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revision 1654, Fri Oct 27 16:58:15 2006 UTC revision 1837, Mon May 14 13:17:37 2007 UTC
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1    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.99875-1
4            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
5    
6    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
9            indexing
10            * tests/indexing.R: test set for that.
11    
12    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
15            entries.
16            * tests/indexing.R(out): add regression test for it
17    
18    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
21            name for "!" method definitions.
22    
23    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R (intI): new utility, used for "[" :
26                    Cleanup up there, and fixes for duplicated indices - more TODO!
27    
28            * tests/indexing.R(out): more tests
29    
30    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
31    
32            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
33            code that is now part of the R Lapack library.
34    
35            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
36            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
37    
38    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
41    
42    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
45            up with extraneous names '0'...'<n-1>'
46    
47    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/dgTMatrix.R (mat2dgT): care about NAs
50    
51    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/kronecker.R: triangularity preserving methods
54    
55    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/kronecker.R: new file collecting kronecker() methods in one
58                    place.  Goal: become much faster!
59    
60    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
63            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
64            can be much faster.
65    
66            * tests/matprod.R: add regression tests for these (upper & lower).
67    
68    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/Matrix.R (diff): method for our Matrices.
71    
72            * R/sparseMatrix.R (isDiagonal): check dim()!
73    
74    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Matrix.R (dim<-): new method for "reshape()" built on a
77            proposal from Tamas Papp.
78    
79    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
82    
83            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
84            rather define and export  cBind() and rBind() only.
85            --> useRs *must* change code that used to have cbind()/rbind() !!
86    
87            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
88            * R/bind.Rout.save: ditto
89    
90    2007-02-16  Douglas Bates  <bates@r-project.org>
91    
92            * DESCRIPTION (Date, Version): 0.9975-11 with new date
93            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
94            const modifier on declaration of the array 'valid'
95    
96    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
97    
98            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
99    
100    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
103    
104            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
105            * tests/simple.R: test the above and some of these coercions:
106    
107            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
108                    be careful to avoid infinite recursion, using new coercions in
109            * R/ngCMatrix.R and nsC... and ntC...
110            * R/lsparseMatrix.R: ditto
111    
112            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
113    
114            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
115            * R/Rsparse.R: reactivate .Call()s
116    
117            * tests/Class+Meth.R: a bit more on actual classes
118    
119    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
122    
123    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * DESCRIPTION (Version): 0.9975-10 to upload
126    
127            * tests/Class+Meth.R (tstMatrixClass): require coercions to
128            specific classes less unconditionally.
129    
130            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
131    
132            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
133    
134            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
135            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
136            R_to_CMatrix segfaults on one platform.
137            Eliminate most coercion method to *specific* classes, and replace
138            with virtual classes coercions.
139    
140    
141    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
142    
143            * src/init.c: export the CHM...._validate() placeholders, since
144            they *are* called.
145    
146            * tests/Class+Meth.R (classCanCoerce): and starting to test
147            all as(<from>, <to>)
148    
149    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
152            * tests/indexing.R: tested now
153            * tests/indexing.Rout.save: updated
154    
155            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
156            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
157            appropriate.
158    
159            * NAMESPACE: export a trivial
160            * R/Matrix.R: drop() Matrix-method
161    
162            * R/AllClass.R: moved all prototypes to virtual super classes.
163    
164            * R/Rsparse.R: many more coercions to have less exceptions in
165            * tests/Class+Meth.R:
166    
167            * R/Ops.R (Compare): tweak for case with NA
168            * tests/simpl.R: hence another 'FIXME' eliminated
169    
170    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
173            objects.
174    
175            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
176              and more of "!", "&", "|", all, any; coercions
177    
178            * R/Rsparse.R: many coercions (which enable quite a few other
179            methods), thanks to enhancements in
180            * src/dgCMatrix.c (R_to_CMatrix): new, and
181            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
182            symmetric & triangular and ..RMatrix objects.
183    
184            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
185            renamed file from src/dsTMatrix.c;
186            now dealing with symmetric and triangular Tsparse coercions, both
187            to dense and general.
188    
189    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
192    
193            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
194            where sensible when the <numeric> is of length > 1.
195    
196    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/Matrix.R ([<-): for M[] <- value: fix length
199    
200    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
203            * R/ndenseMatrix.R: new coercions n* -> l*
204    
205    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
208    
209            * R/Ops.R ("Logic"): and other "Ops", many updates
210    
211    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * src/Mutils.h (SET_DimNames): new utility
214    
215            * R/Auxiliaries.R (nnzero): improved and now exported via
216    
217            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
218    
219    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/diagMatrix.R (!): fix typo.
222    
223    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Auxiliaries.R (as_Csparse): and quite a few others:
226                    allow to pass class definition --> speedup
227            * R/sparseMatrix.R: apply the above
228    
229            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
230    
231            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
232            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
233            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
234    
235            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
236    
237            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
238            and use it for "sparse*" as well, since it's faster than the
239            as_Csparse(.) way.
240    
241    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
244    
245    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
248            as method for   M[ ij ] <- v
249            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
250    
251            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
252            FALSE answer
253    
254            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
255            * tests/indexing.R: test it, and some of the above
256    
257    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Auxiliaries.R (is_duplicatedT): new utility
260    
261    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
262    
263            * src/init.c (R_init_Matrix): export cholmod_scale
264    
265    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
268            base::as.matrix to (x, ...)
269    
270    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
273            file; start using "Logic", hence
274    
275            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
276            * NAMESPACE: import and export "Logic"
277    
278    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
281            only needed previously to R version 2.5.0.
282    
283    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
286    
287            * R/Tsparse.R (replTmat): fix subassignment of triangular
288            * R/Csparse.R (replCmat): ditto
289            * tests/indexing.R: more tests, incl the above fix
290    
291    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (drop0): extend for non CSparse
294            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
295    
296            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
297                    use uplo correctly (!); other places: use uplo_P() macro
298    
299            * R/Csparse.R (replCmat): call diagU2N() when needed
300            * R/Tsparse.R (replTmat): ditto
301    
302            * src/dtCMatrix.c (tCMatrix_validate): new
303            * src/dtTMatrix.c (tTMatrix_validate): new, used in
304            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
305    
306            * R/diagMatrix.R (replDiag): to use in [<-
307    
308    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
311                    also more general diagU2N().
312    
313    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
316            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
317    
318    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * tests/bind.R: a few more cases
321            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
322    
323            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
324            * R/ddenseMatrix.R (cbind2/rbind2)
325            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
326            * tests/indexing.R
327            * tests/indexing.Rout.save: updated
328    
329    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
332            * tests/indexing.R
333    
334    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
337            align with proper position of "0", i.e., right for integers.
338            argument 'align' by default is "fancy".
339    
340    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
343            * R/Csparse.R: and fix "Compare" for more cases.
344            * tests/Class+Meth.R: test some of these (m == m, m != m)
345    
346    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/lsparseMatrix.R: all() and any() methods
349            * R/ldenseMatrix.R:      ditto
350            * NAMESPACE, R/Matrix.R: ditto
351    
352            * man/all-methods.Rd: document them minimally
353    
354            * tests/simple.R: add a few examples for these
355    
356    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/Tsparse.R ([): fix long standing typo in symmetric case
359            * man/dsCMatrix-class.Rd: add example exhibiting the above case
360    
361    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
364            to LL before converting to a sparse matrix. (The LDL form can be
365            converted to a sparse matrix but it is implicitly a unit
366            triangular matrix and a diagonal matrix overwritten on the diagonal.)
367    
368    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
369    
370            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
371    
372    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * DESCRIPTION (Version): updated -> release 0.9975-7
375            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
376    
377    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
378    
379            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
380    
381    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
382    
383            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
384            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
385            is exactly singular.
386    
387    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * DESCRIPTION (Date): updated -> release 0.9975-6
390    
391    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
394            now returns symmetric.
395    
396            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
397    
398            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
399            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
400    
401            * R/Auxiliaries.R (.type.kind): added
402    
403    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
406            running src/CSparse_install.sh
407    
408            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
409    
410    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
413            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
414    
415            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
416    
417            * tests/Class+Meth.R (tstMatrixClass): now assure
418            the (important in method programming) property :
419    
420                    ###>>  Every "Matrix" is either
421                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
422    
423                    (where "*" stands for "Matrix")
424    
425            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
426    
427            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
428            * tests/validObj.R: checks for "comparison"
429    
430            * R/sparseMatrix.R ([): improved indexing for sparse;
431                    trying to keep <symmetric>[ n, n] symmmetric
432    
433            * tests/indexing.R: indexing for logical sparse now ok
434    
435    
436    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * src/Tsparse.c: use xTsparse_validate() , and hence remove
439    
440            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
441    
442    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
445    
446            * tests/simple.R: validObject() checking the above.
447    
448            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
449            replacing both dgCMatrix_validate and lgCM*.
450    
451            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
452            fix dimnames setting in other places.
453            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
454    
455    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
458    
459            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
460            symmetry test, via
461            * R/Auxiliaries.R (.as.dgC.0.factors):
462    
463    2006-11-01  Douglas Bates  <bates@r-project.org>
464    
465            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
466            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
467            <CsparseMatrix>) added
468    
469    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * tests/matprod.R: add a variation of Harri's example
472    
473            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
474            recursive infinitely.
475    
476            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
477    
478            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
479    
480    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
483            matrix if possible; test m+m == 2*m; now test dgRMatrix.
484            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
485            satisfy the above test.
486    
487  2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
490    
491          * R/dgCMatrix.R: solve(a, b="missing") based on          * R/dgCMatrix.R: solve(a, b="missing") based on
492          * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with          * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
493          RHS = NULL.          RHS = NULL.

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