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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 1825, Thu Apr 12 13:21:51 2007 UTC
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1    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgTMatrix.R (mat2dgT): care about NAs
4    
5    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/kronecker.R: triangularity preserving methods
8    
9    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * R/kronecker.R: new file collecting kronecker() methods in one
12                    place.  Goal: become much faster!
13    
14    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
17            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
18            can be much faster.
19    
20            * tests/matprod.R: add regression tests for these (upper & lower).
21    
22    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/Matrix.R (diff): method for our Matrices.
25    
26            * R/sparseMatrix.R (isDiagonal): check dim()!
27    
28    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/Matrix.R (dim<-): new method for "reshape()" built on a
31            proposal from Tamas Papp.
32    
33    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
36    
37            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
38            rather define and export  cBind() and rBind() only.
39            --> useRs *must* change code that used to have cbind()/rbind() !!
40    
41            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
42            * R/bind.Rout.save: ditto
43    
44    2007-02-16  Douglas Bates  <bates@r-project.org>
45    
46            * DESCRIPTION (Date, Version): 0.9975-11 with new date
47            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
48            const modifier on declaration of the array 'valid'
49    
50    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
53    
54    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
57    
58            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
59            * tests/simple.R: test the above and some of these coercions:
60    
61            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
62                    be careful to avoid infinite recursion, using new coercions in
63            * R/ngCMatrix.R and nsC... and ntC...
64            * R/lsparseMatrix.R: ditto
65    
66            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
67    
68            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
69            * R/Rsparse.R: reactivate .Call()s
70    
71            * tests/Class+Meth.R: a bit more on actual classes
72    
73    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
74    
75            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
76    
77    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * DESCRIPTION (Version): 0.9975-10 to upload
80    
81            * tests/Class+Meth.R (tstMatrixClass): require coercions to
82            specific classes less unconditionally.
83    
84            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
85    
86            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
87    
88            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
89            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
90            R_to_CMatrix segfaults on one platform.
91            Eliminate most coercion method to *specific* classes, and replace
92            with virtual classes coercions.
93    
94    
95    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
96    
97            * src/init.c: export the CHM...._validate() placeholders, since
98            they *are* called.
99    
100            * tests/Class+Meth.R (classCanCoerce): and starting to test
101            all as(<from>, <to>)
102    
103    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
106            * tests/indexing.R: tested now
107            * tests/indexing.Rout.save: updated
108    
109            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
110            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
111            appropriate.
112    
113            * NAMESPACE: export a trivial
114            * R/Matrix.R: drop() Matrix-method
115    
116            * R/AllClass.R: moved all prototypes to virtual super classes.
117    
118            * R/Rsparse.R: many more coercions to have less exceptions in
119            * tests/Class+Meth.R:
120    
121            * R/Ops.R (Compare): tweak for case with NA
122            * tests/simpl.R: hence another 'FIXME' eliminated
123    
124    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
127            objects.
128    
129            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
130              and more of "!", "&", "|", all, any; coercions
131    
132            * R/Rsparse.R: many coercions (which enable quite a few other
133            methods), thanks to enhancements in
134            * src/dgCMatrix.c (R_to_CMatrix): new, and
135            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
136            symmetric & triangular and ..RMatrix objects.
137    
138            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
139            renamed file from src/dsTMatrix.c;
140            now dealing with symmetric and triangular Tsparse coercions, both
141            to dense and general.
142    
143    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
146    
147            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
148            where sensible when the <numeric> is of length > 1.
149    
150    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/Matrix.R ([<-): for M[] <- value: fix length
153    
154    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
157            * R/ndenseMatrix.R: new coercions n* -> l*
158    
159    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
162    
163            * R/Ops.R ("Logic"): and other "Ops", many updates
164    
165    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * src/Mutils.h (SET_DimNames): new utility
168    
169            * R/Auxiliaries.R (nnzero): improved and now exported via
170    
171            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
172    
173    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/diagMatrix.R (!): fix typo.
176    
177    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Auxiliaries.R (as_Csparse): and quite a few others:
180                    allow to pass class definition --> speedup
181            * R/sparseMatrix.R: apply the above
182    
183            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
184    
185            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
186            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
187            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
188    
189            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
190    
191            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
192            and use it for "sparse*" as well, since it's faster than the
193            as_Csparse(.) way.
194    
195    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
198    
199    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
202            as method for   M[ ij ] <- v
203            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
204    
205            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
206            FALSE answer
207    
208            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
209            * tests/indexing.R: test it, and some of the above
210    
211    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Auxiliaries.R (is_duplicatedT): new utility
214    
215    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
216    
217            * src/init.c (R_init_Matrix): export cholmod_scale
218    
219    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
222            base::as.matrix to (x, ...)
223    
224    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
227            file; start using "Logic", hence
228    
229            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
230            * NAMESPACE: import and export "Logic"
231    
232    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
235            only needed previously to R version 2.5.0.
236    
237    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
240    
241            * R/Tsparse.R (replTmat): fix subassignment of triangular
242            * R/Csparse.R (replCmat): ditto
243            * tests/indexing.R: more tests, incl the above fix
244    
245    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Auxiliaries.R (drop0): extend for non CSparse
248            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
249    
250            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
251                    use uplo correctly (!); other places: use uplo_P() macro
252    
253            * R/Csparse.R (replCmat): call diagU2N() when needed
254            * R/Tsparse.R (replTmat): ditto
255    
256            * src/dtCMatrix.c (tCMatrix_validate): new
257            * src/dtTMatrix.c (tTMatrix_validate): new, used in
258            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
259    
260            * R/diagMatrix.R (replDiag): to use in [<-
261    
262    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
265                    also more general diagU2N().
266    
267    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
270            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
271    
272    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * tests/bind.R: a few more cases
275            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
276    
277            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
278            * R/ddenseMatrix.R (cbind2/rbind2)
279            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
280            * tests/indexing.R
281            * tests/indexing.Rout.save: updated
282    
283    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
286            * tests/indexing.R
287    
288    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
291            align with proper position of "0", i.e., right for integers.
292            argument 'align' by default is "fancy".
293    
294    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
297            * R/Csparse.R: and fix "Compare" for more cases.
298            * tests/Class+Meth.R: test some of these (m == m, m != m)
299    
300    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/lsparseMatrix.R: all() and any() methods
303            * R/ldenseMatrix.R:      ditto
304            * NAMESPACE, R/Matrix.R: ditto
305    
306            * man/all-methods.Rd: document them minimally
307    
308            * tests/simple.R: add a few examples for these
309    
310    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Tsparse.R ([): fix long standing typo in symmetric case
313            * man/dsCMatrix-class.Rd: add example exhibiting the above case
314    
315    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
316    
317            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
318            to LL before converting to a sparse matrix. (The LDL form can be
319            converted to a sparse matrix but it is implicitly a unit
320            triangular matrix and a diagonal matrix overwritten on the diagonal.)
321    
322    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
323    
324            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
325    
326    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
327    
328            * DESCRIPTION (Version): updated -> release 0.9975-7
329            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
330    
331    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
334    
335    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
338            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
339            is exactly singular.
340    
341    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * DESCRIPTION (Date): updated -> release 0.9975-6
344    
345    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
348            now returns symmetric.
349    
350            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
351    
352            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
353            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
354    
355            * R/Auxiliaries.R (.type.kind): added
356    
357    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
360            running src/CSparse_install.sh
361    
362            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
363    
364    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
367            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
368    
369            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
370    
371            * tests/Class+Meth.R (tstMatrixClass): now assure
372            the (important in method programming) property :
373    
374                    ###>>  Every "Matrix" is either
375                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
376    
377                    (where "*" stands for "Matrix")
378    
379            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
380    
381            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
382            * tests/validObj.R: checks for "comparison"
383    
384            * R/sparseMatrix.R ([): improved indexing for sparse;
385                    trying to keep <symmetric>[ n, n] symmmetric
386    
387            * tests/indexing.R: indexing for logical sparse now ok
388    
389    
390    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * src/Tsparse.c: use xTsparse_validate() , and hence remove
393    
394            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
395    
396    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
399    
400            * tests/simple.R: validObject() checking the above.
401    
402            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
403            replacing both dgCMatrix_validate and lgCM*.
404    
405            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
406            fix dimnames setting in other places.
407            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
408    
409    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
412    
413            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
414            symmetry test, via
415            * R/Auxiliaries.R (.as.dgC.0.factors):
416    
417    2006-11-01  Douglas Bates  <bates@r-project.org>
418    
419            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
420            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
421            <CsparseMatrix>) added
422    
423    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * tests/matprod.R: add a variation of Harri's example
426    
427            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
428            recursive infinitely.
429    
430            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
431    
432            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
433    
434    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
437            matrix if possible; test m+m == 2*m; now test dgRMatrix.
438            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
439            satisfy the above test.
440    
441    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
444    
445            * R/dgCMatrix.R: solve(a, b="missing") based on
446            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
447            RHS = NULL.
448    
449            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
450            add more (needed) [t]crossprod() methods.
451    
452            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
453    
454            * R/Auxiliaries.R (as_CspClass): cleanup
455            (drop0): internal utility for "Csparse_drop(*, 0)"
456            (.bail.out.2): encourage active feedback
457    
458    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/dMatrix.R(Compare): new(), then slots [no validity check]
461    
462            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
463            non-valid or 'sorted' case).
464    
465            * R/dsparseMatrix.R: add "chol" method.
466            * R/ddenseMatrix.R: ditto
467    
468            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
469            * NAMESPACE (Ops)
470            * R/diagMatrix.R (diag2T): simple utility used "higher level"
471            coercion; deprecating direct lower level coercions.
472    
473            * R/*.R (seq): use seq_len() and seq_along() where possible.
474    
475    
476    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * DESCRIPTION (Version): 0.9975-5 ready for release
479    
480    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
481    
482            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
483    
484    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/AllClass.R (corMatrix): add 'validity' check;
487                    comment out unused "LDL" class definition
488            * NAMESPACE: mention, but do not export "LDL" class
489            * R/corMatrix.R: new (simple), needed for R-devel with
490            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
491              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
492    
493    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
494    
495            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
496            use Rprintf and R's error handling.
497    
498    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
501            * tests/matprod.R: add tests for the bug fixed.
502    
503    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
504    
505            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
506            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
507    
508    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
509    
510            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
511    
512    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * DESCRIPTION (Version): 0.9975-3
515    
516            * R/diagMatrix.R (bdiag): new function constructing block diagonal
517            (sparse) matrices.
518            * man/bdiag.Rd: docu + examples
519    
520            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
521    
522            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
523            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
524    
525            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
526            that result is sparse or diagonal (and not dense).
527    
528            * man/Subassign-methods.Rd: fix examples
529    
530            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
531            should always return a sparse (and not sometimes a diagonal) matrix.
532    
533    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
536    
537    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
538    
539            * DESCRIPTION (Version): 0.9975-2
540    
541            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
542    
543    2006-10-02  Douglas Bates  <bates@R-project.org>
544    
545            * tests/dg_Matrix.R: Simplify test taking into account new code.
546    
547    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
550    
551            * R/lsTMatrix.R: new files w/ missing methods
552            * R/nsTMatrix.R:  "  'for completeness'
553    
554            * tests/Class+Meth.R: a bit less 'not.ok.classes'
555    
556            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
557    
558    
559    2006-09-28  Douglas Bates  <bates@R-project.org>
560    
561            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
562            included.
563    
564            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
565            Export C-callable functions used in Zt_create in lme4.
566    
567    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * DESCRIPTION (Version): 0.9975-1
570    
571            * tests/simple.R: less checks fail; using NA, found that our
572                    kronecker() is not base-compatible with NA's.
573    
574            * R/dMatrix.R: "Compare" method now implemented for all cases
575    
576            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
577    
578            * man/dtpMatrix-class.Rd: mention length of 'x' slot
579    
580            * src/dtpMatrix.c (dtpMatrix_validate): fix check
581            * src/dspMatrix.c (dspMatrix_validate): ditto
582    
583            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
584              including coercion to [nl]tTMatrix.
585    
586            * R/diagMatrix.R (show): print a header line as for other classes.
587    
588    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * src/Makefile.win (SUBDIRS): fix typo
591    
592    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
595    
596    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
597    
598            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
599            symmetric and y missing in R code using %*% (cholmod_aat doesn't
600            accept a symmetric matrix).
601            * tests/group-methods.R: Uncomment test of crossprod applied to
602            lsCMatrix objects.
603    
604    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/AllClass.R (symmetricMatrix): add validity method (available
607            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
608    
609            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
610    
611            * tests/indexing.Rout.save:
612            * tests/indexing.R: additions, mainly for 'lsparse'
613    
614            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
615            case.
616    
617            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
618    
619    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
622                    as 'N' (1-letter - Ok?)
623    
624            * tests/group-methods.R: add test for logical + NAs
625    
626            * R/dMatrix.R ("Compare"): fix to work with NA's
627    
628            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
629    
630            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
631                    which is implemented.
632    
633    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * src/chm_common.c: coerce logical <-> double instead of
636            typecasting;  needed for "l" matrix handling in cholmod.
637    
638            * tests/other-pkgs.R (graph): small extension in "graph" checks.
639    
640            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
641            (Tsp2grNEL): other fixes needed
642    
643    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
646                    Matrices, since "lMatrix", also "lsparseM" can have NA
647            * R/ndenseMatrix.R, etc: new source files
648            * man/nsparseMatrix-classes.Rd, etc: new help files
649            * tests/: adaptions
650            * src/chm_common.c (chm_dense_to_SEXP): and others:
651                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
652            * src/Csparse.c, etc: ditto
653    
654    2006-09-11  Douglas Bates  <bates@R-project.org>
655    
656            * src/Mutils.[ch],init.c inst/include/*.h: Move the
657            alloc_d**Matrix functions to the lme4 package.
658    
659    2006-09-09  Douglas Bates  <bates@R-project.org>
660    
661            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
662            fixed
663    
664    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/lMatrix.R: new
667    
668            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
669    
670            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
671            * man/tcrossprod.Rd: ditto
672    
673    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
674    
675            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
676            for exported functions
677            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
678            Remove partitioning algorithms for sparse matrix reordering.  The
679            copyright on the Metis code was problematic and the methods were
680            rarely used.
681            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
682            operations are now done entirely in CHOLMOD code.
683    
684    2006-09-06  Douglas Bates  <bates@R-project.org>
685    
686            * src/Mutils.h: Remove functions that are no longer used.
687    
688    2006-09-04  Douglas Bates  <bates@R-project.org>
689    
690            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
691            * src/DEPS.mkf: update
692    
693    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * created branches/Matrix-for-R-2.3.x;  on trunk: do
696            * DESCRIPTION (Version): 0.9975-0
697            (Depends): R (>= 2.4.0)
698    
699    2006-09-01  Douglas Bates  <bates@R-project.org>
700    
701            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
702    
703    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
706            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
707    
708            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
709    
710    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
713            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
714            * R/dsparseMatrix.R: ditto
715            * R/Csparse.R: ditto
716    
717    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/dMatrix.R (Compare): improve availability of "<", etc
720            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
721    
722    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
725            of a 0-index which was used as 1-index (..hmm)
726    
727            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
728    
729            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
730            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
731            (.is.diagonal): ditto
732    
733            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
734    
735            * R/Matrix.R (Matrix): also work for NA data
736    
737  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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