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revision 1654, Fri Oct 27 16:58:15 2006 UTC revision 1803, Tue Mar 27 16:43:22 2007 UTC
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1    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/kronecker.R: new file collecting kronecker() methods in one
4                    place.  Goal: become much faster!
5    
6    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
9            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
10            can be much faster.
11    
12            * tests/matprod.R: add regression tests for these (upper & lower).
13    
14    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Matrix.R (diff): method for our Matrices.
17    
18            * R/sparseMatrix.R (isDiagonal): check dim()!
19    
20    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R (dim<-): new method for "reshape()" built on a
23            proposal from Tamas Papp.
24    
25    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
28    
29            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
30            rather define and export  cBind() and rBind() only.
31            --> useRs *must* change code that used to have cbind()/rbind() !!
32    
33            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
34            * R/bind.Rout.save: ditto
35    
36    2007-02-16  Douglas Bates  <bates@r-project.org>
37    
38            * DESCRIPTION (Date, Version): 0.9975-11 with new date
39            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
40            const modifier on declaration of the array 'valid'
41    
42    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
45    
46    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
49    
50            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
51            * tests/simple.R: test the above and some of these coercions:
52    
53            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
54                    be careful to avoid infinite recursion, using new coercions in
55            * R/ngCMatrix.R and nsC... and ntC...
56            * R/lsparseMatrix.R: ditto
57    
58            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
59    
60            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
61            * R/Rsparse.R: reactivate .Call()s
62    
63            * tests/Class+Meth.R: a bit more on actual classes
64    
65    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
68    
69    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * DESCRIPTION (Version): 0.9975-10 to upload
72    
73            * tests/Class+Meth.R (tstMatrixClass): require coercions to
74            specific classes less unconditionally.
75    
76            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
77    
78            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
79    
80            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
81            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
82            R_to_CMatrix segfaults on one platform.
83            Eliminate most coercion method to *specific* classes, and replace
84            with virtual classes coercions.
85    
86    
87    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
88    
89            * src/init.c: export the CHM...._validate() placeholders, since
90            they *are* called.
91    
92            * tests/Class+Meth.R (classCanCoerce): and starting to test
93            all as(<from>, <to>)
94    
95    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
98            * tests/indexing.R: tested now
99            * tests/indexing.Rout.save: updated
100    
101            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
102            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
103            appropriate.
104    
105            * NAMESPACE: export a trivial
106            * R/Matrix.R: drop() Matrix-method
107    
108            * R/AllClass.R: moved all prototypes to virtual super classes.
109    
110            * R/Rsparse.R: many more coercions to have less exceptions in
111            * tests/Class+Meth.R:
112    
113            * R/Ops.R (Compare): tweak for case with NA
114            * tests/simpl.R: hence another 'FIXME' eliminated
115    
116    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
119            objects.
120    
121            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
122              and more of "!", "&", "|", all, any; coercions
123    
124            * R/Rsparse.R: many coercions (which enable quite a few other
125            methods), thanks to enhancements in
126            * src/dgCMatrix.c (R_to_CMatrix): new, and
127            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
128            symmetric & triangular and ..RMatrix objects.
129    
130            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
131            renamed file from src/dsTMatrix.c;
132            now dealing with symmetric and triangular Tsparse coercions, both
133            to dense and general.
134    
135    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
138    
139            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
140            where sensible when the <numeric> is of length > 1.
141    
142    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R ([<-): for M[] <- value: fix length
145    
146    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
149            * R/ndenseMatrix.R: new coercions n* -> l*
150    
151    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
154    
155            * R/Ops.R ("Logic"): and other "Ops", many updates
156    
157    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * src/Mutils.h (SET_DimNames): new utility
160    
161            * R/Auxiliaries.R (nnzero): improved and now exported via
162    
163            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
164    
165    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/diagMatrix.R (!): fix typo.
168    
169    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Auxiliaries.R (as_Csparse): and quite a few others:
172                    allow to pass class definition --> speedup
173            * R/sparseMatrix.R: apply the above
174    
175            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
176    
177            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
178            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
179            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
180    
181            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
182    
183            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
184            and use it for "sparse*" as well, since it's faster than the
185            as_Csparse(.) way.
186    
187    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
190    
191    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
194            as method for   M[ ij ] <- v
195            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
196    
197            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
198            FALSE answer
199    
200            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
201            * tests/indexing.R: test it, and some of the above
202    
203    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Auxiliaries.R (is_duplicatedT): new utility
206    
207    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * src/init.c (R_init_Matrix): export cholmod_scale
210    
211    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
214            base::as.matrix to (x, ...)
215    
216    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
219            file; start using "Logic", hence
220    
221            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
222            * NAMESPACE: import and export "Logic"
223    
224    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
227            only needed previously to R version 2.5.0.
228    
229    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
232    
233            * R/Tsparse.R (replTmat): fix subassignment of triangular
234            * R/Csparse.R (replCmat): ditto
235            * tests/indexing.R: more tests, incl the above fix
236    
237    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/Auxiliaries.R (drop0): extend for non CSparse
240            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
241    
242            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
243                    use uplo correctly (!); other places: use uplo_P() macro
244    
245            * R/Csparse.R (replCmat): call diagU2N() when needed
246            * R/Tsparse.R (replTmat): ditto
247    
248            * src/dtCMatrix.c (tCMatrix_validate): new
249            * src/dtTMatrix.c (tTMatrix_validate): new, used in
250            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
251    
252            * R/diagMatrix.R (replDiag): to use in [<-
253    
254    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
257                    also more general diagU2N().
258    
259    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
262            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
263    
264    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/bind.R: a few more cases
267            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
268    
269            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
270            * R/ddenseMatrix.R (cbind2/rbind2)
271            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
272            * tests/indexing.R
273            * tests/indexing.Rout.save: updated
274    
275    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
278            * tests/indexing.R
279    
280    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
283            align with proper position of "0", i.e., right for integers.
284            argument 'align' by default is "fancy".
285    
286    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
289            * R/Csparse.R: and fix "Compare" for more cases.
290            * tests/Class+Meth.R: test some of these (m == m, m != m)
291    
292    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/lsparseMatrix.R: all() and any() methods
295            * R/ldenseMatrix.R:      ditto
296            * NAMESPACE, R/Matrix.R: ditto
297    
298            * man/all-methods.Rd: document them minimally
299    
300            * tests/simple.R: add a few examples for these
301    
302    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Tsparse.R ([): fix long standing typo in symmetric case
305            * man/dsCMatrix-class.Rd: add example exhibiting the above case
306    
307    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
308    
309            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
310            to LL before converting to a sparse matrix. (The LDL form can be
311            converted to a sparse matrix but it is implicitly a unit
312            triangular matrix and a diagonal matrix overwritten on the diagonal.)
313    
314    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
315    
316            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
317    
318    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * DESCRIPTION (Version): updated -> release 0.9975-7
321            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
322    
323    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
326    
327    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
330            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
331            is exactly singular.
332    
333    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * DESCRIPTION (Date): updated -> release 0.9975-6
336    
337    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
340            now returns symmetric.
341    
342            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
343    
344            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
345            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
346    
347            * R/Auxiliaries.R (.type.kind): added
348    
349    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
352            running src/CSparse_install.sh
353    
354            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
355    
356    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
359            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
360    
361            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
362    
363            * tests/Class+Meth.R (tstMatrixClass): now assure
364            the (important in method programming) property :
365    
366                    ###>>  Every "Matrix" is either
367                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
368    
369                    (where "*" stands for "Matrix")
370    
371            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
372    
373            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
374            * tests/validObj.R: checks for "comparison"
375    
376            * R/sparseMatrix.R ([): improved indexing for sparse;
377                    trying to keep <symmetric>[ n, n] symmmetric
378    
379            * tests/indexing.R: indexing for logical sparse now ok
380    
381    
382    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * src/Tsparse.c: use xTsparse_validate() , and hence remove
385    
386            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
387    
388    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
391    
392            * tests/simple.R: validObject() checking the above.
393    
394            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
395            replacing both dgCMatrix_validate and lgCM*.
396    
397            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
398            fix dimnames setting in other places.
399            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
400    
401    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
404    
405            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
406            symmetry test, via
407            * R/Auxiliaries.R (.as.dgC.0.factors):
408    
409    2006-11-01  Douglas Bates  <bates@r-project.org>
410    
411            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
412            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
413            <CsparseMatrix>) added
414    
415    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * tests/matprod.R: add a variation of Harri's example
418    
419            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
420            recursive infinitely.
421    
422            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
423    
424            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
425    
426    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
429            matrix if possible; test m+m == 2*m; now test dgRMatrix.
430            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
431            satisfy the above test.
432    
433  2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
436    
437          * R/dgCMatrix.R: solve(a, b="missing") based on          * R/dgCMatrix.R: solve(a, b="missing") based on
438          * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with          * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
439          RHS = NULL.          RHS = NULL.

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