SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1360, Tue Aug 8 17:29:03 2006 UTC revision 1966, Sat Jul 7 20:07:58 2007 UTC
# Line 1  Line 1 
1    2007-07-07 18:23  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
4              lgRMatrix
5            * [r4568] DESCRIPTION: Prepare for bug-fix release
6            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
7              for declaration of cholmod_symmetry
8    
9    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
12            release.
13    
14    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
15    
16            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
17              functions - no longer used
18            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
19              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
20              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
21              Alloca
22    
23    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
24    
25            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
26              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
27              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
28              src/t_gCMatrix_colSums.c: more R_CheckStack()s
29    
30    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
31    
32            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
33              the required amount of memory then call M_numeric_as_chm_dense.
34            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
35              (like Calloc but calling alloca)
36    
37    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
40            and extended with more sophisticated 'col.names' option.
41            * NAMESPACE: export  printSparseMatrix()
42            * man/printSpMatrix.Rd: document, incl. examples
43    
44    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
45    
46            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
47              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
48              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
49    
50    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * DESCRIPTION (Version): 0.99875-4
53    
54            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
55            some dimnames perservation.
56    
57            * R/dsTMatrix.R (t-method): keep dimnames
58            * R/dtTMatrix.R:  ditto
59    
60            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
61            and ncol(.) < 10
62    
63            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
64            from Mutils.h
65    
66            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
67            e.g. in as(<ngCMatrix>, "matrix")
68    
69    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
70    
71            * [r4529] .: Create a branch for the API changes from the 0.99875
72              series to the 0.999375 series
73            * [r4530] DESCRIPTION, inst/include/Matrix.h,
74              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
75              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
76              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
77              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
78              as_cholmod_x functions
79    
80    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
81    
82            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
83              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
84              to Comparisons
85    
86    >>>>>>> .merge-right.r4561
87    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * DESCRIPTION (Version): 0.99875-3 ready to be released.
90    
91            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
92    
93            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
94            that should also work in a future version of R.
95    
96    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
99    
100            * R/sparseVector.R: more *sparseVector coercions, notably for
101            non - double ones.
102    
103    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
106              notably the new ones building on the new .Call(.)s:
107    
108            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
109            all 4 of [dlin]gCMatrix_colSums().
110    
111    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
112    
113            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
114            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
115              result
116    
117    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/kronecker.R: fix typo (could lead to inf.recursion)
120            * test/simple.R: testing that
121    
122            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
123            method as well (which can have arguments, show() can't).
124    
125    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
126    
127            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
128              added dgCMatrix_colSums for [col,row][Sums,Means]
129    
130    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
131    
132            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
133              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
134              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
135            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
136              class
137            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
138              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
139              row names to store the levels - duh!  Added an example.
140    
141    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * src/Csparse.c (Csparse_validate): check for *repeated* entries
144            thanks to example from Christian Buchta; with a test here:
145            * tests/simple.R:
146    
147    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
150            of colSums(*, sparseResult = TRUE)
151    
152    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
155            'na.rm = FALSE' as "everywhere" else in R.
156    
157    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
158    
159            * [r4421] src/CSparse_install.sh: Modify for new organization of
160              CSparse package
161            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
162              SuiteSparse
163            * [r4426] src/Makefile: add ./UFconfig to the include path for
164              compilation
165            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
166            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
167              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
168    
169    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
172            * R/sparseMatrix.R (prSpMatrix): now gives a message about
173            suppressed column names.
174    
175    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
178              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
179              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
180              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
181              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
182              Remove warnings after change to const char* CHAR
183    
184    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
185    
186            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
187              type of M_cholmod_ssmult
188    
189    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
190    
191            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
192              src/init.c: Yet another cholmod export - cholmod_ssmult
193    
194    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * NAMESPACE: exported drop0(), since
197            * man/drop0.Rd: I have seen several cases, I really wanted to use
198            it, so our users may want too.
199    
200    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * man/colSums.Rd: separately document colSums() etc, since these
203            have the extra argument 'sparseResult'.
204    
205    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
208            * man/spMatrix.Rd: docu., including examples
209    
210            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
211            in order to make colMeans() etc fast *and* correct.
212            * R/sparseVector.R (replSPvec): "[<-" functionality for
213            sparseVectors; tested in
214            * tests/simple.R:
215    
216    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
219            (very) sparse Matrices; output similar to Matlab's print().
220    
221    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
222    
223            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
224            0-based, indices (Jose Quesada <quesada@gmail.com>).
225    
226    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
227    
228            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
229    
230    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Auxiliaries.R (sparsapply): new utility, much faster than
233            tapply1() for large sparse matrices.
234    
235    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Matrix.R (dim<-): reshape now via sparseVector.
238    
239            * R/sparseVector.R: methods and function for
240            * R/AllClass.R: new "sparseVector" class and daughters.
241            * NAMESPACE: export new classes
242    
243    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * DESCRIPTION (Version): 0.99875-1
246            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
247    
248    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
251            indexing
252            * tests/indexing.R: test set for that.
253    
254    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
257            entries.
258            * tests/indexing.R(out): add regression test for it
259    
260    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
263            name for "!" method definitions.
264    
265    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Tsparse.R (intI): new utility, used for "[" :
268                    Cleanup up there, and fixes for duplicated indices - more TODO!
269    
270            * tests/indexing.R(out): more tests
271    
272    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
273    
274            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
275            code that is now part of the R Lapack library.
276    
277            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
278            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
279    
280    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
283    
284    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
287            up with extraneous names '0'...'<n-1>'
288    
289    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/dgTMatrix.R (mat2dgT): care about NAs
292    
293    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/kronecker.R: triangularity preserving methods
296    
297    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/kronecker.R: new file collecting kronecker() methods in one
300                    place.  Goal: become much faster!
301    
302    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
305            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
306            can be much faster.
307    
308            * tests/matprod.R: add regression tests for these (upper & lower).
309    
310    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Matrix.R (diff): method for our Matrices.
313    
314            * R/sparseMatrix.R (isDiagonal): check dim()!
315    
316    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * R/Matrix.R (dim<-): new method for "reshape()" built on a
319            proposal from Tamas Papp.
320    
321    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
324    
325            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
326            rather define and export  cBind() and rBind() only.
327            --> useRs *must* change code that used to have cbind()/rbind() !!
328    
329            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
330            * R/bind.Rout.save: ditto
331    
332    2007-02-16  Douglas Bates  <bates@r-project.org>
333    
334            * DESCRIPTION (Date, Version): 0.9975-11 with new date
335            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
336            const modifier on declaration of the array 'valid'
337    
338    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
339    
340            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
341    
342    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
345    
346            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
347            * tests/simple.R: test the above and some of these coercions:
348    
349            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
350                    be careful to avoid infinite recursion, using new coercions in
351            * R/ngCMatrix.R and nsC... and ntC...
352            * R/lsparseMatrix.R: ditto
353    
354            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
355    
356            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
357            * R/Rsparse.R: reactivate .Call()s
358    
359            * tests/Class+Meth.R: a bit more on actual classes
360    
361    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
364    
365    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * DESCRIPTION (Version): 0.9975-10 to upload
368    
369            * tests/Class+Meth.R (tstMatrixClass): require coercions to
370            specific classes less unconditionally.
371    
372            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
373    
374            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
375    
376            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
377            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
378            R_to_CMatrix segfaults on one platform.
379            Eliminate most coercion method to *specific* classes, and replace
380            with virtual classes coercions.
381    
382    
383    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
384    
385            * src/init.c: export the CHM...._validate() placeholders, since
386            they *are* called.
387    
388            * tests/Class+Meth.R (classCanCoerce): and starting to test
389            all as(<from>, <to>)
390    
391    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
394            * tests/indexing.R: tested now
395            * tests/indexing.Rout.save: updated
396    
397            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
398            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
399            appropriate.
400    
401            * NAMESPACE: export a trivial
402            * R/Matrix.R: drop() Matrix-method
403    
404            * R/AllClass.R: moved all prototypes to virtual super classes.
405    
406            * R/Rsparse.R: many more coercions to have less exceptions in
407            * tests/Class+Meth.R:
408    
409            * R/Ops.R (Compare): tweak for case with NA
410            * tests/simpl.R: hence another 'FIXME' eliminated
411    
412    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
415            objects.
416    
417            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
418              and more of "!", "&", "|", all, any; coercions
419    
420            * R/Rsparse.R: many coercions (which enable quite a few other
421            methods), thanks to enhancements in
422            * src/dgCMatrix.c (R_to_CMatrix): new, and
423            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
424            symmetric & triangular and ..RMatrix objects.
425    
426            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
427            renamed file from src/dsTMatrix.c;
428            now dealing with symmetric and triangular Tsparse coercions, both
429            to dense and general.
430    
431    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
434    
435            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
436            where sensible when the <numeric> is of length > 1.
437    
438    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
439    
440            * R/Matrix.R ([<-): for M[] <- value: fix length
441    
442    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
445            * R/ndenseMatrix.R: new coercions n* -> l*
446    
447    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
450    
451            * R/Ops.R ("Logic"): and other "Ops", many updates
452    
453    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * src/Mutils.h (SET_DimNames): new utility
456    
457            * R/Auxiliaries.R (nnzero): improved and now exported via
458    
459            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
460    
461    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/diagMatrix.R (!): fix typo.
464    
465    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/Auxiliaries.R (as_Csparse): and quite a few others:
468                    allow to pass class definition --> speedup
469            * R/sparseMatrix.R: apply the above
470    
471            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
472    
473            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
474            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
475            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
476    
477            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
478    
479            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
480            and use it for "sparse*" as well, since it's faster than the
481            as_Csparse(.) way.
482    
483    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
484    
485            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
486    
487    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
490            as method for   M[ ij ] <- v
491            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
492    
493            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
494            FALSE answer
495    
496            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
497            * tests/indexing.R: test it, and some of the above
498    
499    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * R/Auxiliaries.R (is_duplicatedT): new utility
502    
503    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
504    
505            * src/init.c (R_init_Matrix): export cholmod_scale
506    
507    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
510            base::as.matrix to (x, ...)
511    
512    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
515            file; start using "Logic", hence
516    
517            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
518            * NAMESPACE: import and export "Logic"
519    
520    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
523            only needed previously to R version 2.5.0.
524    
525    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
528    
529            * R/Tsparse.R (replTmat): fix subassignment of triangular
530            * R/Csparse.R (replCmat): ditto
531            * tests/indexing.R: more tests, incl the above fix
532    
533    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/Auxiliaries.R (drop0): extend for non CSparse
536            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
537    
538            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
539                    use uplo correctly (!); other places: use uplo_P() macro
540    
541            * R/Csparse.R (replCmat): call diagU2N() when needed
542            * R/Tsparse.R (replTmat): ditto
543    
544            * src/dtCMatrix.c (tCMatrix_validate): new
545            * src/dtTMatrix.c (tTMatrix_validate): new, used in
546            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
547    
548            * R/diagMatrix.R (replDiag): to use in [<-
549    
550    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
553                    also more general diagU2N().
554    
555    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
558            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
559    
560    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * tests/bind.R: a few more cases
563            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
564    
565            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
566            * R/ddenseMatrix.R (cbind2/rbind2)
567            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
568            * tests/indexing.R
569            * tests/indexing.Rout.save: updated
570    
571    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
574            * tests/indexing.R
575    
576    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
579            align with proper position of "0", i.e., right for integers.
580            argument 'align' by default is "fancy".
581    
582    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
585            * R/Csparse.R: and fix "Compare" for more cases.
586            * tests/Class+Meth.R: test some of these (m == m, m != m)
587    
588    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/lsparseMatrix.R: all() and any() methods
591            * R/ldenseMatrix.R:      ditto
592            * NAMESPACE, R/Matrix.R: ditto
593    
594            * man/all-methods.Rd: document them minimally
595    
596            * tests/simple.R: add a few examples for these
597    
598    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/Tsparse.R ([): fix long standing typo in symmetric case
601            * man/dsCMatrix-class.Rd: add example exhibiting the above case
602    
603    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
604    
605            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
606            to LL before converting to a sparse matrix. (The LDL form can be
607            converted to a sparse matrix but it is implicitly a unit
608            triangular matrix and a diagonal matrix overwritten on the diagonal.)
609    
610    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
611    
612            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
613    
614    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
615    
616            * DESCRIPTION (Version): updated -> release 0.9975-7
617            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
618    
619    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
622    
623    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
624    
625            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
626            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
627            is exactly singular.
628    
629    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * DESCRIPTION (Date): updated -> release 0.9975-6
632    
633    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
636            now returns symmetric.
637    
638            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
639    
640            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
641            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
642    
643            * R/Auxiliaries.R (.type.kind): added
644    
645    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
648            running src/CSparse_install.sh
649    
650            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
651    
652    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
655            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
656    
657            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
658    
659            * tests/Class+Meth.R (tstMatrixClass): now assure
660            the (important in method programming) property :
661    
662                    ###>>  Every "Matrix" is either
663                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
664    
665                    (where "*" stands for "Matrix")
666    
667            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
668    
669            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
670            * tests/validObj.R: checks for "comparison"
671    
672            * R/sparseMatrix.R ([): improved indexing for sparse;
673                    trying to keep <symmetric>[ n, n] symmmetric
674    
675            * tests/indexing.R: indexing for logical sparse now ok
676    
677    
678    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * src/Tsparse.c: use xTsparse_validate() , and hence remove
681    
682            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
683    
684    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
687    
688            * tests/simple.R: validObject() checking the above.
689    
690            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
691            replacing both dgCMatrix_validate and lgCM*.
692    
693            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
694            fix dimnames setting in other places.
695            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
696    
697    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
700    
701            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
702            symmetry test, via
703            * R/Auxiliaries.R (.as.dgC.0.factors):
704    
705    2006-11-01  Douglas Bates  <bates@r-project.org>
706    
707            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
708            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
709            <CsparseMatrix>) added
710    
711    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * tests/matprod.R: add a variation of Harri's example
714    
715            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
716            recursive infinitely.
717    
718            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
719    
720            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
721    
722    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
725            matrix if possible; test m+m == 2*m; now test dgRMatrix.
726            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
727            satisfy the above test.
728    
729    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
732    
733            * R/dgCMatrix.R: solve(a, b="missing") based on
734            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
735            RHS = NULL.
736    
737            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
738            add more (needed) [t]crossprod() methods.
739    
740            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
741    
742            * R/Auxiliaries.R (as_CspClass): cleanup
743            (drop0): internal utility for "Csparse_drop(*, 0)"
744            (.bail.out.2): encourage active feedback
745    
746    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/dMatrix.R(Compare): new(), then slots [no validity check]
749    
750            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
751            non-valid or 'sorted' case).
752    
753            * R/dsparseMatrix.R: add "chol" method.
754            * R/ddenseMatrix.R: ditto
755    
756            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
757            * NAMESPACE (Ops)
758            * R/diagMatrix.R (diag2T): simple utility used "higher level"
759            coercion; deprecating direct lower level coercions.
760    
761            * R/*.R (seq): use seq_len() and seq_along() where possible.
762    
763    
764    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * DESCRIPTION (Version): 0.9975-5 ready for release
767    
768    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
769    
770            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
771    
772    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/AllClass.R (corMatrix): add 'validity' check;
775                    comment out unused "LDL" class definition
776            * NAMESPACE: mention, but do not export "LDL" class
777            * R/corMatrix.R: new (simple), needed for R-devel with
778            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
779              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
780    
781    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
782    
783            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
784            use Rprintf and R's error handling.
785    
786    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
789            * tests/matprod.R: add tests for the bug fixed.
790    
791    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
792    
793            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
794            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
795    
796    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
797    
798            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
799    
800    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * DESCRIPTION (Version): 0.9975-3
803    
804            * R/diagMatrix.R (bdiag): new function constructing block diagonal
805            (sparse) matrices.
806            * man/bdiag.Rd: docu + examples
807    
808            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
809    
810            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
811            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
812    
813            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
814            that result is sparse or diagonal (and not dense).
815    
816            * man/Subassign-methods.Rd: fix examples
817    
818            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
819            should always return a sparse (and not sometimes a diagonal) matrix.
820    
821    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
824    
825    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
826    
827            * DESCRIPTION (Version): 0.9975-2
828    
829            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
830    
831    2006-10-02  Douglas Bates  <bates@R-project.org>
832    
833            * tests/dg_Matrix.R: Simplify test taking into account new code.
834    
835    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
838    
839            * R/lsTMatrix.R: new files w/ missing methods
840            * R/nsTMatrix.R:  "  'for completeness'
841    
842            * tests/Class+Meth.R: a bit less 'not.ok.classes'
843    
844            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
845    
846    
847    2006-09-28  Douglas Bates  <bates@R-project.org>
848    
849            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
850            included.
851    
852            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
853            Export C-callable functions used in Zt_create in lme4.
854    
855    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * DESCRIPTION (Version): 0.9975-1
858    
859            * tests/simple.R: less checks fail; using NA, found that our
860                    kronecker() is not base-compatible with NA's.
861    
862            * R/dMatrix.R: "Compare" method now implemented for all cases
863    
864            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
865    
866            * man/dtpMatrix-class.Rd: mention length of 'x' slot
867    
868            * src/dtpMatrix.c (dtpMatrix_validate): fix check
869            * src/dspMatrix.c (dspMatrix_validate): ditto
870    
871            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
872              including coercion to [nl]tTMatrix.
873    
874            * R/diagMatrix.R (show): print a header line as for other classes.
875    
876    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * src/Makefile.win (SUBDIRS): fix typo
879    
880    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
883    
884    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
885    
886            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
887            symmetric and y missing in R code using %*% (cholmod_aat doesn't
888            accept a symmetric matrix).
889            * tests/group-methods.R: Uncomment test of crossprod applied to
890            lsCMatrix objects.
891    
892    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
893    
894            * R/AllClass.R (symmetricMatrix): add validity method (available
895            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
896    
897            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
898    
899            * tests/indexing.Rout.save:
900            * tests/indexing.R: additions, mainly for 'lsparse'
901    
902            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
903            case.
904    
905            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
906    
907    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
908    
909            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
910                    as 'N' (1-letter - Ok?)
911    
912            * tests/group-methods.R: add test for logical + NAs
913    
914            * R/dMatrix.R ("Compare"): fix to work with NA's
915    
916            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
917    
918            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
919                    which is implemented.
920    
921    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
922    
923            * src/chm_common.c: coerce logical <-> double instead of
924            typecasting;  needed for "l" matrix handling in cholmod.
925    
926            * tests/other-pkgs.R (graph): small extension in "graph" checks.
927    
928            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
929            (Tsp2grNEL): other fixes needed
930    
931    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
934                    Matrices, since "lMatrix", also "lsparseM" can have NA
935            * R/ndenseMatrix.R, etc: new source files
936            * man/nsparseMatrix-classes.Rd, etc: new help files
937            * tests/: adaptions
938            * src/chm_common.c (chm_dense_to_SEXP): and others:
939                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
940            * src/Csparse.c, etc: ditto
941    
942    2006-09-11  Douglas Bates  <bates@R-project.org>
943    
944            * src/Mutils.[ch],init.c inst/include/*.h: Move the
945            alloc_d**Matrix functions to the lme4 package.
946    
947    2006-09-09  Douglas Bates  <bates@R-project.org>
948    
949            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
950            fixed
951    
952    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * R/lMatrix.R: new
955    
956            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
957    
958            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
959            * man/tcrossprod.Rd: ditto
960    
961    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
962    
963            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
964            for exported functions
965            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
966            Remove partitioning algorithms for sparse matrix reordering.  The
967            copyright on the Metis code was problematic and the methods were
968            rarely used.
969            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
970            operations are now done entirely in CHOLMOD code.
971    
972    2006-09-06  Douglas Bates  <bates@R-project.org>
973    
974            * src/Mutils.h: Remove functions that are no longer used.
975    
976    2006-09-04  Douglas Bates  <bates@R-project.org>
977    
978            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
979            * src/DEPS.mkf: update
980    
981    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
982    
983            * created branches/Matrix-for-R-2.3.x;  on trunk: do
984            * DESCRIPTION (Version): 0.9975-0
985            (Depends): R (>= 2.4.0)
986    
987    2006-09-01  Douglas Bates  <bates@R-project.org>
988    
989            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
990    
991    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
994            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
995    
996            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
997    
998    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1001            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1002            * R/dsparseMatrix.R: ditto
1003            * R/Csparse.R: ditto
1004    
1005    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/dMatrix.R (Compare): improve availability of "<", etc
1008            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1009    
1010    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1013            of a 0-index which was used as 1-index (..hmm)
1014    
1015            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1016    
1017            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1018            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1019            (.is.diagonal): ditto
1020    
1021            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1022    
1023            * R/Matrix.R (Matrix): also work for NA data
1024    
1025    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1028            in all cases.
1029    
1030    2006-08-27  Douglas Bates  <bates@R-project.org>
1031    
1032            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1033            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1034    
1035    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1038            subclasses of "ddenseMatrix"
1039            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1040            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1041            instead of half dozen specialized ones.
1042    
1043    2006-08-25  Douglas Bates  <bates@R-project.org>
1044    
1045            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1046            <tillard@cirad.fr> - ordering standard errors to match effects.
1047    
1048    2006-08-24  Douglas Bates  <bates@R-project.org>
1049    
1050            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1051            on R_ldl.
1052            * R/lCholCMatrix.R,
1053            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1054            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1055            * many files in ./R and ./src: Use more general version of
1056            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1057            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1058            dtpMatrix, dspMatrix and dppMatrix conversions.
1059    
1060    
1061    2006-08-23  Douglas Bates  <bates@R-project.org>
1062    
1063            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1064            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1065            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1066            dgeMatrix_crossprod (may need to do this in other places).
1067            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1068            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1069    
1070    2006-08-22  Douglas Bates  <bates@R-project.org>
1071    
1072            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1073            types of classed Matrices, matrices or numeric or logical vectors.
1074            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1075            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1076            to Mutils.h (as an inline) and change name to Matrix_check_class;
1077            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1078            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1079            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1080            * src/Csparse.c: use diag_P and uplo_P macros.
1081    
1082    2006-08-21  Douglas Bates  <bates@R-project.org>
1083    
1084            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1085            valgrind.
1086            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1087            inverses.
1088            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1089            -Wall warnings.
1090            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1091            Use dup_mMatrix_as_dgeMatrix.
1092    
1093    2006-08-20  Douglas Bates  <bates@R-project.org>
1094    
1095            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1096            * tests/sparseQR.R: Added
1097            * man/sparseQR-class.Rd: Document methods for qr.* generics
1098            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1099    
1100    2006-08-19  Douglas Bates  <bates@R-project.org>
1101    
1102            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1103            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1104            and qr.fitted.
1105            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1106            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1107    
1108    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1109    
1110            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1111            the base version has no "..." argument.
1112    
1113            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1114    
1115            * R/Matrix.R: define and
1116            * NAMESPACE: export as.numeric() and as.logical() methods.
1117                    Let's hope these do not badly slow down something...
1118            Finally export the zapsmall() method.
1119    
1120    2006-08-17  Douglas Bates  <bates@R-project.org>
1121    
1122            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1123            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1124            * src/dtCMatrix.c :Remove code that is no longer used
1125            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1126    
1127    2006-08-14  Douglas Bates  <bates@R-project.org>
1128    
1129            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1130            Csparse_to_logical and Csparse_symmetric_to_general.
1131            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1132            coercion methods between CsparseMatrix and TsparseMatrix.
1133    
1134    2006-08-14  Douglas Bates  <bates@R-project.org>
1135    
1136            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1137            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1138            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1139            possible.
1140    
1141    2006-08-12  Douglas Bates  <bates@R-project.org>
1142    
1143            * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,
1144              dgTMatrix.c,dgCMatrix.c,dsCMatrix.c,dtTMatrix.c, R/dsTMatrix.R,
1145              Tsparse.R,Csparse.R,dgTMatrix.R,dsCMatrix.R,lsCMatrix.R:
1146              generalize conversions between TsparseMatrix, CsparseMatrix,
1147              denseMatrix and matrix.  Preserve triangularity property and
1148              propagate Dimnames in the easy cases.
1149    
1150    2006-08-10  Douglas Bates  <bates@R-project.org>
1151    
1152            * src/lmer.c: adjust checks in glmer_init for S4SXP
1153            * tests/validObj.R: check of all(eq) should be all(eq@x) - worked
1154            before S4SXP but for the wrong reasons.
1155    
1156  2006-08-08  Douglas Bates  <bates@R-project.org>  2006-08-08  Douglas Bates  <bates@R-project.org>
1157    
1158          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.          * src/Csparse.c (Csparse_crossprod): tcrossprod result has stype = -1.

Legend:
Removed from v.1360  
changed lines
  Added in v.1966

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge