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revision 1360, Tue Aug 8 17:29:03 2006 UTC revision 1877, Tue Jun 5 17:06:34 2007 UTC
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1    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
4              SuiteSparse
5            * [r4426] src/Makefile: add ./UFconfig to the include path for
6              compilation
7            * [r4427] src/cs.c, src/cs.h: update to CSparse version 2.2.0
8            * [r4428] inst/doc/UFsparse/* src/AMD/* src/CHOLMOD/*
9              src/COLAMD/* src/UFconfig/UFconfig.h: Update to version 3.0.0 of
10              SuiteSparse
11    
12    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
15            * R/sparseMatrix.R (prSpMatrix): now gives a message about
16            suppressed column names.
17    
18    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
19    
20            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
21              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
22              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
23              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
24              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
25              Remove warnings after change to const char* CHAR
26    
27    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
28    
29            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
30              type of M_cholmod_ssmult
31    
32    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
33    
34            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
35              src/init.c: Yet another cholmod export - cholmod_ssmult
36    
37    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * NAMESPACE: exported drop0(), since
40            * man/drop0.Rd: I have seen several cases, I really wanted to use
41            it, so our users may want too.
42    
43    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * man/colSums.Rd: separately document colSums() etc, since these
46            have the extra argument 'sparseResult'.
47    
48    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
51            * man/spMatrix.Rd: docu., including examples
52    
53            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
54            in order to make colMeans() etc fast *and* correct.
55            * R/sparseVector.R (replSPvec): "[<-" functionality for
56            sparseVectors; tested in
57            * tests/simple.R:
58    
59    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
62            (very) sparse Matrices; output similar to Matlab's print().
63    
64    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
65    
66            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
67            0-based, indices (Jose Quesada <quesada@gmail.com>).
68    
69    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
70    
71            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
72    
73    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/Auxiliaries.R (sparsapply): new utility, much faster than
76            tapply1() for large sparse matrices.
77    
78    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/Matrix.R (dim<-): reshape now via sparseVector.
81    
82            * R/sparseVector.R: methods and function for
83            * R/AllClass.R: new "sparseVector" class and daughters.
84            * NAMESPACE: export new classes
85    
86    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * DESCRIPTION (Version): 0.99875-1
89            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
90    
91    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
94            indexing
95            * tests/indexing.R: test set for that.
96    
97    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
100            entries.
101            * tests/indexing.R(out): add regression test for it
102    
103    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
106            name for "!" method definitions.
107    
108    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Tsparse.R (intI): new utility, used for "[" :
111                    Cleanup up there, and fixes for duplicated indices - more TODO!
112    
113            * tests/indexing.R(out): more tests
114    
115    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
116    
117            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
118            code that is now part of the R Lapack library.
119    
120            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
121            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
122    
123    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
126    
127    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
130            up with extraneous names '0'...'<n-1>'
131    
132    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/dgTMatrix.R (mat2dgT): care about NAs
135    
136    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/kronecker.R: triangularity preserving methods
139    
140    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/kronecker.R: new file collecting kronecker() methods in one
143                    place.  Goal: become much faster!
144    
145    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
148            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
149            can be much faster.
150    
151            * tests/matprod.R: add regression tests for these (upper & lower).
152    
153    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Matrix.R (diff): method for our Matrices.
156    
157            * R/sparseMatrix.R (isDiagonal): check dim()!
158    
159    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R (dim<-): new method for "reshape()" built on a
162            proposal from Tamas Papp.
163    
164    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
167    
168            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
169            rather define and export  cBind() and rBind() only.
170            --> useRs *must* change code that used to have cbind()/rbind() !!
171    
172            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
173            * R/bind.Rout.save: ditto
174    
175    2007-02-16  Douglas Bates  <bates@r-project.org>
176    
177            * DESCRIPTION (Date, Version): 0.9975-11 with new date
178            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
179            const modifier on declaration of the array 'valid'
180    
181    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
182    
183            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
184    
185    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
188    
189            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
190            * tests/simple.R: test the above and some of these coercions:
191    
192            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
193                    be careful to avoid infinite recursion, using new coercions in
194            * R/ngCMatrix.R and nsC... and ntC...
195            * R/lsparseMatrix.R: ditto
196    
197            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
198    
199            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
200            * R/Rsparse.R: reactivate .Call()s
201    
202            * tests/Class+Meth.R: a bit more on actual classes
203    
204    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
205    
206            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
207    
208    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * DESCRIPTION (Version): 0.9975-10 to upload
211    
212            * tests/Class+Meth.R (tstMatrixClass): require coercions to
213            specific classes less unconditionally.
214    
215            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
216    
217            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
218    
219            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
220            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
221            R_to_CMatrix segfaults on one platform.
222            Eliminate most coercion method to *specific* classes, and replace
223            with virtual classes coercions.
224    
225    
226    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
227    
228            * src/init.c: export the CHM...._validate() placeholders, since
229            they *are* called.
230    
231            * tests/Class+Meth.R (classCanCoerce): and starting to test
232            all as(<from>, <to>)
233    
234    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
237            * tests/indexing.R: tested now
238            * tests/indexing.Rout.save: updated
239    
240            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
241            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
242            appropriate.
243    
244            * NAMESPACE: export a trivial
245            * R/Matrix.R: drop() Matrix-method
246    
247            * R/AllClass.R: moved all prototypes to virtual super classes.
248    
249            * R/Rsparse.R: many more coercions to have less exceptions in
250            * tests/Class+Meth.R:
251    
252            * R/Ops.R (Compare): tweak for case with NA
253            * tests/simpl.R: hence another 'FIXME' eliminated
254    
255    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
258            objects.
259    
260            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
261              and more of "!", "&", "|", all, any; coercions
262    
263            * R/Rsparse.R: many coercions (which enable quite a few other
264            methods), thanks to enhancements in
265            * src/dgCMatrix.c (R_to_CMatrix): new, and
266            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
267            symmetric & triangular and ..RMatrix objects.
268    
269            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
270            renamed file from src/dsTMatrix.c;
271            now dealing with symmetric and triangular Tsparse coercions, both
272            to dense and general.
273    
274    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
277    
278            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
279            where sensible when the <numeric> is of length > 1.
280    
281    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/Matrix.R ([<-): for M[] <- value: fix length
284    
285    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
288            * R/ndenseMatrix.R: new coercions n* -> l*
289    
290    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
293    
294            * R/Ops.R ("Logic"): and other "Ops", many updates
295    
296    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * src/Mutils.h (SET_DimNames): new utility
299    
300            * R/Auxiliaries.R (nnzero): improved and now exported via
301    
302            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
303    
304    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/diagMatrix.R (!): fix typo.
307    
308    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Auxiliaries.R (as_Csparse): and quite a few others:
311                    allow to pass class definition --> speedup
312            * R/sparseMatrix.R: apply the above
313    
314            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
315    
316            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
317            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
318            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
319    
320            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
321    
322            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
323            and use it for "sparse*" as well, since it's faster than the
324            as_Csparse(.) way.
325    
326    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
329    
330    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
333            as method for   M[ ij ] <- v
334            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
335    
336            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
337            FALSE answer
338    
339            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
340            * tests/indexing.R: test it, and some of the above
341    
342    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/Auxiliaries.R (is_duplicatedT): new utility
345    
346    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * src/init.c (R_init_Matrix): export cholmod_scale
349    
350    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
353            base::as.matrix to (x, ...)
354    
355    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
358            file; start using "Logic", hence
359    
360            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
361            * NAMESPACE: import and export "Logic"
362    
363    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
366            only needed previously to R version 2.5.0.
367    
368    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
371    
372            * R/Tsparse.R (replTmat): fix subassignment of triangular
373            * R/Csparse.R (replCmat): ditto
374            * tests/indexing.R: more tests, incl the above fix
375    
376    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/Auxiliaries.R (drop0): extend for non CSparse
379            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
380    
381            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
382                    use uplo correctly (!); other places: use uplo_P() macro
383    
384            * R/Csparse.R (replCmat): call diagU2N() when needed
385            * R/Tsparse.R (replTmat): ditto
386    
387            * src/dtCMatrix.c (tCMatrix_validate): new
388            * src/dtTMatrix.c (tTMatrix_validate): new, used in
389            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
390    
391            * R/diagMatrix.R (replDiag): to use in [<-
392    
393    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
396                    also more general diagU2N().
397    
398    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
401            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
402    
403    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * tests/bind.R: a few more cases
406            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
407    
408            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
409            * R/ddenseMatrix.R (cbind2/rbind2)
410            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
411            * tests/indexing.R
412            * tests/indexing.Rout.save: updated
413    
414    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
417            * tests/indexing.R
418    
419    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
422            align with proper position of "0", i.e., right for integers.
423            argument 'align' by default is "fancy".
424    
425    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
428            * R/Csparse.R: and fix "Compare" for more cases.
429            * tests/Class+Meth.R: test some of these (m == m, m != m)
430    
431    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/lsparseMatrix.R: all() and any() methods
434            * R/ldenseMatrix.R:      ditto
435            * NAMESPACE, R/Matrix.R: ditto
436    
437            * man/all-methods.Rd: document them minimally
438    
439            * tests/simple.R: add a few examples for these
440    
441    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Tsparse.R ([): fix long standing typo in symmetric case
444            * man/dsCMatrix-class.Rd: add example exhibiting the above case
445    
446    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
447    
448            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
449            to LL before converting to a sparse matrix. (The LDL form can be
450            converted to a sparse matrix but it is implicitly a unit
451            triangular matrix and a diagonal matrix overwritten on the diagonal.)
452    
453    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
454    
455            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
456    
457    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
458    
459            * DESCRIPTION (Version): updated -> release 0.9975-7
460            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
461    
462    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
465    
466    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
467    
468            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
469            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
470            is exactly singular.
471    
472    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * DESCRIPTION (Date): updated -> release 0.9975-6
475    
476    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
479            now returns symmetric.
480    
481            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
482    
483            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
484            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
485    
486            * R/Auxiliaries.R (.type.kind): added
487    
488    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
491            running src/CSparse_install.sh
492    
493            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
494    
495    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
498            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
499    
500            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
501    
502            * tests/Class+Meth.R (tstMatrixClass): now assure
503            the (important in method programming) property :
504    
505                    ###>>  Every "Matrix" is either
506                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
507    
508                    (where "*" stands for "Matrix")
509    
510            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
511    
512            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
513            * tests/validObj.R: checks for "comparison"
514    
515            * R/sparseMatrix.R ([): improved indexing for sparse;
516                    trying to keep <symmetric>[ n, n] symmmetric
517    
518            * tests/indexing.R: indexing for logical sparse now ok
519    
520    
521    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * src/Tsparse.c: use xTsparse_validate() , and hence remove
524    
525            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
526    
527    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
530    
531            * tests/simple.R: validObject() checking the above.
532    
533            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
534            replacing both dgCMatrix_validate and lgCM*.
535    
536            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
537            fix dimnames setting in other places.
538            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
539    
540    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
543    
544            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
545            symmetry test, via
546            * R/Auxiliaries.R (.as.dgC.0.factors):
547    
548    2006-11-01  Douglas Bates  <bates@r-project.org>
549    
550            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
551            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
552            <CsparseMatrix>) added
553    
554    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * tests/matprod.R: add a variation of Harri's example
557    
558            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
559            recursive infinitely.
560    
561            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
562    
563            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
564    
565    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
566    
567            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
568            matrix if possible; test m+m == 2*m; now test dgRMatrix.
569            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
570            satisfy the above test.
571    
572    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
575    
576            * R/dgCMatrix.R: solve(a, b="missing") based on
577            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
578            RHS = NULL.
579    
580            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
581            add more (needed) [t]crossprod() methods.
582    
583            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
584    
585            * R/Auxiliaries.R (as_CspClass): cleanup
586            (drop0): internal utility for "Csparse_drop(*, 0)"
587            (.bail.out.2): encourage active feedback
588    
589    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/dMatrix.R(Compare): new(), then slots [no validity check]
592    
593            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
594            non-valid or 'sorted' case).
595    
596            * R/dsparseMatrix.R: add "chol" method.
597            * R/ddenseMatrix.R: ditto
598    
599            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
600            * NAMESPACE (Ops)
601            * R/diagMatrix.R (diag2T): simple utility used "higher level"
602            coercion; deprecating direct lower level coercions.
603    
604            * R/*.R (seq): use seq_len() and seq_along() where possible.
605    
606    
607    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * DESCRIPTION (Version): 0.9975-5 ready for release
610    
611    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
612    
613            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
614    
615    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
616    
617            * R/AllClass.R (corMatrix): add 'validity' check;
618                    comment out unused "LDL" class definition
619            * NAMESPACE: mention, but do not export "LDL" class
620            * R/corMatrix.R: new (simple), needed for R-devel with
621            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
622              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
623    
624    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
625    
626            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
627            use Rprintf and R's error handling.
628    
629    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
632            * tests/matprod.R: add tests for the bug fixed.
633    
634    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
637            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
638    
639    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
642    
643    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * DESCRIPTION (Version): 0.9975-3
646    
647            * R/diagMatrix.R (bdiag): new function constructing block diagonal
648            (sparse) matrices.
649            * man/bdiag.Rd: docu + examples
650    
651            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
652    
653            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
654            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
655    
656            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
657            that result is sparse or diagonal (and not dense).
658    
659            * man/Subassign-methods.Rd: fix examples
660    
661            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
662            should always return a sparse (and not sometimes a diagonal) matrix.
663    
664    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
667    
668    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
669    
670            * DESCRIPTION (Version): 0.9975-2
671    
672            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
673    
674    2006-10-02  Douglas Bates  <bates@R-project.org>
675    
676            * tests/dg_Matrix.R: Simplify test taking into account new code.
677    
678    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
681    
682            * R/lsTMatrix.R: new files w/ missing methods
683            * R/nsTMatrix.R:  "  'for completeness'
684    
685            * tests/Class+Meth.R: a bit less 'not.ok.classes'
686    
687            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
688    
689    
690    2006-09-28  Douglas Bates  <bates@R-project.org>
691    
692            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
693            included.
694    
695            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
696            Export C-callable functions used in Zt_create in lme4.
697    
698    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * DESCRIPTION (Version): 0.9975-1
701    
702            * tests/simple.R: less checks fail; using NA, found that our
703                    kronecker() is not base-compatible with NA's.
704    
705            * R/dMatrix.R: "Compare" method now implemented for all cases
706    
707            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
708    
709            * man/dtpMatrix-class.Rd: mention length of 'x' slot
710    
711            * src/dtpMatrix.c (dtpMatrix_validate): fix check
712            * src/dspMatrix.c (dspMatrix_validate): ditto
713    
714            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
715              including coercion to [nl]tTMatrix.
716    
717            * R/diagMatrix.R (show): print a header line as for other classes.
718    
719    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * src/Makefile.win (SUBDIRS): fix typo
722    
723    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
726    
727    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
730            symmetric and y missing in R code using %*% (cholmod_aat doesn't
731            accept a symmetric matrix).
732            * tests/group-methods.R: Uncomment test of crossprod applied to
733            lsCMatrix objects.
734    
735    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/AllClass.R (symmetricMatrix): add validity method (available
738            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
739    
740            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
741    
742            * tests/indexing.Rout.save:
743            * tests/indexing.R: additions, mainly for 'lsparse'
744    
745            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
746            case.
747    
748            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
749    
750    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
753                    as 'N' (1-letter - Ok?)
754    
755            * tests/group-methods.R: add test for logical + NAs
756    
757            * R/dMatrix.R ("Compare"): fix to work with NA's
758    
759            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
760    
761            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
762                    which is implemented.
763    
764    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * src/chm_common.c: coerce logical <-> double instead of
767            typecasting;  needed for "l" matrix handling in cholmod.
768    
769            * tests/other-pkgs.R (graph): small extension in "graph" checks.
770    
771            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
772            (Tsp2grNEL): other fixes needed
773    
774    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
777                    Matrices, since "lMatrix", also "lsparseM" can have NA
778            * R/ndenseMatrix.R, etc: new source files
779            * man/nsparseMatrix-classes.Rd, etc: new help files
780            * tests/: adaptions
781            * src/chm_common.c (chm_dense_to_SEXP): and others:
782                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
783            * src/Csparse.c, etc: ditto
784    
785    2006-09-11  Douglas Bates  <bates@R-project.org>
786    
787            * src/Mutils.[ch],init.c inst/include/*.h: Move the
788            alloc_d**Matrix functions to the lme4 package.
789    
790    2006-09-09  Douglas Bates  <bates@R-project.org>
791    
792            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
793            fixed
794    
795    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/lMatrix.R: new
798    
799            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
800    
801            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
802            * man/tcrossprod.Rd: ditto
803    
804    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
805    
806            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
807            for exported functions
808            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
809            Remove partitioning algorithms for sparse matrix reordering.  The
810            copyright on the Metis code was problematic and the methods were
811            rarely used.
812            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
813            operations are now done entirely in CHOLMOD code.
814    
815    2006-09-06  Douglas Bates  <bates@R-project.org>
816    
817            * src/Mutils.h: Remove functions that are no longer used.
818    
819    2006-09-04  Douglas Bates  <bates@R-project.org>
820    
821            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
822            * src/DEPS.mkf: update
823    
824    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * created branches/Matrix-for-R-2.3.x;  on trunk: do
827            * DESCRIPTION (Version): 0.9975-0
828            (Depends): R (>= 2.4.0)
829    
830    2006-09-01  Douglas Bates  <bates@R-project.org>
831    
832            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
833    
834    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
837            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
838    
839            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
840    
841    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
842    
843            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
844            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
845            * R/dsparseMatrix.R: ditto
846            * R/Csparse.R: ditto
847    
848    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/dMatrix.R (Compare): improve availability of "<", etc
851            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
852    
853    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
856            of a 0-index which was used as 1-index (..hmm)
857    
858            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
859    
860            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
861            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
862            (.is.diagonal): ditto
863    
864            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
865    
866            * R/Matrix.R (Matrix): also work for NA data
867    
868    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
871            in all cases.
872    
873    2006-08-27  Douglas Bates  <bates@R-project.org>
874    
875            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
876            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
877    
878    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
881            subclasses of "ddenseMatrix"
882            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
883            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
884            instead of half dozen specialized ones.
885    
886    2006-08-25  Douglas Bates  <bates@R-project.org>
887    
888            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
889            <tillard@cirad.fr> - ordering standard errors to match effects.
890    
891    2006-08-24  Douglas Bates  <bates@R-project.org>
892    
893            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
894            on R_ldl.
895            * R/lCholCMatrix.R,
896            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
897            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
898            * many files in ./R and ./src: Use more general version of
899            dup_mMatrix_as_dgeMatrix to simplify method definitions.
900            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
901            dtpMatrix, dspMatrix and dppMatrix conversions.
902    
903    
904    2006-08-23  Douglas Bates  <bates@R-project.org>
905    
906            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
907            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
908            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
909            dgeMatrix_crossprod (may need to do this in other places).
910            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
911            generic and method for dsCMatrix.  Use CHOLMOD for chol().
912    
913    2006-08-22  Douglas Bates  <bates@R-project.org>
914    
915            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
916            types of classed Matrices, matrices or numeric or logical vectors.
917            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
918            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
919            to Mutils.h (as an inline) and change name to Matrix_check_class;
920            fixes in as_cholmod_factor and chm_factor_to_SEXP.
921            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
922            dsCMatrix_matrix_solve.  Comment out vestigial functions.
923            * src/Csparse.c: use diag_P and uplo_P macros.
924    
925    2006-08-21  Douglas Bates  <bates@R-project.org>
926    
927            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
928            valgrind.
929            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
930            inverses.
931            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
932            -Wall warnings.
933            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
934            Use dup_mMatrix_as_dgeMatrix.
935    
936    2006-08-20  Douglas Bates  <bates@R-project.org>
937    
938            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
939            * tests/sparseQR.R: Added
940            * man/sparseQR-class.Rd: Document methods for qr.* generics
941            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
942    
943    2006-08-19  Douglas Bates  <bates@R-project.org>
944    
945            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
946            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
947            and qr.fitted.
948            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
949            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
950    
951    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
954            the base version has no "..." argument.
955    
956            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
957    
958            * R/Matrix.R: define and
959            * NAMESPACE: export as.numeric() and as.logical() methods.
960                    Let's hope these do not badly slow down something...
961            Finally export the zapsmall() method.
962    
963    2006-08-17  Douglas Bates  <bates@R-project.org>
964    
965            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
966            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
967            * src/dtCMatrix.c :Remove code that is no longer used
968            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
969    
970    2006-08-14  Douglas Bates  <bates@R-project.org>
971    
972            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
973            Csparse_to_logical and Csparse_symmetric_to_general.
974            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
975            coercion methods between CsparseMatrix and TsparseMatrix.
976    
977    2006-08-14  Douglas Bates  <bates@R-project.org>
978    
979            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
980            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
981            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
982            possible.
983    
984    2006-08-12  Douglas Bates  <bates@R-project.org>
985    
986            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
987              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
988              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
989              generalize conversions between TsparseMatrix, CsparseMatrix,
990              denseMatrix and matrix.  Preserve triangularity property and
991              propagate Dimnames in the easy cases.
992    
993    2006-08-10  Douglas Bates  <bates@R-project.org>
994    
995            * src/lmer.c: adjust checks in glmer_init for S4SXP
996            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
997            before S4SXP but for the wrong reasons.
998    
999  2006-08-08  Douglas Bates  <bates@R-project.org>  2006-08-08  Douglas Bates  <bates@R-project.org>
1000    
1001          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.

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