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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 1960, Fri Jul 6 16:54:43 2007 UTC
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1    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
4              functions - no longer used
5            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
6              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
7              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
8              Alloca
9    
10    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
11    
12            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
13              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
14              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
15              src/t_gCMatrix_colSums.c: more R_CheckStack()s
16    
17    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
18    
19            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
20              the required amount of memory then call M_numeric_as_chm_dense.
21            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
22              (like Calloc but calling alloca)
23    
24    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
27            and extended with more sophisticated 'col.names' option.
28            * NAMESPACE: export  printSparseMatrix()
29            * man/printSpMatrix.Rd: document, incl. examples
30    
31    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
32    
33            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
34              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
35              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
36    
37    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * DESCRIPTION (Version): 0.99875-4
40    
41            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
42            some dimnames perservation.
43    
44            * R/dsTMatrix.R (t-method): keep dimnames
45            * R/dtTMatrix.R:  ditto
46    
47            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
48            and ncol(.) < 10
49    
50            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
51            from Mutils.h
52    
53            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
54            e.g. in as(<ngCMatrix>, "matrix")
55    
56    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4529] .: Create a branch for the API changes from the 0.99875
59              series to the 0.999375 series
60            * [r4530] DESCRIPTION, inst/include/Matrix.h,
61              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
62              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
63              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
64              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
65              as_cholmod_x functions
66    
67    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
68    
69            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
70              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
71              to Comparisons
72    
73    >>>>>>> .merge-right.r4561
74    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * DESCRIPTION (Version): 0.99875-3 ready to be released.
77    
78            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
79    
80            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
81            that should also work in a future version of R.
82    
83    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
86    
87            * R/sparseVector.R: more *sparseVector coercions, notably for
88            non - double ones.
89    
90    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
93              notably the new ones building on the new .Call(.)s:
94    
95            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
96            all 4 of [dlin]gCMatrix_colSums().
97    
98    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
101            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
102              result
103    
104    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/kronecker.R: fix typo (could lead to inf.recursion)
107            * test/simple.R: testing that
108    
109            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
110            method as well (which can have arguments, show() can't).
111    
112    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
115              added dgCMatrix_colSums for [col,row][Sums,Means]
116    
117    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
118    
119            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
120              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
121              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
122            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
123              class
124            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
125              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
126              row names to store the levels - duh!  Added an example.
127    
128    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/Csparse.c (Csparse_validate): check for *repeated* entries
131            thanks to example from Christian Buchta; with a test here:
132            * tests/simple.R:
133    
134    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
137            of colSums(*, sparseResult = TRUE)
138    
139    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
142            'na.rm = FALSE' as "everywhere" else in R.
143    
144    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r4421] src/CSparse_install.sh: Modify for new organization of
147              CSparse package
148            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
149              SuiteSparse
150            * [r4426] src/Makefile: add ./UFconfig to the include path for
151              compilation
152            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
153            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
154              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
155    
156    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
159            * R/sparseMatrix.R (prSpMatrix): now gives a message about
160            suppressed column names.
161    
162    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
163    
164            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
165              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
166              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
167              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
168              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
169              Remove warnings after change to const char* CHAR
170    
171    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
174              type of M_cholmod_ssmult
175    
176    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
177    
178            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
179              src/init.c: Yet another cholmod export - cholmod_ssmult
180    
181    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * NAMESPACE: exported drop0(), since
184            * man/drop0.Rd: I have seen several cases, I really wanted to use
185            it, so our users may want too.
186    
187    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * man/colSums.Rd: separately document colSums() etc, since these
190            have the extra argument 'sparseResult'.
191    
192    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
195            * man/spMatrix.Rd: docu., including examples
196    
197            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
198            in order to make colMeans() etc fast *and* correct.
199            * R/sparseVector.R (replSPvec): "[<-" functionality for
200            sparseVectors; tested in
201            * tests/simple.R:
202    
203    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
206            (very) sparse Matrices; output similar to Matlab's print().
207    
208    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
209    
210            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
211            0-based, indices (Jose Quesada <quesada@gmail.com>).
212    
213    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
216    
217    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (sparsapply): new utility, much faster than
220            tapply1() for large sparse matrices.
221    
222    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Matrix.R (dim<-): reshape now via sparseVector.
225    
226            * R/sparseVector.R: methods and function for
227            * R/AllClass.R: new "sparseVector" class and daughters.
228            * NAMESPACE: export new classes
229    
230    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Version): 0.99875-1
233            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
234    
235    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
238            indexing
239            * tests/indexing.R: test set for that.
240    
241    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
244            entries.
245            * tests/indexing.R(out): add regression test for it
246    
247    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
250            name for "!" method definitions.
251    
252    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Tsparse.R (intI): new utility, used for "[" :
255                    Cleanup up there, and fixes for duplicated indices - more TODO!
256    
257            * tests/indexing.R(out): more tests
258    
259    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
262            code that is now part of the R Lapack library.
263    
264            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
265            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
266    
267    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
270    
271    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
274            up with extraneous names '0'...'<n-1>'
275    
276    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/dgTMatrix.R (mat2dgT): care about NAs
279    
280    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/kronecker.R: triangularity preserving methods
283    
284    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/kronecker.R: new file collecting kronecker() methods in one
287                    place.  Goal: become much faster!
288    
289    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
292            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
293            can be much faster.
294    
295            * tests/matprod.R: add regression tests for these (upper & lower).
296    
297    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Matrix.R (diff): method for our Matrices.
300    
301            * R/sparseMatrix.R (isDiagonal): check dim()!
302    
303    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/Matrix.R (dim<-): new method for "reshape()" built on a
306            proposal from Tamas Papp.
307    
308    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
311    
312            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
313            rather define and export  cBind() and rBind() only.
314            --> useRs *must* change code that used to have cbind()/rbind() !!
315    
316            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
317            * R/bind.Rout.save: ditto
318    
319    2007-02-16  Douglas Bates  <bates@r-project.org>
320    
321            * DESCRIPTION (Date, Version): 0.9975-11 with new date
322            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
323            const modifier on declaration of the array 'valid'
324    
325    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
326    
327            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
328    
329    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
332    
333            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
334            * tests/simple.R: test the above and some of these coercions:
335    
336            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
337                    be careful to avoid infinite recursion, using new coercions in
338            * R/ngCMatrix.R and nsC... and ntC...
339            * R/lsparseMatrix.R: ditto
340    
341            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
342    
343            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
344            * R/Rsparse.R: reactivate .Call()s
345    
346            * tests/Class+Meth.R: a bit more on actual classes
347    
348    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
349    
350            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
351    
352    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * DESCRIPTION (Version): 0.9975-10 to upload
355    
356            * tests/Class+Meth.R (tstMatrixClass): require coercions to
357            specific classes less unconditionally.
358    
359            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
360    
361            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
362    
363            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
364            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
365            R_to_CMatrix segfaults on one platform.
366            Eliminate most coercion method to *specific* classes, and replace
367            with virtual classes coercions.
368    
369    
370    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
371    
372            * src/init.c: export the CHM...._validate() placeholders, since
373            they *are* called.
374    
375            * tests/Class+Meth.R (classCanCoerce): and starting to test
376            all as(<from>, <to>)
377    
378    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
381            * tests/indexing.R: tested now
382            * tests/indexing.Rout.save: updated
383    
384            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
385            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
386            appropriate.
387    
388            * NAMESPACE: export a trivial
389            * R/Matrix.R: drop() Matrix-method
390    
391            * R/AllClass.R: moved all prototypes to virtual super classes.
392    
393            * R/Rsparse.R: many more coercions to have less exceptions in
394            * tests/Class+Meth.R:
395    
396            * R/Ops.R (Compare): tweak for case with NA
397            * tests/simpl.R: hence another 'FIXME' eliminated
398    
399    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
402            objects.
403    
404            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
405              and more of "!", "&", "|", all, any; coercions
406    
407            * R/Rsparse.R: many coercions (which enable quite a few other
408            methods), thanks to enhancements in
409            * src/dgCMatrix.c (R_to_CMatrix): new, and
410            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
411            symmetric & triangular and ..RMatrix objects.
412    
413            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
414            renamed file from src/dsTMatrix.c;
415            now dealing with symmetric and triangular Tsparse coercions, both
416            to dense and general.
417    
418    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
421    
422            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
423            where sensible when the <numeric> is of length > 1.
424    
425    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/Matrix.R ([<-): for M[] <- value: fix length
428    
429    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
432            * R/ndenseMatrix.R: new coercions n* -> l*
433    
434    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
437    
438            * R/Ops.R ("Logic"): and other "Ops", many updates
439    
440    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/Mutils.h (SET_DimNames): new utility
443    
444            * R/Auxiliaries.R (nnzero): improved and now exported via
445    
446            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
447    
448    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/diagMatrix.R (!): fix typo.
451    
452    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/Auxiliaries.R (as_Csparse): and quite a few others:
455                    allow to pass class definition --> speedup
456            * R/sparseMatrix.R: apply the above
457    
458            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
459    
460            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
461            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
462            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
463    
464            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
465    
466            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
467            and use it for "sparse*" as well, since it's faster than the
468            as_Csparse(.) way.
469    
470    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
473    
474    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
477            as method for   M[ ij ] <- v
478            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
479    
480            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
481            FALSE answer
482    
483            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
484            * tests/indexing.R: test it, and some of the above
485    
486    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/Auxiliaries.R (is_duplicatedT): new utility
489    
490    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
491    
492            * src/init.c (R_init_Matrix): export cholmod_scale
493    
494    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
497            base::as.matrix to (x, ...)
498    
499    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
502            file; start using "Logic", hence
503    
504            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
505            * NAMESPACE: import and export "Logic"
506    
507    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
510            only needed previously to R version 2.5.0.
511    
512    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
515    
516            * R/Tsparse.R (replTmat): fix subassignment of triangular
517            * R/Csparse.R (replCmat): ditto
518            * tests/indexing.R: more tests, incl the above fix
519    
520    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Auxiliaries.R (drop0): extend for non CSparse
523            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
524    
525            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
526                    use uplo correctly (!); other places: use uplo_P() macro
527    
528            * R/Csparse.R (replCmat): call diagU2N() when needed
529            * R/Tsparse.R (replTmat): ditto
530    
531            * src/dtCMatrix.c (tCMatrix_validate): new
532            * src/dtTMatrix.c (tTMatrix_validate): new, used in
533            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
534    
535            * R/diagMatrix.R (replDiag): to use in [<-
536    
537    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
540                    also more general diagU2N().
541    
542    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
545            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
546    
547    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * tests/bind.R: a few more cases
550            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
551    
552            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
553            * R/ddenseMatrix.R (cbind2/rbind2)
554            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
555            * tests/indexing.R
556            * tests/indexing.Rout.save: updated
557    
558    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
561            * tests/indexing.R
562    
563    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
566            align with proper position of "0", i.e., right for integers.
567            argument 'align' by default is "fancy".
568    
569    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
572            * R/Csparse.R: and fix "Compare" for more cases.
573            * tests/Class+Meth.R: test some of these (m == m, m != m)
574    
575    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/lsparseMatrix.R: all() and any() methods
578            * R/ldenseMatrix.R:      ditto
579            * NAMESPACE, R/Matrix.R: ditto
580    
581            * man/all-methods.Rd: document them minimally
582    
583            * tests/simple.R: add a few examples for these
584    
585    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/Tsparse.R ([): fix long standing typo in symmetric case
588            * man/dsCMatrix-class.Rd: add example exhibiting the above case
589    
590    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
591    
592            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
593            to LL before converting to a sparse matrix. (The LDL form can be
594            converted to a sparse matrix but it is implicitly a unit
595            triangular matrix and a diagonal matrix overwritten on the diagonal.)
596    
597    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
598    
599            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
600    
601    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * DESCRIPTION (Version): updated -> release 0.9975-7
604            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
605    
606    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
609    
610    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
611    
612            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
613            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
614            is exactly singular.
615    
616    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * DESCRIPTION (Date): updated -> release 0.9975-6
619    
620    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
621    
622            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
623            now returns symmetric.
624    
625            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
626    
627            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
628            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
629    
630            * R/Auxiliaries.R (.type.kind): added
631    
632    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
635            running src/CSparse_install.sh
636    
637            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
638    
639    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
642            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
643    
644            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
645    
646            * tests/Class+Meth.R (tstMatrixClass): now assure
647            the (important in method programming) property :
648    
649                    ###>>  Every "Matrix" is either
650                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
651    
652                    (where "*" stands for "Matrix")
653    
654            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
655    
656            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
657            * tests/validObj.R: checks for "comparison"
658    
659            * R/sparseMatrix.R ([): improved indexing for sparse;
660                    trying to keep <symmetric>[ n, n] symmmetric
661    
662            * tests/indexing.R: indexing for logical sparse now ok
663    
664    
665    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * src/Tsparse.c: use xTsparse_validate() , and hence remove
668    
669            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
670    
671    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
674    
675            * tests/simple.R: validObject() checking the above.
676    
677            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
678            replacing both dgCMatrix_validate and lgCM*.
679    
680            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
681            fix dimnames setting in other places.
682            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
683    
684    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
687    
688            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
689            symmetry test, via
690            * R/Auxiliaries.R (.as.dgC.0.factors):
691    
692    2006-11-01  Douglas Bates  <bates@r-project.org>
693    
694            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
695            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
696            <CsparseMatrix>) added
697    
698    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * tests/matprod.R: add a variation of Harri's example
701    
702            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
703            recursive infinitely.
704    
705            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
706    
707            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
708    
709    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
712            matrix if possible; test m+m == 2*m; now test dgRMatrix.
713            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
714            satisfy the above test.
715    
716    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
719    
720            * R/dgCMatrix.R: solve(a, b="missing") based on
721            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
722            RHS = NULL.
723    
724            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
725            add more (needed) [t]crossprod() methods.
726    
727            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
728    
729            * R/Auxiliaries.R (as_CspClass): cleanup
730            (drop0): internal utility for "Csparse_drop(*, 0)"
731            (.bail.out.2): encourage active feedback
732    
733    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/dMatrix.R(Compare): new(), then slots [no validity check]
736    
737            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
738            non-valid or 'sorted' case).
739    
740            * R/dsparseMatrix.R: add "chol" method.
741            * R/ddenseMatrix.R: ditto
742    
743            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
744            * NAMESPACE (Ops)
745            * R/diagMatrix.R (diag2T): simple utility used "higher level"
746            coercion; deprecating direct lower level coercions.
747    
748            * R/*.R (seq): use seq_len() and seq_along() where possible.
749    
750    
751    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * DESCRIPTION (Version): 0.9975-5 ready for release
754    
755  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
756    
757          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.

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