kronecker.R: triangularity preserving methods
141    
142    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/kronecker.R: new file collecting kronecker() methods in one
145                    place.  Goal: become much faster!
146    
147    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
150            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
151            can be much faster.
152    
153            * tests/matprod.R: add regression tests for these (upper & lower).
154    
155    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Matrix.R (diff): method for our Matrices.
158    
159            * R/sparseMatrix.R (isDiagonal): check dim()!
160    
161    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Matrix.R (dim<-): new method for "reshape()" built on a
164            proposal from Tamas Papp.
165    
166    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
169    
170            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
171            rather define and export  cBind() and rBind() only.
172            --> useRs *must* change code that used to have cbind()/rbind() !!
173    
174            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
175            * R/bind.Rout.save: ditto
176    
177    2007-02-16  Douglas Bates  <bates@r-project.org>
178    
179            * DESCRIPTION (Date, Version): 0.9975-11 with new date
180            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
181            const modifier on declaration of the array 'valid'
182    
183    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
184    
185            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
186    
187    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
190    
191            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
192            * tests/simple.R: test the above and some of these coercions:
193    
194            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
195                    be careful to avoid infinite recursion, using new coercions in
196            * R/ngCMatrix.R and nsC... and ntC...
197            * R/lsparseMatrix.R: ditto
198    
199            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
200    
201            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
202            * R/Rsparse.R: reactivate .Call()s
203    
204            * tests/Class+Meth.R: a bit more on actual classes
205    
206    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
209    
210    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * DESCRIPTION (Version): 0.9975-10 to upload
213    
214            * tests/Class+Meth.R (tstMatrixClass): require coercions to
215            specific classes less unconditionally.
216    
217            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
218    
219            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
220    
221            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
222            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
223            R_to_CMatrix segfaults on one platform.
224            Eliminate most coercion method to *specific* classes, and replace
225            with virtual classes coercions.
226    
227    
228    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
229    
230            * src/init.c: export the CHM...._validate() placeholders, since
231            they *are* called.
232    
233            * tests/Class+Meth.R (classCanCoerce): and starting to test
234            all as(<from>, <to>)
235    
236    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
239            * tests/indexing.R: tested now
240            * tests/indexing.Rout.save: updated
241    
242            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
243            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
244            appropriate.
245    
246            * NAMESPACE: export a trivial
247            * R/Matrix.R: drop() Matrix-method
248    
249            * R/AllClass.R: moved all prototypes to virtual super classes.
250    
251            * R/Rsparse.R: many more coercions to have less exceptions in
252            * tests/Class+Meth.R:
253    
254            * R/Ops.R (Compare): tweak for case with NA
255            * tests/simpl.R: hence another 'FIXME' eliminated
256    
257    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
260            objects.
261    
262            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
263              and more of "!", "&", "|", all, any; coercions
264    
265            * R/Rsparse.R: many coercions (which enable quite a few other
266            methods), thanks to enhancements in
267            * src/dgCMatrix.c (R_to_CMatrix): new, and
268            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
269            symmetric & triangular and ..RMatrix objects.
270    
271            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
272            renamed file from src/dsTMatrix.c;
273            now dealing with symmetric and triangular Tsparse coercions, both
274            to dense and general.
275    
276    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
279    
280            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
281            where sensible when the <numeric> is of length > 1.
282    
283    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Matrix.R ([<-): for M[] <- value: fix length
286    
287    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
290            * R/ndenseMatrix.R: new coercions n* -> l*
291    
292    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
295    
296            * R/Ops.R ("Logic"): and other "Ops", many updates
297    
298    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * src/Mutils.h (SET_DimNames): new utility
301    
302            * R/Auxiliaries.R (nnzero): improved and now exported via
303    
304            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
305    
306    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/diagMatrix.R (!): fix typo.
309    
310    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Auxiliaries.R (as_Csparse): and quite a few others:
313                    allow to pass class definition --> speedup
314            * R/sparseMatrix.R: apply the above
315    
316            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
317    
318            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
319            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
320            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
321    
322            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
323    
324            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
325            and use it for "sparse*" as well, since it's faster than the
326            as_Csparse(.) way.
327    
328    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
331    
332    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
335            as method for   M[ ij ] <- v
336            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
337    
338            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
339            FALSE answer
340    
341            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
342            * tests/indexing.R: test it, and some of the above
343    
344    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/Auxiliaries.R (is_duplicatedT): new utility
347    
348    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * src/init.c (R_init_Matrix): export cholmod_scale
351    
352    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
355            base::as.matrix to (x, ...)
356    
357    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
360            file; start using "Logic", hence
361    
362            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
363            * NAMESPACE: import and export "Logic"
364    
365    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
368            only needed previously to R version 2.5.0.
369    
370    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
373    
374            * R/Tsparse.R (replTmat): fix subassignment of triangular
375            * R/Csparse.R (replCmat): ditto
376            * tests/indexing.R: more tests, incl the above fix
377    
378    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Auxiliaries.R (drop0): extend for non CSparse
381            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
382    
383            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
384                    use uplo correctly (!); other places: use uplo_P() macro
385    
386            * R/Csparse.R (replCmat): call diagU2N() when needed
387            * R/Tsparse.R (replTmat): ditto
388    
389            * src/dtCMatrix.c (tCMatrix_validate): new
390            * src/dtTMatrix.c (tTMatrix_validate): new, used in
391            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
392    
393            * R/diagMatrix.R (replDiag): to use in [<-
394    
395    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
398                    also more general diagU2N().
399    
400    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
403            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
404    
405    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * tests/bind.R: a few more cases
408            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
409    
410            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
411            * R/ddenseMatrix.R (cbind2/rbind2)
412            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
413            * tests/indexing.R
414            * tests/indexing.Rout.save: updated
415    
416    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
419            * tests/indexing.R
420    
421    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
424            align with proper position of "0", i.e., right for integers.
425            argument 'align' by default is "fancy".
426    
427    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
430            * R/Csparse.R: and fix "Compare" for more cases.
431            * tests/Class+Meth.R: test some of these (m == m, m != m)
432    
433    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/lsparseMatrix.R: all() and any() methods
436            * R/ldenseMatrix.R:      ditto
437            * NAMESPACE, R/Matrix.R: ditto
438    
439            * man/all-methods.Rd: document them minimally
440    
441            * tests/simple.R: add a few examples for these
442    
443    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/Tsparse.R ([): fix long standing typo in symmetric case
446            * man/dsCMatrix-class.Rd: add example exhibiting the above case
447    
448    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
449    
450            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
451            to LL before converting to a sparse matrix. (The LDL form can be
452            converted to a sparse matrix but it is implicitly a unit
453            triangular matrix and a diagonal matrix overwritten on the diagonal.)
454    
455    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
456    
457            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
458    
459    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
460    
461            * DESCRIPTION (Version): updated -> release 0.9975-7
462            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
463    
464    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
467    
468    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
469    
470            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
471            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
472            is exactly singular.
473    
474    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * DESCRIPTION (Date): updated -> release 0.9975-6
477    
478    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
481            now returns symmetric.
482    
483            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
484    
485            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
486            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
487    
488            * R/Auxiliaries.R (.type.kind): added
489    
490    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
493            running src/CSparse_install.sh
494    
495            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
496    
497    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
500            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
501    
502            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
503    
504            * tests/Class+Meth.R (tstMatrixClass): now assure
505            the (important in method programming) property :
506    
507                    ###>>  Every "Matrix" is either
508                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
509    
510                    (where "*" stands for "Matrix")
511    
512            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
513    
514            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
515            * tests/validObj.R: checks for "comparison"
516    
517            * R/sparseMatrix.R ([): improved indexing for sparse;
518                    trying to keep <symmetric>[ n, n] symmmetric
519    
520            * tests/indexing.R: indexing for logical sparse now ok
521    
522    
523    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * src/Tsparse.c: use xTsparse_validate() , and hence remove
526    
527            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
528    
529    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
532    
533            * tests/simple.R: validObject() checking the above.
534    
535            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
536            replacing both dgCMatrix_validate and lgCM*.
537    
538            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
539            fix dimnames setting in other places.
540            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
541    
542    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
545    
546            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
547            symmetry test, via
548            * R/Auxiliaries.R (.as.dgC.0.factors):
549    
550    2006-11-01  Douglas Bates  <bates@r-project.org>
551    
552            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
553            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
554            <CsparseMatrix>) added
555    
556    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * tests/matprod.R: add a variation of Harri's example
559    
560            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
561            recursive infinitely.
562    
563            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
564    
565            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
566    
567    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
570            matrix if possible; test m+m == 2*m; now test dgRMatrix.
571            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
572            satisfy the above test.
573    
574    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
577    
578            * R/dgCMatrix.R: solve(a, b="missing") based on
579            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
580            RHS = NULL.
581    
582            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
583            add more (needed) [t]crossprod() methods.
584    
585            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
586    
587            * R/Auxiliaries.R (as_CspClass): cleanup
588            (drop0): internal utility for "Csparse_drop(*, 0)"
589            (.bail.out.2): encourage active feedback
590    
591    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
592    
593            * R/dMatrix.R(Compare): new(), then slots [no validity check]
594    
595            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
596            non-valid or 'sorted' case).
597    
598            * R/dsparseMatrix.R: add "chol" method.
599            * R/ddenseMatrix.R: ditto
600    
601            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
602            * NAMESPACE (Ops)
603            * R/diagMatrix.R (diag2T): simple utility used "higher level"
604            coercion; deprecating direct lower level coercions.
605    
606            * R/*.R (seq): use seq_len() and seq_along() where possible.
607    
608    
609    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * DESCRIPTION (Version): 0.9975-5 ready for release
612    
613    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
614    
615            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
616    
617    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/AllClass.R (corMatrix): add 'validity' check;
620                    comment out unused "LDL" class definition
621            * NAMESPACE: mention, but do not export "LDL" class
622            * R/corMatrix.R: new (simple), needed for R-devel with
623            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
624              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
625    
626    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
627    
628            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
629            use Rprintf and R's error handling.
630    
631    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
634            * tests/matprod.R: add tests for the bug fixed.
635    
636    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
637    
638            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
639            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
640    
641    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
642    
643            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
644    
645    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * DESCRIPTION (Version): 0.9975-3
648    
649            * R/diagMatrix.R (bdiag): new function constructing block diagonal
650            (sparse) matrices.
651            * man/bdiag.Rd: docu + examples
652    
653            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
654    
655            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
656            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
657    
658            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
659            that result is sparse or diagonal (and not dense).
660    
661            * man/Subassign-methods.Rd: fix examples
662    
663            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
664            should always return a sparse (and not sometimes a diagonal) matrix.
665    
666    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
669    
670    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
671    
672            * DESCRIPTION (Version): 0.9975-2
673    
674            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
675    
676    2006-10-02  Douglas Bates  <bates@R-project.org>
677    
678            * tests/dg_Matrix.R: Simplify test taking into account new code.
679    
680    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
683    
684            * R/lsTMatrix.R: new files w/ missing methods
685            * R/nsTMatrix.R:  "  'for completeness'
686    
687            * tests/Class+Meth.R: a bit less 'not.ok.classes'
688    
689            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
690    
691    
692    2006-09-28  Douglas Bates  <bates@R-project.org>
693    
694            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
695            included.
696    
697            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
698            Export C-callable functions used in Zt_create in lme4.
699    
700    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * DESCRIPTION (Version): 0.9975-1
703    
704            * tests/simple.R: less checks fail; using NA, found that our
705                    kronecker() is not base-compatible with NA's.
706    
707            * R/dMatrix.R: "Compare" method now implemented for all cases
708    
709            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
710    
711            * man/dtpMatrix-class.Rd: mention length of 'x' slot
712    
713            * src/dtpMatrix.c (dtpMatrix_validate): fix check
714            * src/dspMatrix.c (dspMatrix_validate): ditto
715    
716            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
717              including coercion to [nl]tTMatrix.
718    
719            * R/diagMatrix.R (show): print a header line as for other classes.
720    
721    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * src/Makefile.win (SUBDIRS): fix typo
724    
725    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
728    
729    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
730    
731            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
732            symmetric and y missing in R code using %*% (cholmod_aat doesn't
733            accept a symmetric matrix).
734            * tests/group-methods.R: Uncomment test of crossprod applied to
735            lsCMatrix objects.
736    
737    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/AllClass.R (symmetricMatrix): add validity method (available
740            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
741    
742            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
743    
744            * tests/indexing.Rout.save:
745            * tests/indexing.R: additions, mainly for 'lsparse'
746    
747            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
748            case.
749    
750            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
751    
752    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
755                    as 'N' (1-letter - Ok?)
756    
757            * tests/group-methods.R: add test for logical + NAs
758    
759            * R/dMatrix.R ("Compare"): fix to work with NA's
760    
761            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
762    
763            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
764                    which is implemented.
765    
766    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * src/chm_common.c: coerce logical <-> double instead of
769            typecasting;  needed for "l" matrix handling in cholmod.
770    
771            * tests/other-pkgs.R (graph): small extension in "graph" checks.
772    
773            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
774            (Tsp2grNEL): other fixes needed
775    
776    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
779                    Matrices, since "lMatrix", also "lsparseM" can have NA
780            * R/ndenseMatrix.R, etc: new source files
781            * man/nsparseMatrix-classes.Rd, etc: new help files
782            * tests/: adaptions
783            * src/chm_common.c (chm_dense_to_SEXP): and others:
784                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
785            * src/Csparse.c, etc: ditto
786    
787    2006-09-11  Douglas Bates  <bates@R-project.org>
788    
789            * src/Mutils.[ch],init.c inst/include/*.h: Move the
790            alloc_d**Matrix functions to the lme4 package.
791    
792    2006-09-09  Douglas Bates  <bates@R-project.org>
793    
794            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
795            fixed
796    
797    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/lMatrix.R: new
800    
801            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
802    
803            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
804            * man/tcrossprod.Rd: ditto
805    
806    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
807    
808            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
809            for exported functions
810            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
811            Remove partitioning algorithms for sparse matrix reordering.  The
812            copyright on the Metis code was problematic and the methods were
813            rarely used.
814            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
815            operations are now done entirely in CHOLMOD code.
816    
817    2006-09-06  Douglas Bates  <bates@R-project.org>
818    
819            * src/Mutils.h: Remove functions that are no longer used.
820    
821    2006-09-04  Douglas Bates  <bates@R-project.org>
822    
823            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
824            * src/DEPS.mkf: update
825    
826    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * created branches/Matrix-for-R-2.3.x;  on trunk: do
829            * DESCRIPTION (Version): 0.9975-0
830            (Depends): R (>= 2.4.0)
831    
832    2006-09-01  Douglas Bates  <bates@R-project.org>
833    
834            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
835    
836    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
839            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
840    
841            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
842    
843    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
846            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
847            * R/dsparseMatrix.R: ditto
848            * R/Csparse.R: ditto
849    
850    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * R/dMatrix.R (Compare): improve availability of "<", etc
853            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
854    
855    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
858            of a 0-index which was used as 1-index (..hmm)
859    
860            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
861    
862            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
863            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
864            (.is.diagonal): ditto
865    
866            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
867    
868            * R/Matrix.R (Matrix): also work for NA data
869    
870    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
873            in all cases.
874    
875    2006-08-27  Douglas Bates  <bates@R-project.org>
876    
877            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
878            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
879    
880    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
883            subclasses of "ddenseMatrix"
884            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
885            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
886            instead of half dozen specialized ones.
887    
888    2006-08-25  Douglas Bates  <bates@R-project.org>
889    
890            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
891            <tillard@cirad.fr> - ordering standard errors to match effects.
892    
893    2006-08-24  Douglas Bates  <bates@R-project.org>
894    
895            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
896            on R_ldl.
897            * R/lCholCMatrix.R,
898            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
899            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
900            * many files in ./R and ./src: Use more general version of
901            dup_mMatrix_as_dgeMatrix to simplify method definitions.
902            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
903            dtpMatrix, dspMatrix and dppMatrix conversions.
904    
905    
906    2006-08-23  Douglas Bates  <bates@R-project.org>
907    
908            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
909            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
910            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
911            dgeMatrix_crossprod (may need to do this in other places).
912            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
913            generic and method for dsCMatrix.  Use CHOLMOD for chol().
914    
915    2006-08-22  Douglas Bates  <bates@R-project.org>
916    
917            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
918            types of classed Matrices, matrices or numeric or logical vectors.
919            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
920            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
921            to Mutils.h (as an inline) and change name to Matrix_check_class;
922            fixes in as_cholmod_factor and chm_factor_to_SEXP.
923            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
924            dsCMatrix_matrix_solve.  Comment out vestigial functions.
925            * src/Csparse.c: use diag_P and uplo_P macros.
926    
927  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
928    
929          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
930          valgrind.          valgrind.
931            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
932            inverses.
933            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
934            -Wall warnings.
935            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
936            Use dup_mMatrix_as_dgeMatrix.
937    
938  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
939    

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