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revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 1902, Sat Jun 16 15:54:54 2007 UTC
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1    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
4              added dgCMatrix_colSums for [col,row][Sums,Means]
5    
6    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
7    
8            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
9              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
10              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
11            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
12              class
13            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
14              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
15              row names to store the levels - duh!  Added an example.
16    
17    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * src/Csparse.c (Csparse_validate): check for *repeated* entries
20            thanks to example from Christian Buchta; with a test here:
21            * tests/simple.R:
22    
23    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
26            of colSums(*, sparseResult = TRUE)
27    
28    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
31            'na.rm = FALSE' as "everywhere" else in R.
32    
33    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
34    
35            * [r4421] src/CSparse_install.sh: Modify for new organization of
36              CSparse package
37            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
38              SuiteSparse
39            * [r4426] src/Makefile: add ./UFconfig to the include path for
40              compilation
41            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
42            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
43              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
44    
45    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
48            * R/sparseMatrix.R (prSpMatrix): now gives a message about
49            suppressed column names.
50    
51    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
52    
53            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
54              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
55              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
56              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
57              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
58              Remove warnings after change to const char* CHAR
59    
60    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
61    
62            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
63              type of M_cholmod_ssmult
64    
65    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
68              src/init.c: Yet another cholmod export - cholmod_ssmult
69    
70    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * NAMESPACE: exported drop0(), since
73            * man/drop0.Rd: I have seen several cases, I really wanted to use
74            it, so our users may want too.
75    
76    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * man/colSums.Rd: separately document colSums() etc, since these
79            have the extra argument 'sparseResult'.
80    
81    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
84            * man/spMatrix.Rd: docu., including examples
85    
86            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
87            in order to make colMeans() etc fast *and* correct.
88            * R/sparseVector.R (replSPvec): "[<-" functionality for
89            sparseVectors; tested in
90            * tests/simple.R:
91    
92    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
95            (very) sparse Matrices; output similar to Matlab's print().
96    
97    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
100            0-based, indices (Jose Quesada <quesada@gmail.com>).
101    
102    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
105    
106    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Auxiliaries.R (sparsapply): new utility, much faster than
109            tapply1() for large sparse matrices.
110    
111    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Matrix.R (dim<-): reshape now via sparseVector.
114    
115            * R/sparseVector.R: methods and function for
116            * R/AllClass.R: new "sparseVector" class and daughters.
117            * NAMESPACE: export new classes
118    
119    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * DESCRIPTION (Version): 0.99875-1
122            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
123    
124    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
127            indexing
128            * tests/indexing.R: test set for that.
129    
130    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
133            entries.
134            * tests/indexing.R(out): add regression test for it
135    
136    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
139            name for "!" method definitions.
140    
141    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Tsparse.R (intI): new utility, used for "[" :
144                    Cleanup up there, and fixes for duplicated indices - more TODO!
145    
146            * tests/indexing.R(out): more tests
147    
148    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
149    
150            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
151            code that is now part of the R Lapack library.
152    
153            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
154            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
155    
156    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
159    
160    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
163            up with extraneous names '0'...'<n-1>'
164    
165    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/dgTMatrix.R (mat2dgT): care about NAs
168    
169    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/kronecker.R: triangularity preserving methods
172    
173    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/kronecker.R: new file collecting kronecker() methods in one
176                    place.  Goal: become much faster!
177    
178    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
181            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
182            can be much faster.
183    
184            * tests/matprod.R: add regression tests for these (upper & lower).
185    
186    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * R/Matrix.R (diff): method for our Matrices.
189    
190            * R/sparseMatrix.R (isDiagonal): check dim()!
191    
192    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/Matrix.R (dim<-): new method for "reshape()" built on a
195            proposal from Tamas Papp.
196    
197    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
200    
201            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
202            rather define and export  cBind() and rBind() only.
203            --> useRs *must* change code that used to have cbind()/rbind() !!
204    
205            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
206            * R/bind.Rout.save: ditto
207    
208    2007-02-16  Douglas Bates  <bates@r-project.org>
209    
210            * DESCRIPTION (Date, Version): 0.9975-11 with new date
211            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
212            const modifier on declaration of the array 'valid'
213    
214    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
215    
216            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
217    
218    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
221    
222            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
223            * tests/simple.R: test the above and some of these coercions:
224    
225            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
226                    be careful to avoid infinite recursion, using new coercions in
227            * R/ngCMatrix.R and nsC... and ntC...
228            * R/lsparseMatrix.R: ditto
229    
230            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
231    
232            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
233            * R/Rsparse.R: reactivate .Call()s
234    
235            * tests/Class+Meth.R: a bit more on actual classes
236    
237    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
240    
241    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION (Version): 0.9975-10 to upload
244    
245            * tests/Class+Meth.R (tstMatrixClass): require coercions to
246            specific classes less unconditionally.
247    
248            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
249    
250            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
251    
252            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
253            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
254            R_to_CMatrix segfaults on one platform.
255            Eliminate most coercion method to *specific* classes, and replace
256            with virtual classes coercions.
257    
258    
259    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
260    
261            * src/init.c: export the CHM...._validate() placeholders, since
262            they *are* called.
263    
264            * tests/Class+Meth.R (classCanCoerce): and starting to test
265            all as(<from>, <to>)
266    
267    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
270            * tests/indexing.R: tested now
271            * tests/indexing.Rout.save: updated
272    
273            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
274            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
275            appropriate.
276    
277            * NAMESPACE: export a trivial
278            * R/Matrix.R: drop() Matrix-method
279    
280            * R/AllClass.R: moved all prototypes to virtual super classes.
281    
282            * R/Rsparse.R: many more coercions to have less exceptions in
283            * tests/Class+Meth.R:
284    
285            * R/Ops.R (Compare): tweak for case with NA
286            * tests/simpl.R: hence another 'FIXME' eliminated
287    
288    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
291            objects.
292    
293            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
294              and more of "!", "&", "|", all, any; coercions
295    
296            * R/Rsparse.R: many coercions (which enable quite a few other
297            methods), thanks to enhancements in
298            * src/dgCMatrix.c (R_to_CMatrix): new, and
299            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
300            symmetric & triangular and ..RMatrix objects.
301    
302            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
303            renamed file from src/dsTMatrix.c;
304            now dealing with symmetric and triangular Tsparse coercions, both
305            to dense and general.
306    
307    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
310    
311            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
312            where sensible when the <numeric> is of length > 1.
313    
314    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Matrix.R ([<-): for M[] <- value: fix length
317    
318    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
321            * R/ndenseMatrix.R: new coercions n* -> l*
322    
323    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
326    
327            * R/Ops.R ("Logic"): and other "Ops", many updates
328    
329    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/Mutils.h (SET_DimNames): new utility
332    
333            * R/Auxiliaries.R (nnzero): improved and now exported via
334    
335            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
336    
337    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/diagMatrix.R (!): fix typo.
340    
341    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/Auxiliaries.R (as_Csparse): and quite a few others:
344                    allow to pass class definition --> speedup
345            * R/sparseMatrix.R: apply the above
346    
347            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
348    
349            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
350            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
351            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
352    
353            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
354    
355            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
356            and use it for "sparse*" as well, since it's faster than the
357            as_Csparse(.) way.
358    
359    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
362    
363    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
366            as method for   M[ ij ] <- v
367            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
368    
369            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
370            FALSE answer
371    
372            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
373            * tests/indexing.R: test it, and some of the above
374    
375    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/Auxiliaries.R (is_duplicatedT): new utility
378    
379    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
380    
381            * src/init.c (R_init_Matrix): export cholmod_scale
382    
383    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
386            base::as.matrix to (x, ...)
387    
388    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
391            file; start using "Logic", hence
392    
393            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
394            * NAMESPACE: import and export "Logic"
395    
396    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
399            only needed previously to R version 2.5.0.
400    
401    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
404    
405            * R/Tsparse.R (replTmat): fix subassignment of triangular
406            * R/Csparse.R (replCmat): ditto
407            * tests/indexing.R: more tests, incl the above fix
408    
409    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/Auxiliaries.R (drop0): extend for non CSparse
412            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
413    
414            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
415                    use uplo correctly (!); other places: use uplo_P() macro
416    
417            * R/Csparse.R (replCmat): call diagU2N() when needed
418            * R/Tsparse.R (replTmat): ditto
419    
420            * src/dtCMatrix.c (tCMatrix_validate): new
421            * src/dtTMatrix.c (tTMatrix_validate): new, used in
422            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
423    
424            * R/diagMatrix.R (replDiag): to use in [<-
425    
426    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
429                    also more general diagU2N().
430    
431    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
434            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
435    
436    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * tests/bind.R: a few more cases
439            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
440    
441            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
442            * R/ddenseMatrix.R (cbind2/rbind2)
443            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
444            * tests/indexing.R
445            * tests/indexing.Rout.save: updated
446    
447    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
450            * tests/indexing.R
451    
452    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
455            align with proper position of "0", i.e., right for integers.
456            argument 'align' by default is "fancy".
457    
458    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
461            * R/Csparse.R: and fix "Compare" for more cases.
462            * tests/Class+Meth.R: test some of these (m == m, m != m)
463    
464    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/lsparseMatrix.R: all() and any() methods
467            * R/ldenseMatrix.R:      ditto
468            * NAMESPACE, R/Matrix.R: ditto
469    
470            * man/all-methods.Rd: document them minimally
471    
472            * tests/simple.R: add a few examples for these
473    
474    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Tsparse.R ([): fix long standing typo in symmetric case
477            * man/dsCMatrix-class.Rd: add example exhibiting the above case
478    
479    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
480    
481            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
482            to LL before converting to a sparse matrix. (The LDL form can be
483            converted to a sparse matrix but it is implicitly a unit
484            triangular matrix and a diagonal matrix overwritten on the diagonal.)
485    
486    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
487    
488            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
489    
490    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
491    
492            * DESCRIPTION (Version): updated -> release 0.9975-7
493            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
494    
495    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
498    
499    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
500    
501            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
502            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
503            is exactly singular.
504    
505    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * DESCRIPTION (Date): updated -> release 0.9975-6
508    
509    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
512            now returns symmetric.
513    
514            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
515    
516            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
517            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
518    
519            * R/Auxiliaries.R (.type.kind): added
520    
521    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
524            running src/CSparse_install.sh
525    
526            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
527    
528    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
531            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
532    
533            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
534    
535            * tests/Class+Meth.R (tstMatrixClass): now assure
536            the (important in method programming) property :
537    
538                    ###>>  Every "Matrix" is either
539                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
540    
541                    (where "*" stands for "Matrix")
542    
543            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
544    
545            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
546            * tests/validObj.R: checks for "comparison"
547    
548            * R/sparseMatrix.R ([): improved indexing for sparse;
549                    trying to keep <symmetric>[ n, n] symmmetric
550    
551            * tests/indexing.R: indexing for logical sparse now ok
552    
553    
554    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * src/Tsparse.c: use xTsparse_validate() , and hence remove
557    
558            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
559    
560    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
563    
564            * tests/simple.R: validObject() checking the above.
565    
566            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
567            replacing both dgCMatrix_validate and lgCM*.
568    
569            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
570            fix dimnames setting in other places.
571            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
572    
573    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
576    
577            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
578            symmetry test, via
579            * R/Auxiliaries.R (.as.dgC.0.factors):
580    
581    2006-11-01  Douglas Bates  <bates@r-project.org>
582    
583            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
584            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
585            <CsparseMatrix>) added
586    
587    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * tests/matprod.R: add a variation of Harri's example
590    
591            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
592            recursive infinitely.
593    
594            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
595    
596            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
597    
598    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
601            matrix if possible; test m+m == 2*m; now test dgRMatrix.
602            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
603            satisfy the above test.
604    
605    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
608    
609            * R/dgCMatrix.R: solve(a, b="missing") based on
610            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
611            RHS = NULL.
612    
613            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
614            add more (needed) [t]crossprod() methods.
615    
616            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
617    
618            * R/Auxiliaries.R (as_CspClass): cleanup
619            (drop0): internal utility for "Csparse_drop(*, 0)"
620            (.bail.out.2): encourage active feedback
621    
622    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * R/dMatrix.R(Compare): new(), then slots [no validity check]
625    
626            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
627            non-valid or 'sorted' case).
628    
629            * R/dsparseMatrix.R: add "chol" method.
630            * R/ddenseMatrix.R: ditto
631    
632            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
633            * NAMESPACE (Ops)
634            * R/diagMatrix.R (diag2T): simple utility used "higher level"
635            coercion; deprecating direct lower level coercions.
636    
637            * R/*.R (seq): use seq_len() and seq_along() where possible.
638    
639    
640    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * DESCRIPTION (Version): 0.9975-5 ready for release
643    
644    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
645    
646            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
647    
648    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/AllClass.R (corMatrix): add 'validity' check;
651                    comment out unused "LDL" class definition
652            * NAMESPACE: mention, but do not export "LDL" class
653            * R/corMatrix.R: new (simple), needed for R-devel with
654            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
655              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
656    
657    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
658    
659            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
660            use Rprintf and R's error handling.
661    
662    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
665            * tests/matprod.R: add tests for the bug fixed.
666    
667    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
670            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
671    
672    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
673    
674            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
675    
676    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * DESCRIPTION (Version): 0.9975-3
679    
680            * R/diagMatrix.R (bdiag): new function constructing block diagonal
681            (sparse) matrices.
682            * man/bdiag.Rd: docu + examples
683    
684            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
685    
686            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
687            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
688    
689            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
690            that result is sparse or diagonal (and not dense).
691    
692            * man/Subassign-methods.Rd: fix examples
693    
694            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
695            should always return a sparse (and not sometimes a diagonal) matrix.
696    
697    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
700    
701    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
702    
703            * DESCRIPTION (Version): 0.9975-2
704    
705            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
706    
707    2006-10-02  Douglas Bates  <bates@R-project.org>
708    
709            * tests/dg_Matrix.R: Simplify test taking into account new code.
710    
711    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
714    
715            * R/lsTMatrix.R: new files w/ missing methods
716            * R/nsTMatrix.R:  "  'for completeness'
717    
718            * tests/Class+Meth.R: a bit less 'not.ok.classes'
719    
720            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
721    
722    
723    2006-09-28  Douglas Bates  <bates@R-project.org>
724    
725            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
726            included.
727    
728            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
729            Export C-callable functions used in Zt_create in lme4.
730    
731    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * DESCRIPTION (Version): 0.9975-1
734    
735            * tests/simple.R: less checks fail; using NA, found that our
736                    kronecker() is not base-compatible with NA's.
737    
738            * R/dMatrix.R: "Compare" method now implemented for all cases
739    
740            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
741    
742            * man/dtpMatrix-class.Rd: mention length of 'x' slot
743    
744            * src/dtpMatrix.c (dtpMatrix_validate): fix check
745            * src/dspMatrix.c (dspMatrix_validate): ditto
746    
747            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
748              including coercion to [nl]tTMatrix.
749    
750            * R/diagMatrix.R (show): print a header line as for other classes.
751    
752    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * src/Makefile.win (SUBDIRS): fix typo
755    
756    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
759    
760    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
761    
762            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
763            symmetric and y missing in R code using %*% (cholmod_aat doesn't
764            accept a symmetric matrix).
765            * tests/group-methods.R: Uncomment test of crossprod applied to
766            lsCMatrix objects.
767    
768    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/AllClass.R (symmetricMatrix): add validity method (available
771            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
772    
773            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
774    
775            * tests/indexing.Rout.save:
776            * tests/indexing.R: additions, mainly for 'lsparse'
777    
778            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
779            case.
780    
781            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
782    
783    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
786                    as 'N' (1-letter - Ok?)
787    
788            * tests/group-methods.R: add test for logical + NAs
789    
790            * R/dMatrix.R ("Compare"): fix to work with NA's
791    
792            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
793    
794            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
795                    which is implemented.
796    
797    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * src/chm_common.c: coerce logical <-> double instead of
800            typecasting;  needed for "l" matrix handling in cholmod.
801    
802            * tests/other-pkgs.R (graph): small extension in "graph" checks.
803    
804            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
805            (Tsp2grNEL): other fixes needed
806    
807    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
810                    Matrices, since "lMatrix", also "lsparseM" can have NA
811            * R/ndenseMatrix.R, etc: new source files
812            * man/nsparseMatrix-classes.Rd, etc: new help files
813            * tests/: adaptions
814            * src/chm_common.c (chm_dense_to_SEXP): and others:
815                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
816            * src/Csparse.c, etc: ditto
817    
818    2006-09-11  Douglas Bates  <bates@R-project.org>
819    
820            * src/Mutils.[ch],init.c inst/include/*.h: Move the
821            alloc_d**Matrix functions to the lme4 package.
822    
823    2006-09-09  Douglas Bates  <bates@R-project.org>
824    
825            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
826            fixed
827    
828    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/lMatrix.R: new
831    
832            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
833    
834            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
835            * man/tcrossprod.Rd: ditto
836    
837    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
838    
839            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
840            for exported functions
841            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
842            Remove partitioning algorithms for sparse matrix reordering.  The
843            copyright on the Metis code was problematic and the methods were
844            rarely used.
845            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
846            operations are now done entirely in CHOLMOD code.
847    
848    2006-09-06  Douglas Bates  <bates@R-project.org>
849    
850            * src/Mutils.h: Remove functions that are no longer used.
851    
852    2006-09-04  Douglas Bates  <bates@R-project.org>
853    
854            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
855            * src/DEPS.mkf: update
856    
857    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * created branches/Matrix-for-R-2.3.x;  on trunk: do
860            * DESCRIPTION (Version): 0.9975-0
861            (Depends): R (>= 2.4.0)
862    
863    2006-09-01  Douglas Bates  <bates@R-project.org>
864    
865            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
866    
867    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
870            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
871    
872            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
873    
874    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
877            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
878            * R/dsparseMatrix.R: ditto
879            * R/Csparse.R: ditto
880    
881    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/dMatrix.R (Compare): improve availability of "<", etc
884            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
885    
886    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
889            of a 0-index which was used as 1-index (..hmm)
890    
891            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
892    
893            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
894            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
895            (.is.diagonal): ditto
896    
897            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
898    
899            * R/Matrix.R (Matrix): also work for NA data
900    
901    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
904            in all cases.
905    
906    2006-08-27  Douglas Bates  <bates@R-project.org>
907    
908            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
909            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
910    
911    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
914            subclasses of "ddenseMatrix"
915            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
916            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
917            instead of half dozen specialized ones.
918    
919    2006-08-25  Douglas Bates  <bates@R-project.org>
920    
921            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
922            <tillard@cirad.fr> - ordering standard errors to match effects.
923    
924    2006-08-24  Douglas Bates  <bates@R-project.org>
925    
926            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
927            on R_ldl.
928            * R/lCholCMatrix.R,
929            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
930            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
931            * many files in ./R and ./src: Use more general version of
932            dup_mMatrix_as_dgeMatrix to simplify method definitions.
933            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
934            dtpMatrix, dspMatrix and dppMatrix conversions.
935    
936    
937    2006-08-23  Douglas Bates  <bates@R-project.org>
938    
939            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
940            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
941            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
942            dgeMatrix_crossprod (may need to do this in other places).
943            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
944            generic and method for dsCMatrix.  Use CHOLMOD for chol().
945    
946    2006-08-22  Douglas Bates  <bates@R-project.org>
947    
948            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
949            types of classed Matrices, matrices or numeric or logical vectors.
950            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
951            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
952            to Mutils.h (as an inline) and change name to Matrix_check_class;
953            fixes in as_cholmod_factor and chm_factor_to_SEXP.
954            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
955            dsCMatrix_matrix_solve.  Comment out vestigial functions.
956            * src/Csparse.c: use diag_P and uplo_P macros.
957    
958  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
959    
960          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
961          valgrind.          valgrind.
962            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
963            inverses.
964            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
965            -Wall warnings.
966            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
967            Use dup_mMatrix_as_dgeMatrix.
968    
969  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
970    

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