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revision 1365, Thu Aug 10 18:52:55 2006 UTC revision 1932, Fri Jun 29 16:43:47 2007 UTC
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1    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.99875-3 ready to be released.
4    
5            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
6    
7            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
8            that should also work in a future version of R.
9    
10    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
13    
14            * R/sparseVector.R: more *sparseVector coercions, notably for
15            non - double ones.
16    
17    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
20              notably the new ones building on the new .Call(.)s:
21    
22            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
23            all 4 of [dlin]gCMatrix_colSums().
24    
25    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
26    
27            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
28            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
29              result
30    
31    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/kronecker.R: fix typo (could lead to inf.recursion)
34            * test/simple.R: testing that
35    
36            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
37            method as well (which can have arguments, show() can't).
38    
39    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
40    
41            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
42              added dgCMatrix_colSums for [col,row][Sums,Means]
43    
44    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
45    
46            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
47              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
48              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
49            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
50              class
51            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
52              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
53              row names to store the levels - duh!  Added an example.
54    
55    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * src/Csparse.c (Csparse_validate): check for *repeated* entries
58            thanks to example from Christian Buchta; with a test here:
59            * tests/simple.R:
60    
61    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
64            of colSums(*, sparseResult = TRUE)
65    
66    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
69            'na.rm = FALSE' as "everywhere" else in R.
70    
71    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
72    
73            * [r4421] src/CSparse_install.sh: Modify for new organization of
74              CSparse package
75            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
76              SuiteSparse
77            * [r4426] src/Makefile: add ./UFconfig to the include path for
78              compilation
79            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
80            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
81              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
82    
83    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
86            * R/sparseMatrix.R (prSpMatrix): now gives a message about
87            suppressed column names.
88    
89    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
90    
91            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
92              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
93              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
94              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
95              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
96              Remove warnings after change to const char* CHAR
97    
98    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
99    
100            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
101              type of M_cholmod_ssmult
102    
103    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
104    
105            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
106              src/init.c: Yet another cholmod export - cholmod_ssmult
107    
108    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * NAMESPACE: exported drop0(), since
111            * man/drop0.Rd: I have seen several cases, I really wanted to use
112            it, so our users may want too.
113    
114    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * man/colSums.Rd: separately document colSums() etc, since these
117            have the extra argument 'sparseResult'.
118    
119    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
122            * man/spMatrix.Rd: docu., including examples
123    
124            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
125            in order to make colMeans() etc fast *and* correct.
126            * R/sparseVector.R (replSPvec): "[<-" functionality for
127            sparseVectors; tested in
128            * tests/simple.R:
129    
130    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
133            (very) sparse Matrices; output similar to Matlab's print().
134    
135    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
136    
137            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
138            0-based, indices (Jose Quesada <quesada@gmail.com>).
139    
140    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
141    
142            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
143    
144    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Auxiliaries.R (sparsapply): new utility, much faster than
147            tapply1() for large sparse matrices.
148    
149    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Matrix.R (dim<-): reshape now via sparseVector.
152    
153            * R/sparseVector.R: methods and function for
154            * R/AllClass.R: new "sparseVector" class and daughters.
155            * NAMESPACE: export new classes
156    
157    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * DESCRIPTION (Version): 0.99875-1
160            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
161    
162    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
165            indexing
166            * tests/indexing.R: test set for that.
167    
168    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
171            entries.
172            * tests/indexing.R(out): add regression test for it
173    
174    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
177            name for "!" method definitions.
178    
179    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/Tsparse.R (intI): new utility, used for "[" :
182                    Cleanup up there, and fixes for duplicated indices - more TODO!
183    
184            * tests/indexing.R(out): more tests
185    
186    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
187    
188            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
189            code that is now part of the R Lapack library.
190    
191            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
192            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
193    
194    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
197    
198    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
201            up with extraneous names '0'...'<n-1>'
202    
203    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/dgTMatrix.R (mat2dgT): care about NAs
206    
207    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/kronecker.R: triangularity preserving methods
210    
211    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/kronecker.R: new file collecting kronecker() methods in one
214                    place.  Goal: become much faster!
215    
216    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
219            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
220            can be much faster.
221    
222            * tests/matprod.R: add regression tests for these (upper & lower).
223    
224    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/Matrix.R (diff): method for our Matrices.
227    
228            * R/sparseMatrix.R (isDiagonal): check dim()!
229    
230    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Matrix.R (dim<-): new method for "reshape()" built on a
233            proposal from Tamas Papp.
234    
235    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
238    
239            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
240            rather define and export  cBind() and rBind() only.
241            --> useRs *must* change code that used to have cbind()/rbind() !!
242    
243            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
244            * R/bind.Rout.save: ditto
245    
246    2007-02-16  Douglas Bates  <bates@r-project.org>
247    
248            * DESCRIPTION (Date, Version): 0.9975-11 with new date
249            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
250            const modifier on declaration of the array 'valid'
251    
252    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
253    
254            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
255    
256    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
259    
260            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
261            * tests/simple.R: test the above and some of these coercions:
262    
263            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
264                    be careful to avoid infinite recursion, using new coercions in
265            * R/ngCMatrix.R and nsC... and ntC...
266            * R/lsparseMatrix.R: ditto
267    
268            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
269    
270            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
271            * R/Rsparse.R: reactivate .Call()s
272    
273            * tests/Class+Meth.R: a bit more on actual classes
274    
275    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
276    
277            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
278    
279    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * DESCRIPTION (Version): 0.9975-10 to upload
282    
283            * tests/Class+Meth.R (tstMatrixClass): require coercions to
284            specific classes less unconditionally.
285    
286            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
287    
288            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
289    
290            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
291            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
292            R_to_CMatrix segfaults on one platform.
293            Eliminate most coercion method to *specific* classes, and replace
294            with virtual classes coercions.
295    
296    
297    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
298    
299            * src/init.c: export the CHM...._validate() placeholders, since
300            they *are* called.
301    
302            * tests/Class+Meth.R (classCanCoerce): and starting to test
303            all as(<from>, <to>)
304    
305    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
308            * tests/indexing.R: tested now
309            * tests/indexing.Rout.save: updated
310    
311            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
312            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
313            appropriate.
314    
315            * NAMESPACE: export a trivial
316            * R/Matrix.R: drop() Matrix-method
317    
318            * R/AllClass.R: moved all prototypes to virtual super classes.
319    
320            * R/Rsparse.R: many more coercions to have less exceptions in
321            * tests/Class+Meth.R:
322    
323            * R/Ops.R (Compare): tweak for case with NA
324            * tests/simpl.R: hence another 'FIXME' eliminated
325    
326    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
329            objects.
330    
331            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
332              and more of "!", "&", "|", all, any; coercions
333    
334            * R/Rsparse.R: many coercions (which enable quite a few other
335            methods), thanks to enhancements in
336            * src/dgCMatrix.c (R_to_CMatrix): new, and
337            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
338            symmetric & triangular and ..RMatrix objects.
339    
340            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
341            renamed file from src/dsTMatrix.c;
342            now dealing with symmetric and triangular Tsparse coercions, both
343            to dense and general.
344    
345    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
348    
349            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
350            where sensible when the <numeric> is of length > 1.
351    
352    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * R/Matrix.R ([<-): for M[] <- value: fix length
355    
356    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
359            * R/ndenseMatrix.R: new coercions n* -> l*
360    
361    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
364    
365            * R/Ops.R ("Logic"): and other "Ops", many updates
366    
367    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * src/Mutils.h (SET_DimNames): new utility
370    
371            * R/Auxiliaries.R (nnzero): improved and now exported via
372    
373            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
374    
375    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/diagMatrix.R (!): fix typo.
378    
379    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Auxiliaries.R (as_Csparse): and quite a few others:
382                    allow to pass class definition --> speedup
383            * R/sparseMatrix.R: apply the above
384    
385            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
386    
387            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
388            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
389            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
390    
391            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
392    
393            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
394            and use it for "sparse*" as well, since it's faster than the
395            as_Csparse(.) way.
396    
397    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
400    
401    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
404            as method for   M[ ij ] <- v
405            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
406    
407            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
408            FALSE answer
409    
410            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
411            * tests/indexing.R: test it, and some of the above
412    
413    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Auxiliaries.R (is_duplicatedT): new utility
416    
417    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
418    
419            * src/init.c (R_init_Matrix): export cholmod_scale
420    
421    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
424            base::as.matrix to (x, ...)
425    
426    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
429            file; start using "Logic", hence
430    
431            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
432            * NAMESPACE: import and export "Logic"
433    
434    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
437            only needed previously to R version 2.5.0.
438    
439    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
442    
443            * R/Tsparse.R (replTmat): fix subassignment of triangular
444            * R/Csparse.R (replCmat): ditto
445            * tests/indexing.R: more tests, incl the above fix
446    
447    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * R/Auxiliaries.R (drop0): extend for non CSparse
450            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
451    
452            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
453                    use uplo correctly (!); other places: use uplo_P() macro
454    
455            * R/Csparse.R (replCmat): call diagU2N() when needed
456            * R/Tsparse.R (replTmat): ditto
457    
458            * src/dtCMatrix.c (tCMatrix_validate): new
459            * src/dtTMatrix.c (tTMatrix_validate): new, used in
460            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
461    
462            * R/diagMatrix.R (replDiag): to use in [<-
463    
464    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
467                    also more general diagU2N().
468    
469    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
472            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
473    
474    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * tests/bind.R: a few more cases
477            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
478    
479            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
480            * R/ddenseMatrix.R (cbind2/rbind2)
481            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
482            * tests/indexing.R
483            * tests/indexing.Rout.save: updated
484    
485    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
488            * tests/indexing.R
489    
490    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
493            align with proper position of "0", i.e., right for integers.
494            argument 'align' by default is "fancy".
495    
496    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
499            * R/Csparse.R: and fix "Compare" for more cases.
500            * tests/Class+Meth.R: test some of these (m == m, m != m)
501    
502    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/lsparseMatrix.R: all() and any() methods
505            * R/ldenseMatrix.R:      ditto
506            * NAMESPACE, R/Matrix.R: ditto
507    
508            * man/all-methods.Rd: document them minimally
509    
510            * tests/simple.R: add a few examples for these
511    
512    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Tsparse.R ([): fix long standing typo in symmetric case
515            * man/dsCMatrix-class.Rd: add example exhibiting the above case
516    
517    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
518    
519            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
520            to LL before converting to a sparse matrix. (The LDL form can be
521            converted to a sparse matrix but it is implicitly a unit
522            triangular matrix and a diagonal matrix overwritten on the diagonal.)
523    
524    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
525    
526            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
527    
528    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * DESCRIPTION (Version): updated -> release 0.9975-7
531            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
532    
533    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
536    
537    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
538    
539            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
540            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
541            is exactly singular.
542    
543    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * DESCRIPTION (Date): updated -> release 0.9975-6
546    
547    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
550            now returns symmetric.
551    
552            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
553    
554            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
555            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
556    
557            * R/Auxiliaries.R (.type.kind): added
558    
559    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
562            running src/CSparse_install.sh
563    
564            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
565    
566    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
569            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
570    
571            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
572    
573            * tests/Class+Meth.R (tstMatrixClass): now assure
574            the (important in method programming) property :
575    
576                    ###>>  Every "Matrix" is either
577                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
578    
579                    (where "*" stands for "Matrix")
580    
581            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
582    
583            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
584            * tests/validObj.R: checks for "comparison"
585    
586            * R/sparseMatrix.R ([): improved indexing for sparse;
587                    trying to keep <symmetric>[ n, n] symmmetric
588    
589            * tests/indexing.R: indexing for logical sparse now ok
590    
591    
592    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * src/Tsparse.c: use xTsparse_validate() , and hence remove
595    
596            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
597    
598    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
601    
602            * tests/simple.R: validObject() checking the above.
603    
604            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
605            replacing both dgCMatrix_validate and lgCM*.
606    
607            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
608            fix dimnames setting in other places.
609            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
610    
611    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
614    
615            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
616            symmetry test, via
617            * R/Auxiliaries.R (.as.dgC.0.factors):
618    
619    2006-11-01  Douglas Bates  <bates@r-project.org>
620    
621            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
622            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
623            <CsparseMatrix>) added
624    
625    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * tests/matprod.R: add a variation of Harri's example
628    
629            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
630            recursive infinitely.
631    
632            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
633    
634            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
635    
636    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
639            matrix if possible; test m+m == 2*m; now test dgRMatrix.
640            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
641            satisfy the above test.
642    
643    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
646    
647            * R/dgCMatrix.R: solve(a, b="missing") based on
648            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
649            RHS = NULL.
650    
651            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
652            add more (needed) [t]crossprod() methods.
653    
654            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
655    
656            * R/Auxiliaries.R (as_CspClass): cleanup
657            (drop0): internal utility for "Csparse_drop(*, 0)"
658            (.bail.out.2): encourage active feedback
659    
660    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/dMatrix.R(Compare): new(), then slots [no validity check]
663    
664            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
665            non-valid or 'sorted' case).
666    
667            * R/dsparseMatrix.R: add "chol" method.
668            * R/ddenseMatrix.R: ditto
669    
670            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
671            * NAMESPACE (Ops)
672            * R/diagMatrix.R (diag2T): simple utility used "higher level"
673            coercion; deprecating direct lower level coercions.
674    
675            * R/*.R (seq): use seq_len() and seq_along() where possible.
676    
677    
678    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * DESCRIPTION (Version): 0.9975-5 ready for release
681    
682    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
683    
684            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
685    
686    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/AllClass.R (corMatrix): add 'validity' check;
689                    comment out unused "LDL" class definition
690            * NAMESPACE: mention, but do not export "LDL" class
691            * R/corMatrix.R: new (simple), needed for R-devel with
692            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
693              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
694    
695    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
696    
697            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
698            use Rprintf and R's error handling.
699    
700    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
703            * tests/matprod.R: add tests for the bug fixed.
704    
705    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
706    
707            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
708            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
709    
710    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
711    
712            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
713    
714    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * DESCRIPTION (Version): 0.9975-3
717    
718            * R/diagMatrix.R (bdiag): new function constructing block diagonal
719            (sparse) matrices.
720            * man/bdiag.Rd: docu + examples
721    
722            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
723    
724            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
725            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
726    
727            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
728            that result is sparse or diagonal (and not dense).
729    
730            * man/Subassign-methods.Rd: fix examples
731    
732            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
733            should always return a sparse (and not sometimes a diagonal) matrix.
734    
735    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
738    
739    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
740    
741            * DESCRIPTION (Version): 0.9975-2
742    
743            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
744    
745    2006-10-02  Douglas Bates  <bates@R-project.org>
746    
747            * tests/dg_Matrix.R: Simplify test taking into account new code.
748    
749    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
752    
753            * R/lsTMatrix.R: new files w/ missing methods
754            * R/nsTMatrix.R:  "  'for completeness'
755    
756            * tests/Class+Meth.R: a bit less 'not.ok.classes'
757    
758            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
759    
760    
761    2006-09-28  Douglas Bates  <bates@R-project.org>
762    
763            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
764            included.
765    
766            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
767            Export C-callable functions used in Zt_create in lme4.
768    
769    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * DESCRIPTION (Version): 0.9975-1
772    
773            * tests/simple.R: less checks fail; using NA, found that our
774                    kronecker() is not base-compatible with NA's.
775    
776            * R/dMatrix.R: "Compare" method now implemented for all cases
777    
778            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
779    
780            * man/dtpMatrix-class.Rd: mention length of 'x' slot
781    
782            * src/dtpMatrix.c (dtpMatrix_validate): fix check
783            * src/dspMatrix.c (dspMatrix_validate): ditto
784    
785            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
786              including coercion to [nl]tTMatrix.
787    
788            * R/diagMatrix.R (show): print a header line as for other classes.
789    
790    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * src/Makefile.win (SUBDIRS): fix typo
793    
794    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
797    
798    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
799    
800            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
801            symmetric and y missing in R code using %*% (cholmod_aat doesn't
802            accept a symmetric matrix).
803            * tests/group-methods.R: Uncomment test of crossprod applied to
804            lsCMatrix objects.
805    
806    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * R/AllClass.R (symmetricMatrix): add validity method (available
809            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
810    
811            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
812    
813            * tests/indexing.Rout.save:
814            * tests/indexing.R: additions, mainly for 'lsparse'
815    
816            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
817            case.
818    
819            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
820    
821    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
824                    as 'N' (1-letter - Ok?)
825    
826            * tests/group-methods.R: add test for logical + NAs
827    
828            * R/dMatrix.R ("Compare"): fix to work with NA's
829    
830            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
831    
832            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
833                    which is implemented.
834    
835    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * src/chm_common.c: coerce logical <-> double instead of
838            typecasting;  needed for "l" matrix handling in cholmod.
839    
840            * tests/other-pkgs.R (graph): small extension in "graph" checks.
841    
842            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
843            (Tsp2grNEL): other fixes needed
844    
845    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
848                    Matrices, since "lMatrix", also "lsparseM" can have NA
849            * R/ndenseMatrix.R, etc: new source files
850            * man/nsparseMatrix-classes.Rd, etc: new help files
851            * tests/: adaptions
852            * src/chm_common.c (chm_dense_to_SEXP): and others:
853                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
854            * src/Csparse.c, etc: ditto
855    
856    2006-09-11  Douglas Bates  <bates@R-project.org>
857    
858            * src/Mutils.[ch],init.c inst/include/*.h: Move the
859            alloc_d**Matrix functions to the lme4 package.
860    
861    2006-09-09  Douglas Bates  <bates@R-project.org>
862    
863            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
864            fixed
865    
866    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * R/lMatrix.R: new
869    
870            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
871    
872            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
873            * man/tcrossprod.Rd: ditto
874    
875    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
876    
877            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
878            for exported functions
879            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
880            Remove partitioning algorithms for sparse matrix reordering.  The
881            copyright on the Metis code was problematic and the methods were
882            rarely used.
883            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
884            operations are now done entirely in CHOLMOD code.
885    
886    2006-09-06  Douglas Bates  <bates@R-project.org>
887    
888            * src/Mutils.h: Remove functions that are no longer used.
889    
890    2006-09-04  Douglas Bates  <bates@R-project.org>
891    
892            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
893            * src/DEPS.mkf: update
894    
895    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * created branches/Matrix-for-R-2.3.x;  on trunk: do
898            * DESCRIPTION (Version): 0.9975-0
899            (Depends): R (>= 2.4.0)
900    
901    2006-09-01  Douglas Bates  <bates@R-project.org>
902    
903            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
904    
905    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
908            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
909    
910            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
911    
912    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
913    
914            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
915            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
916            * R/dsparseMatrix.R: ditto
917            * R/Csparse.R: ditto
918    
919    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/dMatrix.R (Compare): improve availability of "<", etc
922            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
923    
924    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
927            of a 0-index which was used as 1-index (..hmm)
928    
929            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
930    
931            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
932            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
933            (.is.diagonal): ditto
934    
935            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
936    
937            * R/Matrix.R (Matrix): also work for NA data
938    
939    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
940    
941            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
942            in all cases.
943    
944    2006-08-27  Douglas Bates  <bates@R-project.org>
945    
946            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
947            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
948    
949    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
952            subclasses of "ddenseMatrix"
953            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
954            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
955            instead of half dozen specialized ones.
956    
957    2006-08-25  Douglas Bates  <bates@R-project.org>
958    
959            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
960            <tillard@cirad.fr> - ordering standard errors to match effects.
961    
962    2006-08-24  Douglas Bates  <bates@R-project.org>
963    
964            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
965            on R_ldl.
966            * R/lCholCMatrix.R,
967            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
968            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
969            * many files in ./R and ./src: Use more general version of
970            dup_mMatrix_as_dgeMatrix to simplify method definitions.
971            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
972            dtpMatrix, dspMatrix and dppMatrix conversions.
973    
974    
975    2006-08-23  Douglas Bates  <bates@R-project.org>
976    
977            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
978            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
979            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
980            dgeMatrix_crossprod (may need to do this in other places).
981            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
982            generic and method for dsCMatrix.  Use CHOLMOD for chol().
983    
984    2006-08-22  Douglas Bates  <bates@R-project.org>
985    
986            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
987            types of classed Matrices, matrices or numeric or logical vectors.
988            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
989            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
990            to Mutils.h (as an inline) and change name to Matrix_check_class;
991            fixes in as_cholmod_factor and chm_factor_to_SEXP.
992            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
993            dsCMatrix_matrix_solve.  Comment out vestigial functions.
994            * src/Csparse.c: use diag_P and uplo_P macros.
995    
996    2006-08-21  Douglas Bates  <bates@R-project.org>
997    
998            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
999            valgrind.
1000            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1001            inverses.
1002            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1003            -Wall warnings.
1004            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1005            Use dup_mMatrix_as_dgeMatrix.
1006    
1007    2006-08-20  Douglas Bates  <bates@R-project.org>
1008    
1009            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1010            * tests/sparseQR.R: Added
1011            * man/sparseQR-class.Rd: Document methods for qr.* generics
1012            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1013    
1014    2006-08-19  Douglas Bates  <bates@R-project.org>
1015    
1016            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1017            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1018            and qr.fitted.
1019            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1020            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1021    
1022    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1025            the base version has no "..." argument.
1026    
1027            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1028    
1029            * R/Matrix.R: define and
1030            * NAMESPACE: export as.numeric() and as.logical() methods.
1031                    Let's hope these do not badly slow down something...
1032            Finally export the zapsmall() method.
1033    
1034    2006-08-17  Douglas Bates  <bates@R-project.org>
1035    
1036            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1037            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1038            * src/dtCMatrix.c :Remove code that is no longer used
1039            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1040    
1041    2006-08-14  Douglas Bates  <bates@R-project.org>
1042    
1043            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1044            Csparse_to_logical and Csparse_symmetric_to_general.
1045            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1046            coercion methods between CsparseMatrix and TsparseMatrix.
1047    
1048    2006-08-14  Douglas Bates  <bates@R-project.org>
1049    
1050            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1051            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1052            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1053            possible.
1054    
1055    2006-08-12  Douglas Bates  <bates@R-project.org>
1056    
1057            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1058              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1059              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1060              generalize conversions between TsparseMatrix, CsparseMatrix,
1061              denseMatrix and matrix.  Preserve triangularity property and
1062              propagate Dimnames in the easy cases.
1063    
1064  2006-08-10  Douglas Bates  <bates@R-project.org>  2006-08-10  Douglas Bates  <bates@R-project.org>
1065    
1066          * src/lmer.c: adjust checks in glmer_init for S4SXP          * src/lmer.c: adjust checks in glmer_init for S4SXP

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