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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 1799, Sat Mar 24 14:54:00 2007 UTC
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1    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
4            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
5            can be much faster.
6    
7            * tests/matprod.R: add regression tests for these (upper & lower).
8    
9    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/Matrix.R (diff): method for our Matrices.
12    
13            * R/sparseMatrix.R (isDiagonal): check dim()!
14    
15    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Matrix.R (dim<-): new method for "reshape()" built on a
18            proposal from Tamas Papp.
19    
20    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
23    
24            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
25            rather define cBind() and rBind();
26            and also cbind()/rbind {in Matrix, but exported}.
27    
28    
29    2007-02-16  Douglas Bates  <bates@r-project.org>
30    
31            * DESCRIPTION (Date, Version): 0.9975-11 with new date
32            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
33            const modifier on declaration of the array 'valid'
34    
35    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
36    
37            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
38    
39    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
42    
43            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
44            * tests/simple.R: test the above and some of these coercions:
45    
46            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
47                    be careful to avoid infinite recursion, using new coercions in
48            * R/ngCMatrix.R and nsC... and ntC...
49            * R/lsparseMatrix.R: ditto
50    
51            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
52    
53            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
54            * R/Rsparse.R: reactivate .Call()s
55    
56            * tests/Class+Meth.R: a bit more on actual classes
57    
58    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
61    
62    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * DESCRIPTION (Version): 0.9975-10 to upload
65    
66            * tests/Class+Meth.R (tstMatrixClass): require coercions to
67            specific classes less unconditionally.
68    
69            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
70    
71            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
72    
73            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
74            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
75            R_to_CMatrix segfaults on one platform.
76            Eliminate most coercion method to *specific* classes, and replace
77            with virtual classes coercions.
78    
79    
80    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
81    
82            * src/init.c: export the CHM...._validate() placeholders, since
83            they *are* called.
84    
85            * tests/Class+Meth.R (classCanCoerce): and starting to test
86            all as(<from>, <to>)
87    
88    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
91            * tests/indexing.R: tested now
92            * tests/indexing.Rout.save: updated
93    
94            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
95            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
96            appropriate.
97    
98            * NAMESPACE: export a trivial
99            * R/Matrix.R: drop() Matrix-method
100    
101            * R/AllClass.R: moved all prototypes to virtual super classes.
102    
103            * R/Rsparse.R: many more coercions to have less exceptions in
104            * tests/Class+Meth.R:
105    
106            * R/Ops.R (Compare): tweak for case with NA
107            * tests/simpl.R: hence another 'FIXME' eliminated
108    
109    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
112            objects.
113    
114            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
115              and more of "!", "&", "|", all, any; coercions
116    
117            * R/Rsparse.R: many coercions (which enable quite a few other
118            methods), thanks to enhancements in
119            * src/dgCMatrix.c (R_to_CMatrix): new, and
120            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
121            symmetric & triangular and ..RMatrix objects.
122    
123            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
124            renamed file from src/dsTMatrix.c;
125            now dealing with symmetric and triangular Tsparse coercions, both
126            to dense and general.
127    
128    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
131    
132            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
133            where sensible when the <numeric> is of length > 1.
134    
135    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Matrix.R ([<-): for M[] <- value: fix length
138    
139    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
142            * R/ndenseMatrix.R: new coercions n* -> l*
143    
144    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
147    
148            * R/Ops.R ("Logic"): and other "Ops", many updates
149    
150    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * src/Mutils.h (SET_DimNames): new utility
153    
154            * R/Auxiliaries.R (nnzero): improved and now exported via
155    
156            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
157    
158    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/diagMatrix.R (!): fix typo.
161    
162    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/Auxiliaries.R (as_Csparse): and quite a few others:
165                    allow to pass class definition --> speedup
166            * R/sparseMatrix.R: apply the above
167    
168            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
169    
170            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
171            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
172            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
173    
174            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
175    
176            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
177            and use it for "sparse*" as well, since it's faster than the
178            as_Csparse(.) way.
179    
180    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
183    
184    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
187            as method for   M[ ij ] <- v
188            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
189    
190            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
191            FALSE answer
192    
193            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
194            * tests/indexing.R: test it, and some of the above
195    
196    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/Auxiliaries.R (is_duplicatedT): new utility
199    
200    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
201    
202            * src/init.c (R_init_Matrix): export cholmod_scale
203    
204    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
207            base::as.matrix to (x, ...)
208    
209    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
212            file; start using "Logic", hence
213    
214            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
215            * NAMESPACE: import and export "Logic"
216    
217    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
220            only needed previously to R version 2.5.0.
221    
222    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
225    
226            * R/Tsparse.R (replTmat): fix subassignment of triangular
227            * R/Csparse.R (replCmat): ditto
228            * tests/indexing.R: more tests, incl the above fix
229    
230    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Auxiliaries.R (drop0): extend for non CSparse
233            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
234    
235            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
236                    use uplo correctly (!); other places: use uplo_P() macro
237    
238            * R/Csparse.R (replCmat): call diagU2N() when needed
239            * R/Tsparse.R (replTmat): ditto
240    
241            * src/dtCMatrix.c (tCMatrix_validate): new
242            * src/dtTMatrix.c (tTMatrix_validate): new, used in
243            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
244    
245            * R/diagMatrix.R (replDiag): to use in [<-
246    
247    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
250                    also more general diagU2N().
251    
252    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
255            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
256    
257    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * tests/bind.R: a few more cases
260            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
261    
262            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
263            * R/ddenseMatrix.R (cbind2/rbind2)
264            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
265            * tests/indexing.R
266            * tests/indexing.Rout.save: updated
267    
268    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
271            * tests/indexing.R
272    
273    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
276            align with proper position of "0", i.e., right for integers.
277            argument 'align' by default is "fancy".
278    
279    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
282            * R/Csparse.R: and fix "Compare" for more cases.
283            * tests/Class+Meth.R: test some of these (m == m, m != m)
284    
285    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/lsparseMatrix.R: all() and any() methods
288            * R/ldenseMatrix.R:      ditto
289            * NAMESPACE, R/Matrix.R: ditto
290    
291            * man/all-methods.Rd: document them minimally
292    
293            * tests/simple.R: add a few examples for these
294    
295    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Tsparse.R ([): fix long standing typo in symmetric case
298            * man/dsCMatrix-class.Rd: add example exhibiting the above case
299    
300    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
303            to LL before converting to a sparse matrix. (The LDL form can be
304            converted to a sparse matrix but it is implicitly a unit
305            triangular matrix and a diagonal matrix overwritten on the diagonal.)
306    
307    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
308    
309            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
310    
311    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
312    
313            * DESCRIPTION (Version): updated -> release 0.9975-7
314            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
315    
316    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
319    
320    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
321    
322            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
323            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
324            is exactly singular.
325    
326    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * DESCRIPTION (Date): updated -> release 0.9975-6
329    
330    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
333            now returns symmetric.
334    
335            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
336    
337            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
338            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
339    
340            * R/Auxiliaries.R (.type.kind): added
341    
342    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
345            running src/CSparse_install.sh
346    
347            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
348    
349    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
352            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
353    
354            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
355    
356            * tests/Class+Meth.R (tstMatrixClass): now assure
357            the (important in method programming) property :
358    
359                    ###>>  Every "Matrix" is either
360                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
361    
362                    (where "*" stands for "Matrix")
363    
364            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
365    
366            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
367            * tests/validObj.R: checks for "comparison"
368    
369            * R/sparseMatrix.R ([): improved indexing for sparse;
370                    trying to keep <symmetric>[ n, n] symmmetric
371    
372            * tests/indexing.R: indexing for logical sparse now ok
373    
374    
375    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * src/Tsparse.c: use xTsparse_validate() , and hence remove
378    
379            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
380    
381    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
384    
385            * tests/simple.R: validObject() checking the above.
386    
387            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
388            replacing both dgCMatrix_validate and lgCM*.
389    
390            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
391            fix dimnames setting in other places.
392            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
393    
394    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
397    
398            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
399            symmetry test, via
400            * R/Auxiliaries.R (.as.dgC.0.factors):
401    
402    2006-11-01  Douglas Bates  <bates@r-project.org>
403    
404            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
405            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
406            <CsparseMatrix>) added
407    
408    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * tests/matprod.R: add a variation of Harri's example
411    
412            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
413            recursive infinitely.
414    
415            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
416    
417            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
418    
419    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
422            matrix if possible; test m+m == 2*m; now test dgRMatrix.
423            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
424            satisfy the above test.
425    
426    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
429    
430            * R/dgCMatrix.R: solve(a, b="missing") based on
431            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
432            RHS = NULL.
433    
434            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
435            add more (needed) [t]crossprod() methods.
436    
437            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
438    
439            * R/Auxiliaries.R (as_CspClass): cleanup
440            (drop0): internal utility for "Csparse_drop(*, 0)"
441            (.bail.out.2): encourage active feedback
442    
443    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/dMatrix.R(Compare): new(), then slots [no validity check]
446    
447            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
448            non-valid or 'sorted' case).
449    
450            * R/dsparseMatrix.R: add "chol" method.
451            * R/ddenseMatrix.R: ditto
452    
453            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
454            * NAMESPACE (Ops)
455            * R/diagMatrix.R (diag2T): simple utility used "higher level"
456            coercion; deprecating direct lower level coercions.
457    
458            * R/*.R (seq): use seq_len() and seq_along() where possible.
459    
460    
461    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * DESCRIPTION (Version): 0.9975-5 ready for release
464    
465    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
466    
467            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
468    
469    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/AllClass.R (corMatrix): add 'validity' check;
472                    comment out unused "LDL" class definition
473            * NAMESPACE: mention, but do not export "LDL" class
474            * R/corMatrix.R: new (simple), needed for R-devel with
475            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
476              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
477    
478    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
479    
480            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
481            use Rprintf and R's error handling.
482    
483    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
486            * tests/matprod.R: add tests for the bug fixed.
487    
488    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
489    
490            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
491            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
492    
493    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
496    
497    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * DESCRIPTION (Version): 0.9975-3
500    
501            * R/diagMatrix.R (bdiag): new function constructing block diagonal
502            (sparse) matrices.
503            * man/bdiag.Rd: docu + examples
504    
505            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
506    
507            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
508            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
509    
510            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
511            that result is sparse or diagonal (and not dense).
512    
513            * man/Subassign-methods.Rd: fix examples
514    
515            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
516            should always return a sparse (and not sometimes a diagonal) matrix.
517    
518    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
521    
522    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
523    
524            * DESCRIPTION (Version): 0.9975-2
525    
526            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
527    
528    2006-10-02  Douglas Bates  <bates@R-project.org>
529    
530            * tests/dg_Matrix.R: Simplify test taking into account new code.
531    
532    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
535    
536            * R/lsTMatrix.R: new files w/ missing methods
537            * R/nsTMatrix.R:  "  'for completeness'
538    
539            * tests/Class+Meth.R: a bit less 'not.ok.classes'
540    
541            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
542    
543    
544    2006-09-28  Douglas Bates  <bates@R-project.org>
545    
546            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
547            included.
548    
549            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
550            Export C-callable functions used in Zt_create in lme4.
551    
552    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * DESCRIPTION (Version): 0.9975-1
555    
556            * tests/simple.R: less checks fail; using NA, found that our
557                    kronecker() is not base-compatible with NA's.
558    
559            * R/dMatrix.R: "Compare" method now implemented for all cases
560    
561            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
562    
563            * man/dtpMatrix-class.Rd: mention length of 'x' slot
564    
565            * src/dtpMatrix.c (dtpMatrix_validate): fix check
566            * src/dspMatrix.c (dspMatrix_validate): ditto
567    
568            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
569              including coercion to [nl]tTMatrix.
570    
571            * R/diagMatrix.R (show): print a header line as for other classes.
572    
573    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * src/Makefile.win (SUBDIRS): fix typo
576    
577    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
580    
581    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
582    
583            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
584            symmetric and y missing in R code using %*% (cholmod_aat doesn't
585            accept a symmetric matrix).
586            * tests/group-methods.R: Uncomment test of crossprod applied to
587            lsCMatrix objects.
588    
589    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/AllClass.R (symmetricMatrix): add validity method (available
592            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
593    
594            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
595    
596            * tests/indexing.Rout.save:
597            * tests/indexing.R: additions, mainly for 'lsparse'
598    
599            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
600            case.
601    
602            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
603    
604    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
607                    as 'N' (1-letter - Ok?)
608    
609            * tests/group-methods.R: add test for logical + NAs
610    
611            * R/dMatrix.R ("Compare"): fix to work with NA's
612    
613            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
614    
615            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
616                    which is implemented.
617    
618    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * src/chm_common.c: coerce logical <-> double instead of
621            typecasting;  needed for "l" matrix handling in cholmod.
622    
623            * tests/other-pkgs.R (graph): small extension in "graph" checks.
624    
625            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
626            (Tsp2grNEL): other fixes needed
627    
628    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
631                    Matrices, since "lMatrix", also "lsparseM" can have NA
632            * R/ndenseMatrix.R, etc: new source files
633            * man/nsparseMatrix-classes.Rd, etc: new help files
634            * tests/: adaptions
635            * src/chm_common.c (chm_dense_to_SEXP): and others:
636                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
637            * src/Csparse.c, etc: ditto
638    
639    2006-09-11  Douglas Bates  <bates@R-project.org>
640    
641            * src/Mutils.[ch],init.c inst/include/*.h: Move the
642            alloc_d**Matrix functions to the lme4 package.
643    
644    2006-09-09  Douglas Bates  <bates@R-project.org>
645    
646            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
647            fixed
648    
649    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/lMatrix.R: new
652    
653            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
654    
655            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
656            * man/tcrossprod.Rd: ditto
657    
658    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
659    
660            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
661            for exported functions
662            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
663            Remove partitioning algorithms for sparse matrix reordering.  The
664            copyright on the Metis code was problematic and the methods were
665            rarely used.
666            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
667            operations are now done entirely in CHOLMOD code.
668    
669    2006-09-06  Douglas Bates  <bates@R-project.org>
670    
671            * src/Mutils.h: Remove functions that are no longer used.
672    
673  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
674    
675          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 696 
696    
697          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
698          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
699          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
700          * R/Csparse.R: dito          * R/Csparse.R: ditto
701    
702  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
# Line 41  Line 713 
713    
714          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
715          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
716          (.is.diagonal): dito          (.is.diagonal): ditto
717    
718          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
719    

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