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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 1751, Tue Jan 30 17:41:02 2007 UTC
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1    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
4            * tests/indexing.R: tested now
5            * tests/indexing.Rout.save: updated
6    
7            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
8            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
9            appropriate.
10    
11            * NAMESPACE: export a trivial
12            * R/Matrix.R: drop() Matrix-method
13    
14            * R/AllClass.R: moved all prototypes to virtual super classes.
15    
16            * R/Rsparse.R: many more coercions to have less exceptions in
17            * tests/Class+Meth.R:
18    
19            * R/Ops.R (Compare): tweak for case with NA
20            * tests/simpl.R: hence another 'FIXME' eliminated
21    
22    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
25            objects.
26    
27            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
28              and more of "!", "&", "|", all, any; coercions
29    
30            * R/Rsparse.R: many coercions (which enable quite a few other
31            methods), thanks to enhancements in
32            * src/dgCMatrix.c (R_to_CMatrix): new, and
33            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
34            symmetric & triangular and ..RMatrix objects.
35    
36            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
37            renamed file from src/dsTMatrix.c;
38            now dealing with symmetric and triangular Tsparse coercions, both
39            to dense and general.
40    
41    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
44    
45            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
46            where sensible when the <numeric> is of length > 1.
47    
48    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/Matrix.R ([<-): for M[] <- value: fix length
51    
52    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
55            * R/ndenseMatrix.R: new coercions n* -> l*
56    
57    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
60    
61            * R/Ops.R ("Logic"): and other "Ops", many updates
62    
63    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * src/Mutils.h (SET_DimNames): new utility
66    
67            * R/Auxiliaries.R (nnzero): improved and now exported via
68    
69            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
70    
71    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/diagMatrix.R (!): fix typo.
74    
75    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/Auxiliaries.R (as_Csparse): and quite a few others:
78                    allow to pass class definition --> speedup
79            * R/sparseMatrix.R: apply the above
80    
81            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
82    
83            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
84            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
85            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
86    
87            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
88    
89            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
90            and use it for "sparse*" as well, since it's faster than the
91            as_Csparse(.) way.
92    
93    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
96    
97    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
100            as method for   M[ ij ] <- v
101            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
102    
103            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
104            FALSE answer
105    
106            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
107            * tests/indexing.R: test it, and some of the above
108    
109    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Auxiliaries.R (is_duplicatedT): new utility
112    
113    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * src/init.c (R_init_Matrix): export cholmod_scale
116    
117    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
120            base::as.matrix to (x, ...)
121    
122    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
125            file; start using "Logic", hence
126    
127            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
128            * NAMESPACE: import and export "Logic"
129    
130    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
133            only needed previously to R version 2.5.0.
134    
135    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
138    
139            * R/Tsparse.R (replTmat): fix subassignment of triangular
140            * R/Csparse.R (replCmat): ditto
141            * tests/indexing.R: more tests, incl the above fix
142    
143    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/Auxiliaries.R (drop0): extend for non CSparse
146            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
147    
148            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
149                    use uplo correctly (!); other places: use uplo_P() macro
150    
151            * R/Csparse.R (replCmat): call diagU2N() when needed
152            * R/Tsparse.R (replTmat): ditto
153    
154            * src/dtCMatrix.c (tCMatrix_validate): new
155            * src/dtTMatrix.c (tTMatrix_validate): new, used in
156            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
157    
158            * R/diagMatrix.R (replDiag): to use in [<-
159    
160    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
163                    also more general diagU2N().
164    
165    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
168            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
169    
170    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/bind.R: a few more cases
173            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
174    
175            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
176            * R/ddenseMatrix.R (cbind2/rbind2)
177            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
178            * tests/indexing.R
179            * tests/indexing.Rout.save: updated
180    
181    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
184            * tests/indexing.R
185    
186    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
189            align with proper position of "0", i.e., right for integers.
190            argument 'align' by default is "fancy".
191    
192    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
195            * R/Csparse.R: and fix "Compare" for more cases.
196            * tests/Class+Meth.R: test some of these (m == m, m != m)
197    
198    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/lsparseMatrix.R: all() and any() methods
201            * R/ldenseMatrix.R:      ditto
202            * NAMESPACE, R/Matrix.R: ditto
203    
204            * man/all-methods.Rd: document them minimally
205    
206            * tests/simple.R: add a few examples for these
207    
208    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Tsparse.R ([): fix long standing typo in symmetric case
211            * man/dsCMatrix-class.Rd: add example exhibiting the above case
212    
213    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
214    
215            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
216            to LL before converting to a sparse matrix. (The LDL form can be
217            converted to a sparse matrix but it is implicitly a unit
218            triangular matrix and a diagonal matrix overwritten on the diagonal.)
219    
220    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
221    
222            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
223    
224    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
225    
226            * DESCRIPTION (Version): updated -> release 0.9975-7
227            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
228    
229    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
232    
233    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
234    
235            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
236            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
237            is exactly singular.
238    
239    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * DESCRIPTION (Date): updated -> release 0.9975-6
242    
243    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
246            now returns symmetric.
247    
248            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
249    
250            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
251            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
252    
253            * R/Auxiliaries.R (.type.kind): added
254    
255    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
258            running src/CSparse_install.sh
259    
260            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
261    
262    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
265            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
266    
267            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
268    
269            * tests/Class+Meth.R (tstMatrixClass): now assure
270            the (important in method programming) property :
271    
272                    ###>>  Every "Matrix" is either
273                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
274    
275                    (where "*" stands for "Matrix")
276    
277            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
278    
279            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
280            * tests/validObj.R: checks for "comparison"
281    
282            * R/sparseMatrix.R ([): improved indexing for sparse;
283                    trying to keep <symmetric>[ n, n] symmmetric
284    
285            * tests/indexing.R: indexing for logical sparse now ok
286    
287    
288    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * src/Tsparse.c: use xTsparse_validate() , and hence remove
291    
292            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
293    
294    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
297    
298            * tests/simple.R: validObject() checking the above.
299    
300            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
301            replacing both dgCMatrix_validate and lgCM*.
302    
303            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
304            fix dimnames setting in other places.
305            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
306    
307    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
310    
311            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
312            symmetry test, via
313            * R/Auxiliaries.R (.as.dgC.0.factors):
314    
315    2006-11-01  Douglas Bates  <bates@r-project.org>
316    
317            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
318            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
319            <CsparseMatrix>) added
320    
321    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * tests/matprod.R: add a variation of Harri's example
324    
325            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
326            recursive infinitely.
327    
328            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
329    
330            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
331    
332    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
335            matrix if possible; test m+m == 2*m; now test dgRMatrix.
336            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
337            satisfy the above test.
338    
339    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
342    
343            * R/dgCMatrix.R: solve(a, b="missing") based on
344            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
345            RHS = NULL.
346    
347            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
348            add more (needed) [t]crossprod() methods.
349    
350            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
351    
352            * R/Auxiliaries.R (as_CspClass): cleanup
353            (drop0): internal utility for "Csparse_drop(*, 0)"
354            (.bail.out.2): encourage active feedback
355    
356    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/dMatrix.R(Compare): new(), then slots [no validity check]
359    
360            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
361            non-valid or 'sorted' case).
362    
363            * R/dsparseMatrix.R: add "chol" method.
364            * R/ddenseMatrix.R: ditto
365    
366            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
367            * NAMESPACE (Ops)
368            * R/diagMatrix.R (diag2T): simple utility used "higher level"
369            coercion; deprecating direct lower level coercions.
370    
371            * R/*.R (seq): use seq_len() and seq_along() where possible.
372    
373    
374    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * DESCRIPTION (Version): 0.9975-5 ready for release
377    
378  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
379    
380          * 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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