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revision 1660, Thu Nov 2 11:05:35 2006 UTC revision 1847, Sat May 19 19:23:28 2007 UTC
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1    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
4            0-based, indices (Jose Quesada <quesada@gmail.com>).
5    
6    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
7    
8            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
9    
10    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Auxiliaries.R (sparsapply): new utility, much faster than
13            tapply1() for large sparse matrices.
14    
15    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Matrix.R (dim<-): reshape now via sparseVector.
18    
19            * R/sparseVector.R: methods and function for
20            * R/AllClass.R: new "sparseVector" class and daughters.
21            * NAMESPACE: export new classes
22    
23    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * DESCRIPTION (Version): 0.99875-1
26            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
27    
28    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
31            indexing
32            * tests/indexing.R: test set for that.
33    
34    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
37            entries.
38            * tests/indexing.R(out): add regression test for it
39    
40    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
43            name for "!" method definitions.
44    
45    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Tsparse.R (intI): new utility, used for "[" :
48                    Cleanup up there, and fixes for duplicated indices - more TODO!
49    
50            * tests/indexing.R(out): more tests
51    
52    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
55            code that is now part of the R Lapack library.
56    
57            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
58            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
59    
60    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
63    
64    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
67            up with extraneous names '0'...'<n-1>'
68    
69    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * R/dgTMatrix.R (mat2dgT): care about NAs
72    
73    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/kronecker.R: triangularity preserving methods
76    
77    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/kronecker.R: new file collecting kronecker() methods in one
80                    place.  Goal: become much faster!
81    
82    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
85            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
86            can be much faster.
87    
88            * tests/matprod.R: add regression tests for these (upper & lower).
89    
90    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Matrix.R (diff): method for our Matrices.
93    
94            * R/sparseMatrix.R (isDiagonal): check dim()!
95    
96    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Matrix.R (dim<-): new method for "reshape()" built on a
99            proposal from Tamas Papp.
100    
101    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
104    
105            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
106            rather define and export  cBind() and rBind() only.
107            --> useRs *must* change code that used to have cbind()/rbind() !!
108    
109            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
110            * R/bind.Rout.save: ditto
111    
112    2007-02-16  Douglas Bates  <bates@r-project.org>
113    
114            * DESCRIPTION (Date, Version): 0.9975-11 with new date
115            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
116            const modifier on declaration of the array 'valid'
117    
118    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
119    
120            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
121    
122    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
125    
126            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
127            * tests/simple.R: test the above and some of these coercions:
128    
129            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
130                    be careful to avoid infinite recursion, using new coercions in
131            * R/ngCMatrix.R and nsC... and ntC...
132            * R/lsparseMatrix.R: ditto
133    
134            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
135    
136            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
137            * R/Rsparse.R: reactivate .Call()s
138    
139            * tests/Class+Meth.R: a bit more on actual classes
140    
141    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
142    
143            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
144    
145    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * DESCRIPTION (Version): 0.9975-10 to upload
148    
149            * tests/Class+Meth.R (tstMatrixClass): require coercions to
150            specific classes less unconditionally.
151    
152            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
153    
154            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
155    
156            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
157            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
158            R_to_CMatrix segfaults on one platform.
159            Eliminate most coercion method to *specific* classes, and replace
160            with virtual classes coercions.
161    
162    
163    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
164    
165            * src/init.c: export the CHM...._validate() placeholders, since
166            they *are* called.
167    
168            * tests/Class+Meth.R (classCanCoerce): and starting to test
169            all as(<from>, <to>)
170    
171    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
174            * tests/indexing.R: tested now
175            * tests/indexing.Rout.save: updated
176    
177            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
178            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
179            appropriate.
180    
181            * NAMESPACE: export a trivial
182            * R/Matrix.R: drop() Matrix-method
183    
184            * R/AllClass.R: moved all prototypes to virtual super classes.
185    
186            * R/Rsparse.R: many more coercions to have less exceptions in
187            * tests/Class+Meth.R:
188    
189            * R/Ops.R (Compare): tweak for case with NA
190            * tests/simpl.R: hence another 'FIXME' eliminated
191    
192    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
195            objects.
196    
197            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
198              and more of "!", "&", "|", all, any; coercions
199    
200            * R/Rsparse.R: many coercions (which enable quite a few other
201            methods), thanks to enhancements in
202            * src/dgCMatrix.c (R_to_CMatrix): new, and
203            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
204            symmetric & triangular and ..RMatrix objects.
205    
206            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
207            renamed file from src/dsTMatrix.c;
208            now dealing with symmetric and triangular Tsparse coercions, both
209            to dense and general.
210    
211    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
214    
215            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
216            where sensible when the <numeric> is of length > 1.
217    
218    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/Matrix.R ([<-): for M[] <- value: fix length
221    
222    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
225            * R/ndenseMatrix.R: new coercions n* -> l*
226    
227    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
230    
231            * R/Ops.R ("Logic"): and other "Ops", many updates
232    
233    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * src/Mutils.h (SET_DimNames): new utility
236    
237            * R/Auxiliaries.R (nnzero): improved and now exported via
238    
239            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
240    
241    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/diagMatrix.R (!): fix typo.
244    
245    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Auxiliaries.R (as_Csparse): and quite a few others:
248                    allow to pass class definition --> speedup
249            * R/sparseMatrix.R: apply the above
250    
251            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
252    
253            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
254            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
255            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
256    
257            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
258    
259            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
260            and use it for "sparse*" as well, since it's faster than the
261            as_Csparse(.) way.
262    
263    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
266    
267    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
270            as method for   M[ ij ] <- v
271            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
272    
273            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
274            FALSE answer
275    
276            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
277            * tests/indexing.R: test it, and some of the above
278    
279    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Auxiliaries.R (is_duplicatedT): new utility
282    
283    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * src/init.c (R_init_Matrix): export cholmod_scale
286    
287    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
290            base::as.matrix to (x, ...)
291    
292    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
295            file; start using "Logic", hence
296    
297            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
298            * NAMESPACE: import and export "Logic"
299    
300    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
303            only needed previously to R version 2.5.0.
304    
305    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
308    
309            * R/Tsparse.R (replTmat): fix subassignment of triangular
310            * R/Csparse.R (replCmat): ditto
311            * tests/indexing.R: more tests, incl the above fix
312    
313    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Auxiliaries.R (drop0): extend for non CSparse
316            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
317    
318            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
319                    use uplo correctly (!); other places: use uplo_P() macro
320    
321            * R/Csparse.R (replCmat): call diagU2N() when needed
322            * R/Tsparse.R (replTmat): ditto
323    
324            * src/dtCMatrix.c (tCMatrix_validate): new
325            * src/dtTMatrix.c (tTMatrix_validate): new, used in
326            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
327    
328            * R/diagMatrix.R (replDiag): to use in [<-
329    
330    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
333                    also more general diagU2N().
334    
335    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
338            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
339    
340    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * tests/bind.R: a few more cases
343            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
344    
345            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
346            * R/ddenseMatrix.R (cbind2/rbind2)
347            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
348            * tests/indexing.R
349            * tests/indexing.Rout.save: updated
350    
351    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
354            * tests/indexing.R
355    
356    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
359            align with proper position of "0", i.e., right for integers.
360            argument 'align' by default is "fancy".
361    
362    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
365            * R/Csparse.R: and fix "Compare" for more cases.
366            * tests/Class+Meth.R: test some of these (m == m, m != m)
367    
368    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/lsparseMatrix.R: all() and any() methods
371            * R/ldenseMatrix.R:      ditto
372            * NAMESPACE, R/Matrix.R: ditto
373    
374            * man/all-methods.Rd: document them minimally
375    
376            * tests/simple.R: add a few examples for these
377    
378    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Tsparse.R ([): fix long standing typo in symmetric case
381            * man/dsCMatrix-class.Rd: add example exhibiting the above case
382    
383    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
384    
385            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
386            to LL before converting to a sparse matrix. (The LDL form can be
387            converted to a sparse matrix but it is implicitly a unit
388            triangular matrix and a diagonal matrix overwritten on the diagonal.)
389    
390    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
391    
392            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
393    
394    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
395    
396            * DESCRIPTION (Version): updated -> release 0.9975-7
397            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
398    
399    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
402    
403    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
404    
405            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
406            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
407            is exactly singular.
408    
409    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * DESCRIPTION (Date): updated -> release 0.9975-6
412    
413    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
416            now returns symmetric.
417    
418            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
419    
420            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
421            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
422    
423            * R/Auxiliaries.R (.type.kind): added
424    
425    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
428            running src/CSparse_install.sh
429    
430            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
431    
432    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
435            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
436    
437            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
438    
439            * tests/Class+Meth.R (tstMatrixClass): now assure
440            the (important in method programming) property :
441    
442                    ###>>  Every "Matrix" is either
443                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
444    
445                    (where "*" stands for "Matrix")
446    
447            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
448    
449            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
450            * tests/validObj.R: checks for "comparison"
451    
452            * R/sparseMatrix.R ([): improved indexing for sparse;
453                    trying to keep <symmetric>[ n, n] symmmetric
454    
455            * tests/indexing.R: indexing for logical sparse now ok
456    
457    
458    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * src/Tsparse.c: use xTsparse_validate() , and hence remove
461    
462            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
463    
464  2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466          * R/AllClass.R (Matrix-class): check length of dimnames in validity.          * R/AllClass.R (Matrix-class): check length of dimnames in validity.
467    
468          * tests/simple.R: validObject() checking the above.          * tests/simple.R: validObject() checking the above.
469    
470          * src/dgCMatrix.c (gCMatrix_validate): new, small and simple,          * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
471          replacing both dgCMatrix_validate and lgCM*.          replacing both dgCMatrix_validate and lgCM*.
472    
473          * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;          * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;

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