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revision 1642, Fri Oct 20 21:08:28 2006 UTC revision 1829, Thu Apr 26 06:35:20 2007 UTC
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1    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (intI): new utility, used for "[" :
4                    Cleanup up there, and fixes for duplicated indices - more TODO!
5    
6            * tests/indexing.R(out): more tests
7    
8    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
9    
10            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
11            code that is now part of the R Lapack library.
12    
13            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
14            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
15    
16    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
19    
20    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
23            up with extraneous names '0'...'<n-1>'
24    
25    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/dgTMatrix.R (mat2dgT): care about NAs
28    
29    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/kronecker.R: triangularity preserving methods
32    
33    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/kronecker.R: new file collecting kronecker() methods in one
36                    place.  Goal: become much faster!
37    
38    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
41            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
42            can be much faster.
43    
44            * tests/matprod.R: add regression tests for these (upper & lower).
45    
46    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R (diff): method for our Matrices.
49    
50            * R/sparseMatrix.R (isDiagonal): check dim()!
51    
52    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Matrix.R (dim<-): new method for "reshape()" built on a
55            proposal from Tamas Papp.
56    
57    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
60    
61            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
62            rather define and export  cBind() and rBind() only.
63            --> useRs *must* change code that used to have cbind()/rbind() !!
64    
65            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
66            * R/bind.Rout.save: ditto
67    
68    2007-02-16  Douglas Bates  <bates@r-project.org>
69    
70            * DESCRIPTION (Date, Version): 0.9975-11 with new date
71            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
72            const modifier on declaration of the array 'valid'
73    
74    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
75    
76            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
77    
78    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
81    
82            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
83            * tests/simple.R: test the above and some of these coercions:
84    
85            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
86                    be careful to avoid infinite recursion, using new coercions in
87            * R/ngCMatrix.R and nsC... and ntC...
88            * R/lsparseMatrix.R: ditto
89    
90            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
91    
92            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
93            * R/Rsparse.R: reactivate .Call()s
94    
95            * tests/Class+Meth.R: a bit more on actual classes
96    
97    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
100    
101    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * DESCRIPTION (Version): 0.9975-10 to upload
104    
105            * tests/Class+Meth.R (tstMatrixClass): require coercions to
106            specific classes less unconditionally.
107    
108            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
109    
110            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
111    
112            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
113            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
114            R_to_CMatrix segfaults on one platform.
115            Eliminate most coercion method to *specific* classes, and replace
116            with virtual classes coercions.
117    
118    
119    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
120    
121            * src/init.c: export the CHM...._validate() placeholders, since
122            they *are* called.
123    
124            * tests/Class+Meth.R (classCanCoerce): and starting to test
125            all as(<from>, <to>)
126    
127    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
130            * tests/indexing.R: tested now
131            * tests/indexing.Rout.save: updated
132    
133            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
134            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
135            appropriate.
136    
137            * NAMESPACE: export a trivial
138            * R/Matrix.R: drop() Matrix-method
139    
140            * R/AllClass.R: moved all prototypes to virtual super classes.
141    
142            * R/Rsparse.R: many more coercions to have less exceptions in
143            * tests/Class+Meth.R:
144    
145            * R/Ops.R (Compare): tweak for case with NA
146            * tests/simpl.R: hence another 'FIXME' eliminated
147    
148    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
151            objects.
152    
153            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
154              and more of "!", "&", "|", all, any; coercions
155    
156            * R/Rsparse.R: many coercions (which enable quite a few other
157            methods), thanks to enhancements in
158            * src/dgCMatrix.c (R_to_CMatrix): new, and
159            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
160            symmetric & triangular and ..RMatrix objects.
161    
162            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
163            renamed file from src/dsTMatrix.c;
164            now dealing with symmetric and triangular Tsparse coercions, both
165            to dense and general.
166    
167    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
170    
171            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
172            where sensible when the <numeric> is of length > 1.
173    
174    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/Matrix.R ([<-): for M[] <- value: fix length
177    
178    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
181            * R/ndenseMatrix.R: new coercions n* -> l*
182    
183    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
186    
187            * R/Ops.R ("Logic"): and other "Ops", many updates
188    
189    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * src/Mutils.h (SET_DimNames): new utility
192    
193            * R/Auxiliaries.R (nnzero): improved and now exported via
194    
195            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
196    
197    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/diagMatrix.R (!): fix typo.
200    
201    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/Auxiliaries.R (as_Csparse): and quite a few others:
204                    allow to pass class definition --> speedup
205            * R/sparseMatrix.R: apply the above
206    
207            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
208    
209            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
210            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
211            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
212    
213            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
214    
215            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
216            and use it for "sparse*" as well, since it's faster than the
217            as_Csparse(.) way.
218    
219    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
222    
223    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
226            as method for   M[ ij ] <- v
227            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
228    
229            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
230            FALSE answer
231    
232            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
233            * tests/indexing.R: test it, and some of the above
234    
235    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Auxiliaries.R (is_duplicatedT): new utility
238    
239    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
240    
241            * src/init.c (R_init_Matrix): export cholmod_scale
242    
243    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
246            base::as.matrix to (x, ...)
247    
248    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
251            file; start using "Logic", hence
252    
253            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
254            * NAMESPACE: import and export "Logic"
255    
256    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
259            only needed previously to R version 2.5.0.
260    
261    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
264    
265            * R/Tsparse.R (replTmat): fix subassignment of triangular
266            * R/Csparse.R (replCmat): ditto
267            * tests/indexing.R: more tests, incl the above fix
268    
269    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Auxiliaries.R (drop0): extend for non CSparse
272            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
273    
274            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
275                    use uplo correctly (!); other places: use uplo_P() macro
276    
277            * R/Csparse.R (replCmat): call diagU2N() when needed
278            * R/Tsparse.R (replTmat): ditto
279    
280            * src/dtCMatrix.c (tCMatrix_validate): new
281            * src/dtTMatrix.c (tTMatrix_validate): new, used in
282            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
283    
284            * R/diagMatrix.R (replDiag): to use in [<-
285    
286    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
289                    also more general diagU2N().
290    
291    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
294            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
295    
296    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * tests/bind.R: a few more cases
299            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
300    
301            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
302            * R/ddenseMatrix.R (cbind2/rbind2)
303            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
304            * tests/indexing.R
305            * tests/indexing.Rout.save: updated
306    
307    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
310            * tests/indexing.R
311    
312    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
315            align with proper position of "0", i.e., right for integers.
316            argument 'align' by default is "fancy".
317    
318    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
321            * R/Csparse.R: and fix "Compare" for more cases.
322            * tests/Class+Meth.R: test some of these (m == m, m != m)
323    
324    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/lsparseMatrix.R: all() and any() methods
327            * R/ldenseMatrix.R:      ditto
328            * NAMESPACE, R/Matrix.R: ditto
329    
330            * man/all-methods.Rd: document them minimally
331    
332            * tests/simple.R: add a few examples for these
333    
334    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/Tsparse.R ([): fix long standing typo in symmetric case
337            * man/dsCMatrix-class.Rd: add example exhibiting the above case
338    
339    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
340    
341            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
342            to LL before converting to a sparse matrix. (The LDL form can be
343            converted to a sparse matrix but it is implicitly a unit
344            triangular matrix and a diagonal matrix overwritten on the diagonal.)
345    
346    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
349    
350    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * DESCRIPTION (Version): updated -> release 0.9975-7
353            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
354    
355    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
358    
359    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
362            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
363            is exactly singular.
364    
365    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * DESCRIPTION (Date): updated -> release 0.9975-6
368    
369    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
372            now returns symmetric.
373    
374            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
375    
376            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
377            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
378    
379            * R/Auxiliaries.R (.type.kind): added
380    
381    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
384            running src/CSparse_install.sh
385    
386            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
387    
388    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
391            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
392    
393            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
394    
395            * tests/Class+Meth.R (tstMatrixClass): now assure
396            the (important in method programming) property :
397    
398                    ###>>  Every "Matrix" is either
399                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
400    
401                    (where "*" stands for "Matrix")
402    
403            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
404    
405            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
406            * tests/validObj.R: checks for "comparison"
407    
408            * R/sparseMatrix.R ([): improved indexing for sparse;
409                    trying to keep <symmetric>[ n, n] symmmetric
410    
411            * tests/indexing.R: indexing for logical sparse now ok
412    
413    
414    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/Tsparse.c: use xTsparse_validate() , and hence remove
417    
418            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
419    
420    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
423    
424            * tests/simple.R: validObject() checking the above.
425    
426            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
427            replacing both dgCMatrix_validate and lgCM*.
428    
429            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
430            fix dimnames setting in other places.
431            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
432    
433    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
436    
437            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
438            symmetry test, via
439            * R/Auxiliaries.R (.as.dgC.0.factors):
440    
441    2006-11-01  Douglas Bates  <bates@r-project.org>
442    
443            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
444            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
445            <CsparseMatrix>) added
446    
447    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * tests/matprod.R: add a variation of Harri's example
450    
451            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
452            recursive infinitely.
453    
454            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
455    
456            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
457    
458    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
461            matrix if possible; test m+m == 2*m; now test dgRMatrix.
462            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
463            satisfy the above test.
464    
465    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
468    
469            * R/dgCMatrix.R: solve(a, b="missing") based on
470            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
471            RHS = NULL.
472    
473            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
474            add more (needed) [t]crossprod() methods.
475    
476            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
477    
478            * R/Auxiliaries.R (as_CspClass): cleanup
479            (drop0): internal utility for "Csparse_drop(*, 0)"
480            (.bail.out.2): encourage active feedback
481    
482    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/dMatrix.R(Compare): new(), then slots [no validity check]
485    
486            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
487            non-valid or 'sorted' case).
488    
489            * R/dsparseMatrix.R: add "chol" method.
490            * R/ddenseMatrix.R: ditto
491    
492            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
493            * NAMESPACE (Ops)
494            * R/diagMatrix.R (diag2T): simple utility used "higher level"
495            coercion; deprecating direct lower level coercions.
496    
497            * R/*.R (seq): use seq_len() and seq_along() where possible.
498    
499    
500    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * DESCRIPTION (Version): 0.9975-5 ready for release
503    
504    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
505    
506            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
507    
508  2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510          * R/AllClass.R (corMatrix): add 'validity' check;          * R/AllClass.R (corMatrix): add 'validity' check;

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