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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1768, Mon Feb 5 17:49:54 2007 UTC
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1    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
4    
5            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
6            * tests/simple.R: test the above and some of these coercions:
7    
8            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
9                    be careful to avoid infinite recursion, using new coercions in
10            * R/ngCMatrix.R and nsC... and ntC...
11            * R/lsparseMatrix.R: ditto
12    
13            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
14    
15            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
16            * R/Rsparse.R: reactivate .Call()s
17    
18            * tests/Class+Meth.R: a bit more on actual classes
19    
20    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
21    
22            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
23    
24    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * DESCRIPTION (Version): 0.9975-10 to upload
27    
28            * tests/Class+Meth.R (tstMatrixClass): require coercions to
29            specific classes less unconditionally.
30    
31            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
32    
33            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
34    
35            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
36            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
37            R_to_CMatrix segfaults on one platform.
38            Eliminate most coercion method to *specific* classes, and replace
39            with virtual classes coercions.
40    
41    
42    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
43    
44            * src/init.c: export the CHM...._validate() placeholders, since
45            they *are* called.
46    
47            * tests/Class+Meth.R (classCanCoerce): and starting to test
48            all as(<from>, <to>)
49    
50    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
53            * tests/indexing.R: tested now
54            * tests/indexing.Rout.save: updated
55    
56            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
57            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
58            appropriate.
59    
60            * NAMESPACE: export a trivial
61            * R/Matrix.R: drop() Matrix-method
62    
63            * R/AllClass.R: moved all prototypes to virtual super classes.
64    
65            * R/Rsparse.R: many more coercions to have less exceptions in
66            * tests/Class+Meth.R:
67    
68            * R/Ops.R (Compare): tweak for case with NA
69            * tests/simpl.R: hence another 'FIXME' eliminated
70    
71    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
74            objects.
75    
76            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
77              and more of "!", "&", "|", all, any; coercions
78    
79            * R/Rsparse.R: many coercions (which enable quite a few other
80            methods), thanks to enhancements in
81            * src/dgCMatrix.c (R_to_CMatrix): new, and
82            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
83            symmetric & triangular and ..RMatrix objects.
84    
85            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
86            renamed file from src/dsTMatrix.c;
87            now dealing with symmetric and triangular Tsparse coercions, both
88            to dense and general.
89    
90    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
93    
94            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
95            where sensible when the <numeric> is of length > 1.
96    
97    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Matrix.R ([<-): for M[] <- value: fix length
100    
101    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
104            * R/ndenseMatrix.R: new coercions n* -> l*
105    
106    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
109    
110            * R/Ops.R ("Logic"): and other "Ops", many updates
111    
112    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/Mutils.h (SET_DimNames): new utility
115    
116            * R/Auxiliaries.R (nnzero): improved and now exported via
117    
118            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
119    
120    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/diagMatrix.R (!): fix typo.
123    
124    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/Auxiliaries.R (as_Csparse): and quite a few others:
127                    allow to pass class definition --> speedup
128            * R/sparseMatrix.R: apply the above
129    
130            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
131    
132            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
133            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
134            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
135    
136            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
137    
138            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
139            and use it for "sparse*" as well, since it's faster than the
140            as_Csparse(.) way.
141    
142    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
145    
146    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
149            as method for   M[ ij ] <- v
150            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
151    
152            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
153            FALSE answer
154    
155            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
156            * tests/indexing.R: test it, and some of the above
157    
158    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Auxiliaries.R (is_duplicatedT): new utility
161    
162    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
163    
164            * src/init.c (R_init_Matrix): export cholmod_scale
165    
166    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
169            base::as.matrix to (x, ...)
170    
171    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
174            file; start using "Logic", hence
175    
176            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
177            * NAMESPACE: import and export "Logic"
178    
179    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
182            only needed previously to R version 2.5.0.
183    
184    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
187    
188            * R/Tsparse.R (replTmat): fix subassignment of triangular
189            * R/Csparse.R (replCmat): ditto
190            * tests/indexing.R: more tests, incl the above fix
191    
192    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/Auxiliaries.R (drop0): extend for non CSparse
195            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
196    
197            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
198                    use uplo correctly (!); other places: use uplo_P() macro
199    
200            * R/Csparse.R (replCmat): call diagU2N() when needed
201            * R/Tsparse.R (replTmat): ditto
202    
203            * src/dtCMatrix.c (tCMatrix_validate): new
204            * src/dtTMatrix.c (tTMatrix_validate): new, used in
205            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
206    
207            * R/diagMatrix.R (replDiag): to use in [<-
208    
209    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
212                    also more general diagU2N().
213    
214    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
217            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
218    
219    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * tests/bind.R: a few more cases
222            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
223    
224            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
225            * R/ddenseMatrix.R (cbind2/rbind2)
226            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
227            * tests/indexing.R
228            * tests/indexing.Rout.save: updated
229    
230    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
233            * tests/indexing.R
234    
235    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
238            align with proper position of "0", i.e., right for integers.
239            argument 'align' by default is "fancy".
240    
241    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
244            * R/Csparse.R: and fix "Compare" for more cases.
245            * tests/Class+Meth.R: test some of these (m == m, m != m)
246    
247    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/lsparseMatrix.R: all() and any() methods
250            * R/ldenseMatrix.R:      ditto
251            * NAMESPACE, R/Matrix.R: ditto
252    
253            * man/all-methods.Rd: document them minimally
254    
255            * tests/simple.R: add a few examples for these
256    
257    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Tsparse.R ([): fix long standing typo in symmetric case
260            * man/dsCMatrix-class.Rd: add example exhibiting the above case
261    
262    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
263    
264            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
265            to LL before converting to a sparse matrix. (The LDL form can be
266            converted to a sparse matrix but it is implicitly a unit
267            triangular matrix and a diagonal matrix overwritten on the diagonal.)
268    
269    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
270    
271            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
272    
273    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
274    
275            * DESCRIPTION (Version): updated -> release 0.9975-7
276            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
277    
278    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
281    
282    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
283    
284            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
285            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
286            is exactly singular.
287    
288    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * DESCRIPTION (Date): updated -> release 0.9975-6
291    
292    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
295            now returns symmetric.
296    
297            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
298    
299            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
300            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
301    
302            * R/Auxiliaries.R (.type.kind): added
303    
304    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
307            running src/CSparse_install.sh
308    
309            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
310    
311    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
314            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
315    
316            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
317    
318            * tests/Class+Meth.R (tstMatrixClass): now assure
319            the (important in method programming) property :
320    
321                    ###>>  Every "Matrix" is either
322                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
323    
324                    (where "*" stands for "Matrix")
325    
326            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
327    
328            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
329            * tests/validObj.R: checks for "comparison"
330    
331            * R/sparseMatrix.R ([): improved indexing for sparse;
332                    trying to keep <symmetric>[ n, n] symmmetric
333    
334            * tests/indexing.R: indexing for logical sparse now ok
335    
336    
337    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * src/Tsparse.c: use xTsparse_validate() , and hence remove
340    
341            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
342    
343    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
346    
347            * tests/simple.R: validObject() checking the above.
348    
349            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
350            replacing both dgCMatrix_validate and lgCM*.
351    
352            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
353            fix dimnames setting in other places.
354            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
355    
356    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
359    
360            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
361            symmetry test, via
362            * R/Auxiliaries.R (.as.dgC.0.factors):
363    
364    2006-11-01  Douglas Bates  <bates@r-project.org>
365    
366            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
367            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
368            <CsparseMatrix>) added
369    
370    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * tests/matprod.R: add a variation of Harri's example
373    
374            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
375            recursive infinitely.
376    
377            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
378    
379            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
380    
381    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
384            matrix if possible; test m+m == 2*m; now test dgRMatrix.
385            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
386            satisfy the above test.
387    
388    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
391    
392            * R/dgCMatrix.R: solve(a, b="missing") based on
393            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
394            RHS = NULL.
395    
396            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
397            add more (needed) [t]crossprod() methods.
398    
399            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
400    
401            * R/Auxiliaries.R (as_CspClass): cleanup
402            (drop0): internal utility for "Csparse_drop(*, 0)"
403            (.bail.out.2): encourage active feedback
404    
405    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/dMatrix.R(Compare): new(), then slots [no validity check]
408    
409            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
410            non-valid or 'sorted' case).
411    
412            * R/dsparseMatrix.R: add "chol" method.
413            * R/ddenseMatrix.R: ditto
414    
415            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
416            * NAMESPACE (Ops)
417            * R/diagMatrix.R (diag2T): simple utility used "higher level"
418            coercion; deprecating direct lower level coercions.
419    
420            * R/*.R (seq): use seq_len() and seq_along() where possible.
421    
422    
423    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * DESCRIPTION (Version): 0.9975-5 ready for release
426    
427    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
428    
429            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
430    
431    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/AllClass.R (corMatrix): add 'validity' check;
434                    comment out unused "LDL" class definition
435            * NAMESPACE: mention, but do not export "LDL" class
436            * R/corMatrix.R: new (simple), needed for R-devel with
437            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
438              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
439    
440    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
441    
442            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
443            use Rprintf and R's error handling.
444    
445    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
448            * tests/matprod.R: add tests for the bug fixed.
449    
450    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
451    
452            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
453            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
454    
455    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
456    
457            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
458    
459    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * DESCRIPTION (Version): 0.9975-3
462    
463            * R/diagMatrix.R (bdiag): new function constructing block diagonal
464            (sparse) matrices.
465            * man/bdiag.Rd: docu + examples
466    
467            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
468    
469            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
470            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
471    
472            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
473            that result is sparse or diagonal (and not dense).
474    
475            * man/Subassign-methods.Rd: fix examples
476    
477            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
478            should always return a sparse (and not sometimes a diagonal) matrix.
479    
480    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
483    
484    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
485    
486            * DESCRIPTION (Version): 0.9975-2
487    
488            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
489    
490    2006-10-02  Douglas Bates  <bates@R-project.org>
491    
492            * tests/dg_Matrix.R: Simplify test taking into account new code.
493    
494    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
497    
498            * R/lsTMatrix.R: new files w/ missing methods
499            * R/nsTMatrix.R:  "  'for completeness'
500    
501            * tests/Class+Meth.R: a bit less 'not.ok.classes'
502    
503            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
504    
505    
506    2006-09-28  Douglas Bates  <bates@R-project.org>
507    
508            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
509            included.
510    
511            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
512            Export C-callable functions used in Zt_create in lme4.
513    
514    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * DESCRIPTION (Version): 0.9975-1
517    
518            * tests/simple.R: less checks fail; using NA, found that our
519                    kronecker() is not base-compatible with NA's.
520    
521            * R/dMatrix.R: "Compare" method now implemented for all cases
522    
523            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
524    
525            * man/dtpMatrix-class.Rd: mention length of 'x' slot
526    
527            * src/dtpMatrix.c (dtpMatrix_validate): fix check
528            * src/dspMatrix.c (dspMatrix_validate): ditto
529    
530            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
531              including coercion to [nl]tTMatrix.
532    
533            * R/diagMatrix.R (show): print a header line as for other classes.
534    
535    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * src/Makefile.win (SUBDIRS): fix typo
538    
539    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
542    
543    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
544    
545            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
546            symmetric and y missing in R code using %*% (cholmod_aat doesn't
547            accept a symmetric matrix).
548            * tests/group-methods.R: Uncomment test of crossprod applied to
549            lsCMatrix objects.
550    
551    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/AllClass.R (symmetricMatrix): add validity method (available
554            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
555    
556            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
557    
558            * tests/indexing.Rout.save:
559            * tests/indexing.R: additions, mainly for 'lsparse'
560    
561            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
562            case.
563    
564            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
565    
566    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
569                    as 'N' (1-letter - Ok?)
570    
571            * tests/group-methods.R: add test for logical + NAs
572    
573            * R/dMatrix.R ("Compare"): fix to work with NA's
574    
575            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
576    
577            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
578                    which is implemented.
579    
580    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * src/chm_common.c: coerce logical <-> double instead of
583            typecasting;  needed for "l" matrix handling in cholmod.
584    
585            * tests/other-pkgs.R (graph): small extension in "graph" checks.
586    
587            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
588            (Tsp2grNEL): other fixes needed
589    
590    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
593                    Matrices, since "lMatrix", also "lsparseM" can have NA
594            * R/ndenseMatrix.R, etc: new source files
595            * man/nsparseMatrix-classes.Rd, etc: new help files
596            * tests/: adaptions
597            * src/chm_common.c (chm_dense_to_SEXP): and others:
598                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
599            * src/Csparse.c, etc: ditto
600    
601    2006-09-11  Douglas Bates  <bates@R-project.org>
602    
603            * src/Mutils.[ch],init.c inst/include/*.h: Move the
604            alloc_d**Matrix functions to the lme4 package.
605    
606    2006-09-09  Douglas Bates  <bates@R-project.org>
607    
608            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
609            fixed
610    
611    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/lMatrix.R: new
614    
615            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
616    
617            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
618            * man/tcrossprod.Rd: ditto
619    
620    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
621    
622            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
623            for exported functions
624            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
625            Remove partitioning algorithms for sparse matrix reordering.  The
626            copyright on the Metis code was problematic and the methods were
627            rarely used.
628            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
629            operations are now done entirely in CHOLMOD code.
630    
631    2006-09-06  Douglas Bates  <bates@R-project.org>
632    
633            * src/Mutils.h: Remove functions that are no longer used.
634    
635    2006-09-04  Douglas Bates  <bates@R-project.org>
636    
637            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
638            * src/DEPS.mkf: update
639    
640    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * created branches/Matrix-for-R-2.3.x;  on trunk: do
643            * DESCRIPTION (Version): 0.9975-0
644            (Depends): R (>= 2.4.0)
645    
646    2006-09-01  Douglas Bates  <bates@R-project.org>
647    
648            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
649    
650    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
653            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
654    
655            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
656    
657    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
660            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
661            * R/dsparseMatrix.R: ditto
662            * R/Csparse.R: ditto
663    
664    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/dMatrix.R (Compare): improve availability of "<", etc
667            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
668    
669    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
672            of a 0-index which was used as 1-index (..hmm)
673    
674            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
675    
676            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
677            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
678            (.is.diagonal): ditto
679    
680            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
681    
682            * R/Matrix.R (Matrix): also work for NA data
683    
684    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
687            in all cases.
688    
689    2006-08-27  Douglas Bates  <bates@R-project.org>
690    
691            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
692            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
693    
694    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
695    
696            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
697            subclasses of "ddenseMatrix"
698            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
699            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
700            instead of half dozen specialized ones.
701    
702    2006-08-25  Douglas Bates  <bates@R-project.org>
703    
704            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
705            <tillard@cirad.fr> - ordering standard errors to match effects.
706    
707    2006-08-24  Douglas Bates  <bates@R-project.org>
708    
709            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
710            on R_ldl.
711            * R/lCholCMatrix.R,
712            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
713            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
714            * many files in ./R and ./src: Use more general version of
715            dup_mMatrix_as_dgeMatrix to simplify method definitions.
716            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
717            dtpMatrix, dspMatrix and dppMatrix conversions.
718    
719    
720    2006-08-23  Douglas Bates  <bates@R-project.org>
721    
722            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
723            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
724            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
725            dgeMatrix_crossprod (may need to do this in other places).
726            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
727            generic and method for dsCMatrix.  Use CHOLMOD for chol().
728    
729    2006-08-22  Douglas Bates  <bates@R-project.org>
730    
731            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
732            types of classed Matrices, matrices or numeric or logical vectors.
733            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
734            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
735            to Mutils.h (as an inline) and change name to Matrix_check_class;
736            fixes in as_cholmod_factor and chm_factor_to_SEXP.
737            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
738            dsCMatrix_matrix_solve.  Comment out vestigial functions.
739            * src/Csparse.c: use diag_P and uplo_P macros.
740    
741  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
742    
743          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
744          valgrind.          valgrind.
745            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
746            inverses.
747            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
748            -Wall warnings.
749            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
750            Use dup_mMatrix_as_dgeMatrix.
751    
752  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
753    

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