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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 1834, Fri May 11 10:07:17 2007 UTC
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1    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
4            indexing
5            * tests/indexing.R: test set for that.
6    
7    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
10            entries.
11            * tests/indexing.R(out): add regression test for it
12    
13    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
16            name for "!" method definitions.
17    
18    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/Tsparse.R (intI): new utility, used for "[" :
21                    Cleanup up there, and fixes for duplicated indices - more TODO!
22    
23            * tests/indexing.R(out): more tests
24    
25    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
26    
27            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
28            code that is now part of the R Lapack library.
29    
30            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
31            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
32    
33    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
36    
37    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
40            up with extraneous names '0'...'<n-1>'
41    
42    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/dgTMatrix.R (mat2dgT): care about NAs
45    
46    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/kronecker.R: triangularity preserving methods
49    
50    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/kronecker.R: new file collecting kronecker() methods in one
53                    place.  Goal: become much faster!
54    
55    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
58            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
59            can be much faster.
60    
61            * tests/matprod.R: add regression tests for these (upper & lower).
62    
63    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (diff): method for our Matrices.
66    
67            * R/sparseMatrix.R (isDiagonal): check dim()!
68    
69    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/Matrix.R (dim<-): new method for "reshape()" built on a
72            proposal from Tamas Papp.
73    
74    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
77    
78            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
79            rather define and export  cBind() and rBind() only.
80            --> useRs *must* change code that used to have cbind()/rbind() !!
81    
82            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
83            * R/bind.Rout.save: ditto
84    
85    2007-02-16  Douglas Bates  <bates@r-project.org>
86    
87            * DESCRIPTION (Date, Version): 0.9975-11 with new date
88            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
89            const modifier on declaration of the array 'valid'
90    
91    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
92    
93            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
94    
95    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
98    
99            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
100            * tests/simple.R: test the above and some of these coercions:
101    
102            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
103                    be careful to avoid infinite recursion, using new coercions in
104            * R/ngCMatrix.R and nsC... and ntC...
105            * R/lsparseMatrix.R: ditto
106    
107            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
108    
109            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
110            * R/Rsparse.R: reactivate .Call()s
111    
112            * tests/Class+Meth.R: a bit more on actual classes
113    
114    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
115    
116            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
117    
118    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * DESCRIPTION (Version): 0.9975-10 to upload
121    
122            * tests/Class+Meth.R (tstMatrixClass): require coercions to
123            specific classes less unconditionally.
124    
125            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
126    
127            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
128    
129            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
130            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
131            R_to_CMatrix segfaults on one platform.
132            Eliminate most coercion method to *specific* classes, and replace
133            with virtual classes coercions.
134    
135    
136    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
137    
138            * src/init.c: export the CHM...._validate() placeholders, since
139            they *are* called.
140    
141            * tests/Class+Meth.R (classCanCoerce): and starting to test
142            all as(<from>, <to>)
143    
144    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
147            * tests/indexing.R: tested now
148            * tests/indexing.Rout.save: updated
149    
150            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
151            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
152            appropriate.
153    
154            * NAMESPACE: export a trivial
155            * R/Matrix.R: drop() Matrix-method
156    
157            * R/AllClass.R: moved all prototypes to virtual super classes.
158    
159            * R/Rsparse.R: many more coercions to have less exceptions in
160            * tests/Class+Meth.R:
161    
162            * R/Ops.R (Compare): tweak for case with NA
163            * tests/simpl.R: hence another 'FIXME' eliminated
164    
165    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
168            objects.
169    
170            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
171              and more of "!", "&", "|", all, any; coercions
172    
173            * R/Rsparse.R: many coercions (which enable quite a few other
174            methods), thanks to enhancements in
175            * src/dgCMatrix.c (R_to_CMatrix): new, and
176            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
177            symmetric & triangular and ..RMatrix objects.
178    
179            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
180            renamed file from src/dsTMatrix.c;
181            now dealing with symmetric and triangular Tsparse coercions, both
182            to dense and general.
183    
184    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
187    
188            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
189            where sensible when the <numeric> is of length > 1.
190    
191    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R ([<-): for M[] <- value: fix length
194    
195    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
198            * R/ndenseMatrix.R: new coercions n* -> l*
199    
200    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
203    
204            * R/Ops.R ("Logic"): and other "Ops", many updates
205    
206    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * src/Mutils.h (SET_DimNames): new utility
209    
210            * R/Auxiliaries.R (nnzero): improved and now exported via
211    
212            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
213    
214    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/diagMatrix.R (!): fix typo.
217    
218    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Auxiliaries.R (as_Csparse): and quite a few others:
221                    allow to pass class definition --> speedup
222            * R/sparseMatrix.R: apply the above
223    
224            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
225    
226            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
227            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
228            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
229    
230            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
231    
232            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
233            and use it for "sparse*" as well, since it's faster than the
234            as_Csparse(.) way.
235    
236    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
239    
240    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
243            as method for   M[ ij ] <- v
244            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
245    
246            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
247            FALSE answer
248    
249            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
250            * tests/indexing.R: test it, and some of the above
251    
252    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Auxiliaries.R (is_duplicatedT): new utility
255    
256    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
257    
258            * src/init.c (R_init_Matrix): export cholmod_scale
259    
260    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
263            base::as.matrix to (x, ...)
264    
265    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
268            file; start using "Logic", hence
269    
270            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
271            * NAMESPACE: import and export "Logic"
272    
273    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
276            only needed previously to R version 2.5.0.
277    
278    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
281    
282            * R/Tsparse.R (replTmat): fix subassignment of triangular
283            * R/Csparse.R (replCmat): ditto
284            * tests/indexing.R: more tests, incl the above fix
285    
286    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (drop0): extend for non CSparse
289            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
290    
291            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
292                    use uplo correctly (!); other places: use uplo_P() macro
293    
294            * R/Csparse.R (replCmat): call diagU2N() when needed
295            * R/Tsparse.R (replTmat): ditto
296    
297            * src/dtCMatrix.c (tCMatrix_validate): new
298            * src/dtTMatrix.c (tTMatrix_validate): new, used in
299            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
300    
301            * R/diagMatrix.R (replDiag): to use in [<-
302    
303    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
306                    also more general diagU2N().
307    
308    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
311            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
312    
313    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * tests/bind.R: a few more cases
316            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
317    
318            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
319            * R/ddenseMatrix.R (cbind2/rbind2)
320            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
321            * tests/indexing.R
322            * tests/indexing.Rout.save: updated
323    
324    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
327            * tests/indexing.R
328    
329    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
332            align with proper position of "0", i.e., right for integers.
333            argument 'align' by default is "fancy".
334    
335    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
338            * R/Csparse.R: and fix "Compare" for more cases.
339            * tests/Class+Meth.R: test some of these (m == m, m != m)
340    
341    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/lsparseMatrix.R: all() and any() methods
344            * R/ldenseMatrix.R:      ditto
345            * NAMESPACE, R/Matrix.R: ditto
346    
347            * man/all-methods.Rd: document them minimally
348    
349            * tests/simple.R: add a few examples for these
350    
351    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Tsparse.R ([): fix long standing typo in symmetric case
354            * man/dsCMatrix-class.Rd: add example exhibiting the above case
355    
356    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
357    
358            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
359            to LL before converting to a sparse matrix. (The LDL form can be
360            converted to a sparse matrix but it is implicitly a unit
361            triangular matrix and a diagonal matrix overwritten on the diagonal.)
362    
363    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
366    
367    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
368    
369            * DESCRIPTION (Version): updated -> release 0.9975-7
370            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
371    
372    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
375    
376    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
377    
378            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
379            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
380            is exactly singular.
381    
382    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * DESCRIPTION (Date): updated -> release 0.9975-6
385    
386    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
389            now returns symmetric.
390    
391            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
392    
393            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
394            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
395    
396            * R/Auxiliaries.R (.type.kind): added
397    
398    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
401            running src/CSparse_install.sh
402    
403            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
404    
405    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
408            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
409    
410            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
411    
412            * tests/Class+Meth.R (tstMatrixClass): now assure
413            the (important in method programming) property :
414    
415                    ###>>  Every "Matrix" is either
416                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
417    
418                    (where "*" stands for "Matrix")
419    
420            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
421    
422            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
423            * tests/validObj.R: checks for "comparison"
424    
425            * R/sparseMatrix.R ([): improved indexing for sparse;
426                    trying to keep <symmetric>[ n, n] symmmetric
427    
428            * tests/indexing.R: indexing for logical sparse now ok
429    
430    
431    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * src/Tsparse.c: use xTsparse_validate() , and hence remove
434    
435            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
436    
437    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
440    
441            * tests/simple.R: validObject() checking the above.
442    
443            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
444            replacing both dgCMatrix_validate and lgCM*.
445    
446            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
447            fix dimnames setting in other places.
448            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
449    
450    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
453    
454            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
455            symmetry test, via
456            * R/Auxiliaries.R (.as.dgC.0.factors):
457    
458    2006-11-01  Douglas Bates  <bates@r-project.org>
459    
460            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
461            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
462            <CsparseMatrix>) added
463    
464    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * tests/matprod.R: add a variation of Harri's example
467    
468            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
469            recursive infinitely.
470    
471            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
472    
473            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
474    
475    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
478            matrix if possible; test m+m == 2*m; now test dgRMatrix.
479            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
480            satisfy the above test.
481    
482    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
485    
486            * R/dgCMatrix.R: solve(a, b="missing") based on
487            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
488            RHS = NULL.
489    
490            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
491            add more (needed) [t]crossprod() methods.
492    
493            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
494    
495            * R/Auxiliaries.R (as_CspClass): cleanup
496            (drop0): internal utility for "Csparse_drop(*, 0)"
497            (.bail.out.2): encourage active feedback
498    
499    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/dMatrix.R(Compare): new(), then slots [no validity check]
502    
503            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
504            non-valid or 'sorted' case).
505    
506            * R/dsparseMatrix.R: add "chol" method.
507            * R/ddenseMatrix.R: ditto
508    
509            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
510            * NAMESPACE (Ops)
511            * R/diagMatrix.R (diag2T): simple utility used "higher level"
512            coercion; deprecating direct lower level coercions.
513    
514            * R/*.R (seq): use seq_len() and seq_along() where possible.
515    
516    
517    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * DESCRIPTION (Version): 0.9975-5 ready for release
520    
521  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
522    
523          * 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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