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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 1987, Tue Jul 10 19:31:18 2007 UTC
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1    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
4    
5    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
6    
7            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
8              to fix a subtle bug (Kurt Hornik and Ingo Feinerer)
9    
10    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
11    
12            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
13              solve the bug
14    
15    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dgCMatrix.c (compressed_to_TMatrix):
18    
19    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * src/Csparse.c (Rsparse_validate): new, to have some validity
22            checking for RsparseMatrix
23            * src/dgCMatrix.c (xRMatrix_validate): ditto
24            * src/dtCMatrix.c (tRMatrix_validate): ditto
25    
26    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
27    
28            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
29              lgRMatrix
30            * [r4568] DESCRIPTION: Prepare for bug-fix release
31            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
32              for declaration of cholmod_symmetry
33    
34    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
37            release.
38    
39    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
40    
41            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
42              functions - no longer used
43            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
44              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
45              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
46              Alloca
47    
48    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
49    
50            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
51              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
52              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
53              src/t_gCMatrix_colSums.c: more R_CheckStack()s
54    
55    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
58              the required amount of memory then call M_numeric_as_chm_dense.
59            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
60              (like Calloc but calling alloca)
61    
62    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
65            and extended with more sophisticated 'col.names' option.
66            * NAMESPACE: export  printSparseMatrix()
67            * man/printSpMatrix.Rd: document, incl. examples
68    
69    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
70    
71            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
72              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
73              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
74    
75    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * DESCRIPTION (Version): 0.99875-4
78    
79            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
80            some dimnames perservation.
81    
82            * R/dsTMatrix.R (t-method): keep dimnames
83            * R/dtTMatrix.R:  ditto
84    
85            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
86            and ncol(.) < 10
87    
88            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
89            from Mutils.h
90    
91            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
92            e.g. in as(<ngCMatrix>, "matrix")
93    
94    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
95    
96            * [r4529] .: Create a branch for the API changes from the 0.99875
97              series to the 0.999375 series
98            * [r4530] DESCRIPTION, inst/include/Matrix.h,
99              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
100              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
101              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
102              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
103              as_cholmod_x functions
104    
105    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
106    
107            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
108              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
109              to Comparisons
110    
111    >>>>>>> .merge-right.r4561
112    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.99875-3 ready to be released.
115    
116            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
117    
118            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
119            that should also work in a future version of R.
120    
121    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
124    
125            * R/sparseVector.R: more *sparseVector coercions, notably for
126            non - double ones.
127    
128    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
131              notably the new ones building on the new .Call(.)s:
132    
133            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
134            all 4 of [dlin]gCMatrix_colSums().
135    
136    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
139            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
140              result
141    
142    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/kronecker.R: fix typo (could lead to inf.recursion)
145            * test/simple.R: testing that
146    
147            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
148            method as well (which can have arguments, show() can't).
149    
150    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
151    
152            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
153              added dgCMatrix_colSums for [col,row][Sums,Means]
154    
155    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
156    
157            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
158              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
159              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
160            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
161              class
162            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
163              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
164              row names to store the levels - duh!  Added an example.
165    
166    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * src/Csparse.c (Csparse_validate): check for *repeated* entries
169            thanks to example from Christian Buchta; with a test here:
170            * tests/simple.R:
171    
172    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
175            of colSums(*, sparseResult = TRUE)
176    
177    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
180            'na.rm = FALSE' as "everywhere" else in R.
181    
182    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
183    
184            * [r4421] src/CSparse_install.sh: Modify for new organization of
185              CSparse package
186            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
187              SuiteSparse
188            * [r4426] src/Makefile: add ./UFconfig to the include path for
189              compilation
190            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
191            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
192              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
193    
194    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
197            * R/sparseMatrix.R (prSpMatrix): now gives a message about
198            suppressed column names.
199    
200    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
203              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
204              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
205              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
206              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
207              Remove warnings after change to const char* CHAR
208    
209    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
212              type of M_cholmod_ssmult
213    
214    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
215    
216            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
217              src/init.c: Yet another cholmod export - cholmod_ssmult
218    
219    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * NAMESPACE: exported drop0(), since
222            * man/drop0.Rd: I have seen several cases, I really wanted to use
223            it, so our users may want too.
224    
225    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * man/colSums.Rd: separately document colSums() etc, since these
228            have the extra argument 'sparseResult'.
229    
230    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
233            * man/spMatrix.Rd: docu., including examples
234    
235            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
236            in order to make colMeans() etc fast *and* correct.
237            * R/sparseVector.R (replSPvec): "[<-" functionality for
238            sparseVectors; tested in
239            * tests/simple.R:
240    
241    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
244            (very) sparse Matrices; output similar to Matlab's print().
245    
246    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
247    
248            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
249            0-based, indices (Jose Quesada <quesada@gmail.com>).
250    
251    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
252    
253            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
254    
255    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
256    
257            * R/Auxiliaries.R (sparsapply): new utility, much faster than
258            tapply1() for large sparse matrices.
259    
260    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/Matrix.R (dim<-): reshape now via sparseVector.
263    
264            * R/sparseVector.R: methods and function for
265            * R/AllClass.R: new "sparseVector" class and daughters.
266            * NAMESPACE: export new classes
267    
268    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * DESCRIPTION (Version): 0.99875-1
271            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
272    
273    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
276            indexing
277            * tests/indexing.R: test set for that.
278    
279    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
282            entries.
283            * tests/indexing.R(out): add regression test for it
284    
285    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
288            name for "!" method definitions.
289    
290    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Tsparse.R (intI): new utility, used for "[" :
293                    Cleanup up there, and fixes for duplicated indices - more TODO!
294    
295            * tests/indexing.R(out): more tests
296    
297    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
298    
299            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
300            code that is now part of the R Lapack library.
301    
302            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
303            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
304    
305    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
308    
309    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
312            up with extraneous names '0'...'<n-1>'
313    
314    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/dgTMatrix.R (mat2dgT): care about NAs
317    
318    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/kronecker.R: triangularity preserving methods
321    
322    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/kronecker.R: new file collecting kronecker() methods in one
325                    place.  Goal: become much faster!
326    
327    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
330            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
331            can be much faster.
332    
333            * tests/matprod.R: add regression tests for these (upper & lower).
334    
335    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Matrix.R (diff): method for our Matrices.
338    
339            * R/sparseMatrix.R (isDiagonal): check dim()!
340    
341    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/Matrix.R (dim<-): new method for "reshape()" built on a
344            proposal from Tamas Papp.
345    
346    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
349    
350            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
351            rather define and export  cBind() and rBind() only.
352            --> useRs *must* change code that used to have cbind()/rbind() !!
353    
354            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
355            * R/bind.Rout.save: ditto
356    
357    2007-02-16  Douglas Bates  <bates@r-project.org>
358    
359            * DESCRIPTION (Date, Version): 0.9975-11 with new date
360            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
361            const modifier on declaration of the array 'valid'
362    
363    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
364    
365            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
366    
367    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
370    
371            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
372            * tests/simple.R: test the above and some of these coercions:
373    
374            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
375                    be careful to avoid infinite recursion, using new coercions in
376            * R/ngCMatrix.R and nsC... and ntC...
377            * R/lsparseMatrix.R: ditto
378    
379            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
380    
381            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
382            * R/Rsparse.R: reactivate .Call()s
383    
384            * tests/Class+Meth.R: a bit more on actual classes
385    
386    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
387    
388            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
389    
390    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * DESCRIPTION (Version): 0.9975-10 to upload
393    
394            * tests/Class+Meth.R (tstMatrixClass): require coercions to
395            specific classes less unconditionally.
396    
397            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
398    
399            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
400    
401            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
402            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
403            R_to_CMatrix segfaults on one platform.
404            Eliminate most coercion method to *specific* classes, and replace
405            with virtual classes coercions.
406    
407    
408    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
409    
410            * src/init.c: export the CHM...._validate() placeholders, since
411            they *are* called.
412    
413            * tests/Class+Meth.R (classCanCoerce): and starting to test
414            all as(<from>, <to>)
415    
416    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
419            * tests/indexing.R: tested now
420            * tests/indexing.Rout.save: updated
421    
422            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
423            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
424            appropriate.
425    
426            * NAMESPACE: export a trivial
427            * R/Matrix.R: drop() Matrix-method
428    
429            * R/AllClass.R: moved all prototypes to virtual super classes.
430    
431            * R/Rsparse.R: many more coercions to have less exceptions in
432            * tests/Class+Meth.R:
433    
434            * R/Ops.R (Compare): tweak for case with NA
435            * tests/simpl.R: hence another 'FIXME' eliminated
436    
437    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
440            objects.
441    
442            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
443              and more of "!", "&", "|", all, any; coercions
444    
445            * R/Rsparse.R: many coercions (which enable quite a few other
446            methods), thanks to enhancements in
447            * src/dgCMatrix.c (R_to_CMatrix): new, and
448            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
449            symmetric & triangular and ..RMatrix objects.
450    
451            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
452            renamed file from src/dsTMatrix.c;
453            now dealing with symmetric and triangular Tsparse coercions, both
454            to dense and general.
455    
456    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
459    
460            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
461            where sensible when the <numeric> is of length > 1.
462    
463    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/Matrix.R ([<-): for M[] <- value: fix length
466    
467    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
470            * R/ndenseMatrix.R: new coercions n* -> l*
471    
472    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
475    
476            * R/Ops.R ("Logic"): and other "Ops", many updates
477    
478    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * src/Mutils.h (SET_DimNames): new utility
481    
482            * R/Auxiliaries.R (nnzero): improved and now exported via
483    
484            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
485    
486    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/diagMatrix.R (!): fix typo.
489    
490    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/Auxiliaries.R (as_Csparse): and quite a few others:
493                    allow to pass class definition --> speedup
494            * R/sparseMatrix.R: apply the above
495    
496            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
497    
498            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
499            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
500            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
501    
502            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
503    
504            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
505            and use it for "sparse*" as well, since it's faster than the
506            as_Csparse(.) way.
507    
508    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
511    
512    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
515            as method for   M[ ij ] <- v
516            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
517    
518            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
519            FALSE answer
520    
521            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
522            * tests/indexing.R: test it, and some of the above
523    
524    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/Auxiliaries.R (is_duplicatedT): new utility
527    
528    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * src/init.c (R_init_Matrix): export cholmod_scale
531    
532    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
535            base::as.matrix to (x, ...)
536    
537    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
540            file; start using "Logic", hence
541    
542            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
543            * NAMESPACE: import and export "Logic"
544    
545    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
548            only needed previously to R version 2.5.0.
549    
550    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
551    
552            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
553    
554            * R/Tsparse.R (replTmat): fix subassignment of triangular
555            * R/Csparse.R (replCmat): ditto
556            * tests/indexing.R: more tests, incl the above fix
557    
558    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/Auxiliaries.R (drop0): extend for non CSparse
561            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
562    
563            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
564                    use uplo correctly (!); other places: use uplo_P() macro
565    
566            * R/Csparse.R (replCmat): call diagU2N() when needed
567            * R/Tsparse.R (replTmat): ditto
568    
569            * src/dtCMatrix.c (tCMatrix_validate): new
570            * src/dtTMatrix.c (tTMatrix_validate): new, used in
571            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
572    
573            * R/diagMatrix.R (replDiag): to use in [<-
574    
575    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
578                    also more general diagU2N().
579    
580    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
583            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
584    
585    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * tests/bind.R: a few more cases
588            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
589    
590            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
591            * R/ddenseMatrix.R (cbind2/rbind2)
592            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
593            * tests/indexing.R
594            * tests/indexing.Rout.save: updated
595    
596    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
599            * tests/indexing.R
600    
601    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
602    
603            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
604            align with proper position of "0", i.e., right for integers.
605            argument 'align' by default is "fancy".
606    
607    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
610            * R/Csparse.R: and fix "Compare" for more cases.
611            * tests/Class+Meth.R: test some of these (m == m, m != m)
612    
613    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/lsparseMatrix.R: all() and any() methods
616            * R/ldenseMatrix.R:      ditto
617            * NAMESPACE, R/Matrix.R: ditto
618    
619            * man/all-methods.Rd: document them minimally
620    
621            * tests/simple.R: add a few examples for these
622    
623    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/Tsparse.R ([): fix long standing typo in symmetric case
626            * man/dsCMatrix-class.Rd: add example exhibiting the above case
627    
628    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
629    
630            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
631            to LL before converting to a sparse matrix. (The LDL form can be
632            converted to a sparse matrix but it is implicitly a unit
633            triangular matrix and a diagonal matrix overwritten on the diagonal.)
634    
635    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
636    
637            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
638    
639    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
640    
641            * DESCRIPTION (Version): updated -> release 0.9975-7
642            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
643    
644    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
647    
648    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
649    
650            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
651            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
652            is exactly singular.
653    
654    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * DESCRIPTION (Date): updated -> release 0.9975-6
657    
658    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
661            now returns symmetric.
662    
663            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
664    
665            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
666            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
667    
668            * R/Auxiliaries.R (.type.kind): added
669    
670    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
673            running src/CSparse_install.sh
674    
675            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
676    
677    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
680            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
681    
682            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
683    
684            * tests/Class+Meth.R (tstMatrixClass): now assure
685            the (important in method programming) property :
686    
687                    ###>>  Every "Matrix" is either
688                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
689    
690                    (where "*" stands for "Matrix")
691    
692            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
693    
694            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
695            * tests/validObj.R: checks for "comparison"
696    
697            * R/sparseMatrix.R ([): improved indexing for sparse;
698                    trying to keep <symmetric>[ n, n] symmmetric
699    
700            * tests/indexing.R: indexing for logical sparse now ok
701    
702    
703    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * src/Tsparse.c: use xTsparse_validate() , and hence remove
706    
707            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
708    
709    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
712    
713            * tests/simple.R: validObject() checking the above.
714    
715            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
716            replacing both dgCMatrix_validate and lgCM*.
717    
718            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
719            fix dimnames setting in other places.
720            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
721    
722    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
725    
726            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
727            symmetry test, via
728            * R/Auxiliaries.R (.as.dgC.0.factors):
729    
730    2006-11-01  Douglas Bates  <bates@r-project.org>
731    
732            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
733            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
734            <CsparseMatrix>) added
735    
736    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * tests/matprod.R: add a variation of Harri's example
739    
740            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
741            recursive infinitely.
742    
743            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
744    
745            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
746    
747    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
750            matrix if possible; test m+m == 2*m; now test dgRMatrix.
751            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
752            satisfy the above test.
753    
754    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
757    
758            * R/dgCMatrix.R: solve(a, b="missing") based on
759            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
760            RHS = NULL.
761    
762            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
763            add more (needed) [t]crossprod() methods.
764    
765            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
766    
767            * R/Auxiliaries.R (as_CspClass): cleanup
768            (drop0): internal utility for "Csparse_drop(*, 0)"
769            (.bail.out.2): encourage active feedback
770    
771    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/dMatrix.R(Compare): new(), then slots [no validity check]
774    
775            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
776            non-valid or 'sorted' case).
777    
778            * R/dsparseMatrix.R: add "chol" method.
779            * R/ddenseMatrix.R: ditto
780    
781            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
782            * NAMESPACE (Ops)
783            * R/diagMatrix.R (diag2T): simple utility used "higher level"
784            coercion; deprecating direct lower level coercions.
785    
786            * R/*.R (seq): use seq_len() and seq_along() where possible.
787    
788    
789    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * DESCRIPTION (Version): 0.9975-5 ready for release
792    
793    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
794    
795            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
796    
797    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/AllClass.R (corMatrix): add 'validity' check;
800                    comment out unused "LDL" class definition
801            * NAMESPACE: mention, but do not export "LDL" class
802            * R/corMatrix.R: new (simple), needed for R-devel with
803            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
804              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
805    
806    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
807    
808            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
809            use Rprintf and R's error handling.
810    
811    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
814            * tests/matprod.R: add tests for the bug fixed.
815    
816    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
817    
818            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
819            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
820    
821    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
822    
823            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
824    
825    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
826    
827            * DESCRIPTION (Version): 0.9975-3
828    
829            * R/diagMatrix.R (bdiag): new function constructing block diagonal
830            (sparse) matrices.
831            * man/bdiag.Rd: docu + examples
832    
833            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
834    
835            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
836            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
837    
838            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
839            that result is sparse or diagonal (and not dense).
840    
841            * man/Subassign-methods.Rd: fix examples
842    
843            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
844            should always return a sparse (and not sometimes a diagonal) matrix.
845    
846    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
849    
850    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
851    
852            * DESCRIPTION (Version): 0.9975-2
853    
854            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
855    
856    2006-10-02  Douglas Bates  <bates@R-project.org>
857    
858            * tests/dg_Matrix.R: Simplify test taking into account new code.
859    
860    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
863    
864            * R/lsTMatrix.R: new files w/ missing methods
865            * R/nsTMatrix.R:  "  'for completeness'
866    
867            * tests/Class+Meth.R: a bit less 'not.ok.classes'
868    
869            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
870    
871    
872    2006-09-28  Douglas Bates  <bates@R-project.org>
873    
874            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
875            included.
876    
877            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
878            Export C-callable functions used in Zt_create in lme4.
879    
880    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * DESCRIPTION (Version): 0.9975-1
883    
884            * tests/simple.R: less checks fail; using NA, found that our
885                    kronecker() is not base-compatible with NA's.
886    
887            * R/dMatrix.R: "Compare" method now implemented for all cases
888    
889            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
890    
891            * man/dtpMatrix-class.Rd: mention length of 'x' slot
892    
893            * src/dtpMatrix.c (dtpMatrix_validate): fix check
894            * src/dspMatrix.c (dspMatrix_validate): ditto
895    
896            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
897              including coercion to [nl]tTMatrix.
898    
899            * R/diagMatrix.R (show): print a header line as for other classes.
900    
901    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * src/Makefile.win (SUBDIRS): fix typo
904    
905    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
908    
909    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
910    
911            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
912            symmetric and y missing in R code using %*% (cholmod_aat doesn't
913            accept a symmetric matrix).
914            * tests/group-methods.R: Uncomment test of crossprod applied to
915            lsCMatrix objects.
916    
917    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * R/AllClass.R (symmetricMatrix): add validity method (available
920            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
921    
922            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
923    
924            * tests/indexing.Rout.save:
925            * tests/indexing.R: additions, mainly for 'lsparse'
926    
927            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
928            case.
929    
930            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
931    
932    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
935                    as 'N' (1-letter - Ok?)
936    
937            * tests/group-methods.R: add test for logical + NAs
938    
939            * R/dMatrix.R ("Compare"): fix to work with NA's
940    
941            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
942    
943            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
944                    which is implemented.
945    
946    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * src/chm_common.c: coerce logical <-> double instead of
949            typecasting;  needed for "l" matrix handling in cholmod.
950    
951            * tests/other-pkgs.R (graph): small extension in "graph" checks.
952    
953            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
954            (Tsp2grNEL): other fixes needed
955    
956  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 962 
962          * tests/: adaptions          * tests/: adaptions
963          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
964                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
965          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
966    
967  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
968    
# Line 26  Line 981 
981          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
982    
983          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
984          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
985    
986  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
987    
# Line 69  Line 1024 
1024    
1025          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1026          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1027          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1028          * R/Csparse.R: dito          * R/Csparse.R: ditto
1029    
1030  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1031    
# Line 86  Line 1041 
1041    
1042          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1043          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1044          (.is.diagonal): dito          (.is.diagonal): ditto
1045    
1046          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1047    

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