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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 1787, Fri Feb 16 20:02:19 2007 UTC
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1    2007-02-16  Douglas Bates  <bates@r-project.org>
2    
3            * DESCRIPTION (Date, Version): 0.9975-11 with new date
4            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
5            const modifier on declaration of the array 'valid'
6    
7    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
8    
9            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
10    
11    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
14    
15            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
16            * tests/simple.R: test the above and some of these coercions:
17    
18            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
19                    be careful to avoid infinite recursion, using new coercions in
20            * R/ngCMatrix.R and nsC... and ntC...
21            * R/lsparseMatrix.R: ditto
22    
23            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
24    
25            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
26            * R/Rsparse.R: reactivate .Call()s
27    
28            * tests/Class+Meth.R: a bit more on actual classes
29    
30    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
33    
34    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.9975-10 to upload
37    
38            * tests/Class+Meth.R (tstMatrixClass): require coercions to
39            specific classes less unconditionally.
40    
41            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
42    
43            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
44    
45            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
46            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
47            R_to_CMatrix segfaults on one platform.
48            Eliminate most coercion method to *specific* classes, and replace
49            with virtual classes coercions.
50    
51    
52    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
53    
54            * src/init.c: export the CHM...._validate() placeholders, since
55            they *are* called.
56    
57            * tests/Class+Meth.R (classCanCoerce): and starting to test
58            all as(<from>, <to>)
59    
60    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
63            * tests/indexing.R: tested now
64            * tests/indexing.Rout.save: updated
65    
66            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
67            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
68            appropriate.
69    
70            * NAMESPACE: export a trivial
71            * R/Matrix.R: drop() Matrix-method
72    
73            * R/AllClass.R: moved all prototypes to virtual super classes.
74    
75            * R/Rsparse.R: many more coercions to have less exceptions in
76            * tests/Class+Meth.R:
77    
78            * R/Ops.R (Compare): tweak for case with NA
79            * tests/simpl.R: hence another 'FIXME' eliminated
80    
81    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
84            objects.
85    
86            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
87              and more of "!", "&", "|", all, any; coercions
88    
89            * R/Rsparse.R: many coercions (which enable quite a few other
90            methods), thanks to enhancements in
91            * src/dgCMatrix.c (R_to_CMatrix): new, and
92            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
93            symmetric & triangular and ..RMatrix objects.
94    
95            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
96            renamed file from src/dsTMatrix.c;
97            now dealing with symmetric and triangular Tsparse coercions, both
98            to dense and general.
99    
100    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
103    
104            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
105            where sensible when the <numeric> is of length > 1.
106    
107    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Matrix.R ([<-): for M[] <- value: fix length
110    
111    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
114            * R/ndenseMatrix.R: new coercions n* -> l*
115    
116    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
119    
120            * R/Ops.R ("Logic"): and other "Ops", many updates
121    
122    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/Mutils.h (SET_DimNames): new utility
125    
126            * R/Auxiliaries.R (nnzero): improved and now exported via
127    
128            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
129    
130    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/diagMatrix.R (!): fix typo.
133    
134    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/Auxiliaries.R (as_Csparse): and quite a few others:
137                    allow to pass class definition --> speedup
138            * R/sparseMatrix.R: apply the above
139    
140            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
141    
142            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
143            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
144            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
145    
146            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
147    
148            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
149            and use it for "sparse*" as well, since it's faster than the
150            as_Csparse(.) way.
151    
152    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
155    
156    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
159            as method for   M[ ij ] <- v
160            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
161    
162            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
163            FALSE answer
164    
165            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
166            * tests/indexing.R: test it, and some of the above
167    
168    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (is_duplicatedT): new utility
171    
172    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
173    
174            * src/init.c (R_init_Matrix): export cholmod_scale
175    
176    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
179            base::as.matrix to (x, ...)
180    
181    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
184            file; start using "Logic", hence
185    
186            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
187            * NAMESPACE: import and export "Logic"
188    
189    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
192            only needed previously to R version 2.5.0.
193    
194    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
197    
198            * R/Tsparse.R (replTmat): fix subassignment of triangular
199            * R/Csparse.R (replCmat): ditto
200            * tests/indexing.R: more tests, incl the above fix
201    
202    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Auxiliaries.R (drop0): extend for non CSparse
205            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
206    
207            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
208                    use uplo correctly (!); other places: use uplo_P() macro
209    
210            * R/Csparse.R (replCmat): call diagU2N() when needed
211            * R/Tsparse.R (replTmat): ditto
212    
213            * src/dtCMatrix.c (tCMatrix_validate): new
214            * src/dtTMatrix.c (tTMatrix_validate): new, used in
215            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
216    
217            * R/diagMatrix.R (replDiag): to use in [<-
218    
219    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
222                    also more general diagU2N().
223    
224    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
227            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
228    
229    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * tests/bind.R: a few more cases
232            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
233    
234            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
235            * R/ddenseMatrix.R (cbind2/rbind2)
236            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
237            * tests/indexing.R
238            * tests/indexing.Rout.save: updated
239    
240    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
243            * tests/indexing.R
244    
245    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
248            align with proper position of "0", i.e., right for integers.
249            argument 'align' by default is "fancy".
250    
251    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
254            * R/Csparse.R: and fix "Compare" for more cases.
255            * tests/Class+Meth.R: test some of these (m == m, m != m)
256    
257    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/lsparseMatrix.R: all() and any() methods
260            * R/ldenseMatrix.R:      ditto
261            * NAMESPACE, R/Matrix.R: ditto
262    
263            * man/all-methods.Rd: document them minimally
264    
265            * tests/simple.R: add a few examples for these
266    
267    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Tsparse.R ([): fix long standing typo in symmetric case
270            * man/dsCMatrix-class.Rd: add example exhibiting the above case
271    
272    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
275            to LL before converting to a sparse matrix. (The LDL form can be
276            converted to a sparse matrix but it is implicitly a unit
277            triangular matrix and a diagonal matrix overwritten on the diagonal.)
278    
279    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
280    
281            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
282    
283    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * DESCRIPTION (Version): updated -> release 0.9975-7
286            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
287    
288    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
291    
292    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
293    
294            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
295            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
296            is exactly singular.
297    
298    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * DESCRIPTION (Date): updated -> release 0.9975-6
301    
302    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
305            now returns symmetric.
306    
307            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
308    
309            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
310            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
311    
312            * R/Auxiliaries.R (.type.kind): added
313    
314    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
317            running src/CSparse_install.sh
318    
319            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
320    
321    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
324            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
325    
326            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
327    
328            * tests/Class+Meth.R (tstMatrixClass): now assure
329            the (important in method programming) property :
330    
331                    ###>>  Every "Matrix" is either
332                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
333    
334                    (where "*" stands for "Matrix")
335    
336            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
337    
338            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
339            * tests/validObj.R: checks for "comparison"
340    
341            * R/sparseMatrix.R ([): improved indexing for sparse;
342                    trying to keep <symmetric>[ n, n] symmmetric
343    
344            * tests/indexing.R: indexing for logical sparse now ok
345    
346    
347    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * src/Tsparse.c: use xTsparse_validate() , and hence remove
350    
351            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
352    
353    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
356    
357            * tests/simple.R: validObject() checking the above.
358    
359            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
360            replacing both dgCMatrix_validate and lgCM*.
361    
362            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
363            fix dimnames setting in other places.
364            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
365    
366    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
369    
370            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
371            symmetry test, via
372            * R/Auxiliaries.R (.as.dgC.0.factors):
373    
374    2006-11-01  Douglas Bates  <bates@r-project.org>
375    
376            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
377            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
378            <CsparseMatrix>) added
379    
380    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * tests/matprod.R: add a variation of Harri's example
383    
384            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
385            recursive infinitely.
386    
387            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
388    
389            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
390    
391    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
394            matrix if possible; test m+m == 2*m; now test dgRMatrix.
395            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
396            satisfy the above test.
397    
398    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
401    
402            * R/dgCMatrix.R: solve(a, b="missing") based on
403            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
404            RHS = NULL.
405    
406            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
407            add more (needed) [t]crossprod() methods.
408    
409            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
410    
411            * R/Auxiliaries.R (as_CspClass): cleanup
412            (drop0): internal utility for "Csparse_drop(*, 0)"
413            (.bail.out.2): encourage active feedback
414    
415    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/dMatrix.R(Compare): new(), then slots [no validity check]
418    
419            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
420            non-valid or 'sorted' case).
421    
422            * R/dsparseMatrix.R: add "chol" method.
423            * R/ddenseMatrix.R: ditto
424    
425            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
426            * NAMESPACE (Ops)
427            * R/diagMatrix.R (diag2T): simple utility used "higher level"
428            coercion; deprecating direct lower level coercions.
429    
430            * R/*.R (seq): use seq_len() and seq_along() where possible.
431    
432    
433    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * DESCRIPTION (Version): 0.9975-5 ready for release
436    
437  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
438    
439          * 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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