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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 1803, Tue Mar 27 16:43:22 2007 UTC
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1    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/kronecker.R: new file collecting kronecker() methods in one
4                    place.  Goal: become much faster!
5    
6    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
9            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
10            can be much faster.
11    
12            * tests/matprod.R: add regression tests for these (upper & lower).
13    
14    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Matrix.R (diff): method for our Matrices.
17    
18            * R/sparseMatrix.R (isDiagonal): check dim()!
19    
20    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R (dim<-): new method for "reshape()" built on a
23            proposal from Tamas Papp.
24    
25    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
28    
29            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
30            rather define and export  cBind() and rBind() only.
31            --> useRs *must* change code that used to have cbind()/rbind() !!
32    
33            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
34            * R/bind.Rout.save: ditto
35    
36    2007-02-16  Douglas Bates  <bates@r-project.org>
37    
38            * DESCRIPTION (Date, Version): 0.9975-11 with new date
39            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
40            const modifier on declaration of the array 'valid'
41    
42    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
43    
44            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
45    
46    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
49    
50            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
51            * tests/simple.R: test the above and some of these coercions:
52    
53            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
54                    be careful to avoid infinite recursion, using new coercions in
55            * R/ngCMatrix.R and nsC... and ntC...
56            * R/lsparseMatrix.R: ditto
57    
58            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
59    
60            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
61            * R/Rsparse.R: reactivate .Call()s
62    
63            * tests/Class+Meth.R: a bit more on actual classes
64    
65    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
66    
67            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
68    
69    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * DESCRIPTION (Version): 0.9975-10 to upload
72    
73            * tests/Class+Meth.R (tstMatrixClass): require coercions to
74            specific classes less unconditionally.
75    
76            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
77    
78            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
79    
80            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
81            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
82            R_to_CMatrix segfaults on one platform.
83            Eliminate most coercion method to *specific* classes, and replace
84            with virtual classes coercions.
85    
86    
87    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
88    
89            * src/init.c: export the CHM...._validate() placeholders, since
90            they *are* called.
91    
92            * tests/Class+Meth.R (classCanCoerce): and starting to test
93            all as(<from>, <to>)
94    
95    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
98            * tests/indexing.R: tested now
99            * tests/indexing.Rout.save: updated
100    
101            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
102            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
103            appropriate.
104    
105            * NAMESPACE: export a trivial
106            * R/Matrix.R: drop() Matrix-method
107    
108            * R/AllClass.R: moved all prototypes to virtual super classes.
109    
110            * R/Rsparse.R: many more coercions to have less exceptions in
111            * tests/Class+Meth.R:
112    
113            * R/Ops.R (Compare): tweak for case with NA
114            * tests/simpl.R: hence another 'FIXME' eliminated
115    
116    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
119            objects.
120    
121            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
122              and more of "!", "&", "|", all, any; coercions
123    
124            * R/Rsparse.R: many coercions (which enable quite a few other
125            methods), thanks to enhancements in
126            * src/dgCMatrix.c (R_to_CMatrix): new, and
127            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
128            symmetric & triangular and ..RMatrix objects.
129    
130            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
131            renamed file from src/dsTMatrix.c;
132            now dealing with symmetric and triangular Tsparse coercions, both
133            to dense and general.
134    
135    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
138    
139            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
140            where sensible when the <numeric> is of length > 1.
141    
142    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R ([<-): for M[] <- value: fix length
145    
146    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
149            * R/ndenseMatrix.R: new coercions n* -> l*
150    
151    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
154    
155            * R/Ops.R ("Logic"): and other "Ops", many updates
156    
157    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * src/Mutils.h (SET_DimNames): new utility
160    
161            * R/Auxiliaries.R (nnzero): improved and now exported via
162    
163            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
164    
165    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/diagMatrix.R (!): fix typo.
168    
169    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Auxiliaries.R (as_Csparse): and quite a few others:
172                    allow to pass class definition --> speedup
173            * R/sparseMatrix.R: apply the above
174    
175            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
176    
177            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
178            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
179            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
180    
181            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
182    
183            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
184            and use it for "sparse*" as well, since it's faster than the
185            as_Csparse(.) way.
186    
187    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
190    
191    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
194            as method for   M[ ij ] <- v
195            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
196    
197            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
198            FALSE answer
199    
200            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
201            * tests/indexing.R: test it, and some of the above
202    
203    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Auxiliaries.R (is_duplicatedT): new utility
206    
207    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
208    
209            * src/init.c (R_init_Matrix): export cholmod_scale
210    
211    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
214            base::as.matrix to (x, ...)
215    
216    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
219            file; start using "Logic", hence
220    
221            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
222            * NAMESPACE: import and export "Logic"
223    
224    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
227            only needed previously to R version 2.5.0.
228    
229    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
232    
233            * R/Tsparse.R (replTmat): fix subassignment of triangular
234            * R/Csparse.R (replCmat): ditto
235            * tests/indexing.R: more tests, incl the above fix
236    
237    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/Auxiliaries.R (drop0): extend for non CSparse
240            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
241    
242            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
243                    use uplo correctly (!); other places: use uplo_P() macro
244    
245            * R/Csparse.R (replCmat): call diagU2N() when needed
246            * R/Tsparse.R (replTmat): ditto
247    
248            * src/dtCMatrix.c (tCMatrix_validate): new
249            * src/dtTMatrix.c (tTMatrix_validate): new, used in
250            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
251    
252            * R/diagMatrix.R (replDiag): to use in [<-
253    
254    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
257                    also more general diagU2N().
258    
259    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
262            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
263    
264    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * tests/bind.R: a few more cases
267            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
268    
269            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
270            * R/ddenseMatrix.R (cbind2/rbind2)
271            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
272            * tests/indexing.R
273            * tests/indexing.Rout.save: updated
274    
275    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
278            * tests/indexing.R
279    
280    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
283            align with proper position of "0", i.e., right for integers.
284            argument 'align' by default is "fancy".
285    
286    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
289            * R/Csparse.R: and fix "Compare" for more cases.
290            * tests/Class+Meth.R: test some of these (m == m, m != m)
291    
292    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/lsparseMatrix.R: all() and any() methods
295            * R/ldenseMatrix.R:      ditto
296            * NAMESPACE, R/Matrix.R: ditto
297    
298            * man/all-methods.Rd: document them minimally
299    
300            * tests/simple.R: add a few examples for these
301    
302    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Tsparse.R ([): fix long standing typo in symmetric case
305            * man/dsCMatrix-class.Rd: add example exhibiting the above case
306    
307    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
308    
309            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
310            to LL before converting to a sparse matrix. (The LDL form can be
311            converted to a sparse matrix but it is implicitly a unit
312            triangular matrix and a diagonal matrix overwritten on the diagonal.)
313    
314    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
315    
316            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
317    
318    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
319    
320            * DESCRIPTION (Version): updated -> release 0.9975-7
321            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
322    
323    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
326    
327    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
328    
329            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
330            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
331            is exactly singular.
332    
333    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * DESCRIPTION (Date): updated -> release 0.9975-6
336    
337    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
340            now returns symmetric.
341    
342            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
343    
344            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
345            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
346    
347            * R/Auxiliaries.R (.type.kind): added
348    
349    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
352            running src/CSparse_install.sh
353    
354            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
355    
356    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
359            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
360    
361            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
362    
363            * tests/Class+Meth.R (tstMatrixClass): now assure
364            the (important in method programming) property :
365    
366                    ###>>  Every "Matrix" is either
367                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
368    
369                    (where "*" stands for "Matrix")
370    
371            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
372    
373            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
374            * tests/validObj.R: checks for "comparison"
375    
376            * R/sparseMatrix.R ([): improved indexing for sparse;
377                    trying to keep <symmetric>[ n, n] symmmetric
378    
379            * tests/indexing.R: indexing for logical sparse now ok
380    
381    
382    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * src/Tsparse.c: use xTsparse_validate() , and hence remove
385    
386            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
387    
388    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
391    
392            * tests/simple.R: validObject() checking the above.
393    
394            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
395            replacing both dgCMatrix_validate and lgCM*.
396    
397            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
398            fix dimnames setting in other places.
399            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
400    
401    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
404    
405            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
406            symmetry test, via
407            * R/Auxiliaries.R (.as.dgC.0.factors):
408    
409    2006-11-01  Douglas Bates  <bates@r-project.org>
410    
411            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
412            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
413            <CsparseMatrix>) added
414    
415    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * tests/matprod.R: add a variation of Harri's example
418    
419            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
420            recursive infinitely.
421    
422            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
423    
424            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
425    
426    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
429            matrix if possible; test m+m == 2*m; now test dgRMatrix.
430            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
431            satisfy the above test.
432    
433    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
436    
437            * R/dgCMatrix.R: solve(a, b="missing") based on
438            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
439            RHS = NULL.
440    
441            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
442            add more (needed) [t]crossprod() methods.
443    
444            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
445    
446            * R/Auxiliaries.R (as_CspClass): cleanup
447            (drop0): internal utility for "Csparse_drop(*, 0)"
448            (.bail.out.2): encourage active feedback
449    
450    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/dMatrix.R(Compare): new(), then slots [no validity check]
453    
454            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
455            non-valid or 'sorted' case).
456    
457            * R/dsparseMatrix.R: add "chol" method.
458            * R/ddenseMatrix.R: ditto
459    
460            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
461            * NAMESPACE (Ops)
462            * R/diagMatrix.R (diag2T): simple utility used "higher level"
463            coercion; deprecating direct lower level coercions.
464    
465            * R/*.R (seq): use seq_len() and seq_along() where possible.
466    
467    
468    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * DESCRIPTION (Version): 0.9975-5 ready for release
471    
472    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
473    
474            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
475    
476    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/AllClass.R (corMatrix): add 'validity' check;
479                    comment out unused "LDL" class definition
480            * NAMESPACE: mention, but do not export "LDL" class
481            * R/corMatrix.R: new (simple), needed for R-devel with
482            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
483              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
484    
485    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
486    
487            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
488            use Rprintf and R's error handling.
489    
490    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
493            * tests/matprod.R: add tests for the bug fixed.
494    
495    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
496    
497            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
498            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
499    
500    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
501    
502            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
503    
504    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * DESCRIPTION (Version): 0.9975-3
507    
508            * R/diagMatrix.R (bdiag): new function constructing block diagonal
509            (sparse) matrices.
510            * man/bdiag.Rd: docu + examples
511    
512            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
513    
514            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
515            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
516    
517            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
518            that result is sparse or diagonal (and not dense).
519    
520            * man/Subassign-methods.Rd: fix examples
521    
522            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
523            should always return a sparse (and not sometimes a diagonal) matrix.
524    
525    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
528    
529    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
530    
531            * DESCRIPTION (Version): 0.9975-2
532    
533            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
534    
535    2006-10-02  Douglas Bates  <bates@R-project.org>
536    
537            * tests/dg_Matrix.R: Simplify test taking into account new code.
538    
539    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
542    
543            * R/lsTMatrix.R: new files w/ missing methods
544            * R/nsTMatrix.R:  "  'for completeness'
545    
546            * tests/Class+Meth.R: a bit less 'not.ok.classes'
547    
548            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
549    
550    
551    2006-09-28  Douglas Bates  <bates@R-project.org>
552    
553            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
554            included.
555    
556            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
557            Export C-callable functions used in Zt_create in lme4.
558    
559    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * DESCRIPTION (Version): 0.9975-1
562    
563            * tests/simple.R: less checks fail; using NA, found that our
564                    kronecker() is not base-compatible with NA's.
565    
566            * R/dMatrix.R: "Compare" method now implemented for all cases
567    
568            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
569    
570            * man/dtpMatrix-class.Rd: mention length of 'x' slot
571    
572            * src/dtpMatrix.c (dtpMatrix_validate): fix check
573            * src/dspMatrix.c (dspMatrix_validate): ditto
574    
575            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
576              including coercion to [nl]tTMatrix.
577    
578            * R/diagMatrix.R (show): print a header line as for other classes.
579    
580    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * src/Makefile.win (SUBDIRS): fix typo
583    
584    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
587    
588    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
589    
590            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
591            symmetric and y missing in R code using %*% (cholmod_aat doesn't
592            accept a symmetric matrix).
593            * tests/group-methods.R: Uncomment test of crossprod applied to
594            lsCMatrix objects.
595    
596    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/AllClass.R (symmetricMatrix): add validity method (available
599            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
600    
601            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
602    
603            * tests/indexing.Rout.save:
604            * tests/indexing.R: additions, mainly for 'lsparse'
605    
606            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
607            case.
608    
609            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
610    
611    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
614                    as 'N' (1-letter - Ok?)
615    
616            * tests/group-methods.R: add test for logical + NAs
617    
618            * R/dMatrix.R ("Compare"): fix to work with NA's
619    
620            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
621    
622            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
623                    which is implemented.
624    
625    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * src/chm_common.c: coerce logical <-> double instead of
628            typecasting;  needed for "l" matrix handling in cholmod.
629    
630            * tests/other-pkgs.R (graph): small extension in "graph" checks.
631    
632            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
633            (Tsp2grNEL): other fixes needed
634    
635    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
638                    Matrices, since "lMatrix", also "lsparseM" can have NA
639            * R/ndenseMatrix.R, etc: new source files
640            * man/nsparseMatrix-classes.Rd, etc: new help files
641            * tests/: adaptions
642            * src/chm_common.c (chm_dense_to_SEXP): and others:
643                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
644            * src/Csparse.c, etc: ditto
645    
646    2006-09-11  Douglas Bates  <bates@R-project.org>
647    
648            * src/Mutils.[ch],init.c inst/include/*.h: Move the
649            alloc_d**Matrix functions to the lme4 package.
650    
651    2006-09-09  Douglas Bates  <bates@R-project.org>
652    
653            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
654            fixed
655    
656    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/lMatrix.R: new
659    
660            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
661    
662            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
663            * man/tcrossprod.Rd: ditto
664    
665    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
666    
667            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
668            for exported functions
669            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
670            Remove partitioning algorithms for sparse matrix reordering.  The
671            copyright on the Metis code was problematic and the methods were
672            rarely used.
673            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
674            operations are now done entirely in CHOLMOD code.
675    
676    2006-09-06  Douglas Bates  <bates@R-project.org>
677    
678            * src/Mutils.h: Remove functions that are no longer used.
679    
680  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
681    
682          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 703 
703    
704          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
705          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
706          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
707          * R/Csparse.R: dito          * R/Csparse.R: ditto
708    
709  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
# Line 41  Line 720 
720    
721          * 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
722          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
723          (.is.diagonal): dito          (.is.diagonal): ditto
724    
725          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
726    

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