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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 1975, Mon Jul 9 20:52:50 2007 UTC
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1    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
4              to fix a subtle bug (Kurt Hornik and Ingo Feinerer)
5    
6    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
7    
8            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
9              solve the bug
10    
11    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * src/dgCMatrix.c (compressed_to_TMatrix):
14    
15    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/Csparse.c (Rsparse_validate): new, to have some validity
18            checking for RsparseMatrix
19            * src/dgCMatrix.c (xRMatrix_validate): ditto
20            * src/dtCMatrix.c (tRMatrix_validate): ditto
21    
22    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
23    
24            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
25              lgRMatrix
26            * [r4568] DESCRIPTION: Prepare for bug-fix release
27            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
28              for declaration of cholmod_symmetry
29    
30    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
33            release.
34    
35    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
36    
37            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
38              functions - no longer used
39            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
40              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
41              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
42              Alloca
43    
44    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
45    
46            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
47              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
48              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
49              src/t_gCMatrix_colSums.c: more R_CheckStack()s
50    
51    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
52    
53            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
54              the required amount of memory then call M_numeric_as_chm_dense.
55            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
56              (like Calloc but calling alloca)
57    
58    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
61            and extended with more sophisticated 'col.names' option.
62            * NAMESPACE: export  printSparseMatrix()
63            * man/printSpMatrix.Rd: document, incl. examples
64    
65    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
68              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
69              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
70    
71    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * DESCRIPTION (Version): 0.99875-4
74    
75            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
76            some dimnames perservation.
77    
78            * R/dsTMatrix.R (t-method): keep dimnames
79            * R/dtTMatrix.R:  ditto
80    
81            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
82            and ncol(.) < 10
83    
84            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
85            from Mutils.h
86    
87            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
88            e.g. in as(<ngCMatrix>, "matrix")
89    
90    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
91    
92            * [r4529] .: Create a branch for the API changes from the 0.99875
93              series to the 0.999375 series
94            * [r4530] DESCRIPTION, inst/include/Matrix.h,
95              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
96              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
97              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
98              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
99              as_cholmod_x functions
100    
101    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
102    
103            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
104              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
105              to Comparisons
106    
107    >>>>>>> .merge-right.r4561
108    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * DESCRIPTION (Version): 0.99875-3 ready to be released.
111    
112            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
113    
114            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
115            that should also work in a future version of R.
116    
117    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
120    
121            * R/sparseVector.R: more *sparseVector coercions, notably for
122            non - double ones.
123    
124    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
127              notably the new ones building on the new .Call(.)s:
128    
129            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
130            all 4 of [dlin]gCMatrix_colSums().
131    
132    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
133    
134            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
135            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
136              result
137    
138    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/kronecker.R: fix typo (could lead to inf.recursion)
141            * test/simple.R: testing that
142    
143            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
144            method as well (which can have arguments, show() can't).
145    
146    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
147    
148            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
149              added dgCMatrix_colSums for [col,row][Sums,Means]
150    
151    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
152    
153            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
154              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
155              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
156            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
157              class
158            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
159              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
160              row names to store the levels - duh!  Added an example.
161    
162    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * src/Csparse.c (Csparse_validate): check for *repeated* entries
165            thanks to example from Christian Buchta; with a test here:
166            * tests/simple.R:
167    
168    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
171            of colSums(*, sparseResult = TRUE)
172    
173    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
176            'na.rm = FALSE' as "everywhere" else in R.
177    
178    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
179    
180            * [r4421] src/CSparse_install.sh: Modify for new organization of
181              CSparse package
182            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
183              SuiteSparse
184            * [r4426] src/Makefile: add ./UFconfig to the include path for
185              compilation
186            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
187            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
188              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
189    
190    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
193            * R/sparseMatrix.R (prSpMatrix): now gives a message about
194            suppressed column names.
195    
196    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
197    
198            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
199              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
200              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
201              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
202              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
203              Remove warnings after change to const char* CHAR
204    
205    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
206    
207            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
208              type of M_cholmod_ssmult
209    
210    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
211    
212            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
213              src/init.c: Yet another cholmod export - cholmod_ssmult
214    
215    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * NAMESPACE: exported drop0(), since
218            * man/drop0.Rd: I have seen several cases, I really wanted to use
219            it, so our users may want too.
220    
221    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * man/colSums.Rd: separately document colSums() etc, since these
224            have the extra argument 'sparseResult'.
225    
226    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
229            * man/spMatrix.Rd: docu., including examples
230    
231            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
232            in order to make colMeans() etc fast *and* correct.
233            * R/sparseVector.R (replSPvec): "[<-" functionality for
234            sparseVectors; tested in
235            * tests/simple.R:
236    
237    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
240            (very) sparse Matrices; output similar to Matlab's print().
241    
242    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
245            0-based, indices (Jose Quesada <quesada@gmail.com>).
246    
247    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
248    
249            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
250    
251    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Auxiliaries.R (sparsapply): new utility, much faster than
254            tapply1() for large sparse matrices.
255    
256    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/Matrix.R (dim<-): reshape now via sparseVector.
259    
260            * R/sparseVector.R: methods and function for
261            * R/AllClass.R: new "sparseVector" class and daughters.
262            * NAMESPACE: export new classes
263    
264    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * DESCRIPTION (Version): 0.99875-1
267            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
268    
269    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
272            indexing
273            * tests/indexing.R: test set for that.
274    
275    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
278            entries.
279            * tests/indexing.R(out): add regression test for it
280    
281    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
284            name for "!" method definitions.
285    
286    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/Tsparse.R (intI): new utility, used for "[" :
289                    Cleanup up there, and fixes for duplicated indices - more TODO!
290    
291            * tests/indexing.R(out): more tests
292    
293    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
294    
295            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
296            code that is now part of the R Lapack library.
297    
298            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
299            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
300    
301    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
304    
305    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
308            up with extraneous names '0'...'<n-1>'
309    
310    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/dgTMatrix.R (mat2dgT): care about NAs
313    
314    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/kronecker.R: triangularity preserving methods
317    
318    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/kronecker.R: new file collecting kronecker() methods in one
321                    place.  Goal: become much faster!
322    
323    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
326            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
327            can be much faster.
328    
329            * tests/matprod.R: add regression tests for these (upper & lower).
330    
331    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/Matrix.R (diff): method for our Matrices.
334    
335            * R/sparseMatrix.R (isDiagonal): check dim()!
336    
337    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * R/Matrix.R (dim<-): new method for "reshape()" built on a
340            proposal from Tamas Papp.
341    
342    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
345    
346            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
347            rather define and export  cBind() and rBind() only.
348            --> useRs *must* change code that used to have cbind()/rbind() !!
349    
350            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
351            * R/bind.Rout.save: ditto
352    
353    2007-02-16  Douglas Bates  <bates@r-project.org>
354    
355            * DESCRIPTION (Date, Version): 0.9975-11 with new date
356            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
357            const modifier on declaration of the array 'valid'
358    
359    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
362    
363    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
366    
367            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
368            * tests/simple.R: test the above and some of these coercions:
369    
370            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
371                    be careful to avoid infinite recursion, using new coercions in
372            * R/ngCMatrix.R and nsC... and ntC...
373            * R/lsparseMatrix.R: ditto
374    
375            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
376    
377            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
378            * R/Rsparse.R: reactivate .Call()s
379    
380            * tests/Class+Meth.R: a bit more on actual classes
381    
382    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
383    
384            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
385    
386    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * DESCRIPTION (Version): 0.9975-10 to upload
389    
390            * tests/Class+Meth.R (tstMatrixClass): require coercions to
391            specific classes less unconditionally.
392    
393            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
394    
395            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
396    
397            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
398            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
399            R_to_CMatrix segfaults on one platform.
400            Eliminate most coercion method to *specific* classes, and replace
401            with virtual classes coercions.
402    
403    
404    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
405    
406            * src/init.c: export the CHM...._validate() placeholders, since
407            they *are* called.
408    
409            * tests/Class+Meth.R (classCanCoerce): and starting to test
410            all as(<from>, <to>)
411    
412    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
415            * tests/indexing.R: tested now
416            * tests/indexing.Rout.save: updated
417    
418            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
419            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
420            appropriate.
421    
422            * NAMESPACE: export a trivial
423            * R/Matrix.R: drop() Matrix-method
424    
425            * R/AllClass.R: moved all prototypes to virtual super classes.
426    
427            * R/Rsparse.R: many more coercions to have less exceptions in
428            * tests/Class+Meth.R:
429    
430            * R/Ops.R (Compare): tweak for case with NA
431            * tests/simpl.R: hence another 'FIXME' eliminated
432    
433    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
434    
435            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
436            objects.
437    
438            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
439              and more of "!", "&", "|", all, any; coercions
440    
441            * R/Rsparse.R: many coercions (which enable quite a few other
442            methods), thanks to enhancements in
443            * src/dgCMatrix.c (R_to_CMatrix): new, and
444            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
445            symmetric & triangular and ..RMatrix objects.
446    
447            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
448            renamed file from src/dsTMatrix.c;
449            now dealing with symmetric and triangular Tsparse coercions, both
450            to dense and general.
451    
452    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
455    
456            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
457            where sensible when the <numeric> is of length > 1.
458    
459    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/Matrix.R ([<-): for M[] <- value: fix length
462    
463    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
466            * R/ndenseMatrix.R: new coercions n* -> l*
467    
468    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
469    
470            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
471    
472            * R/Ops.R ("Logic"): and other "Ops", many updates
473    
474    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * src/Mutils.h (SET_DimNames): new utility
477    
478            * R/Auxiliaries.R (nnzero): improved and now exported via
479    
480            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
481    
482    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
483    
484            * R/diagMatrix.R (!): fix typo.
485    
486    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/Auxiliaries.R (as_Csparse): and quite a few others:
489                    allow to pass class definition --> speedup
490            * R/sparseMatrix.R: apply the above
491    
492            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
493    
494            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
495            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
496            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
497    
498            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
499    
500            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
501            and use it for "sparse*" as well, since it's faster than the
502            as_Csparse(.) way.
503    
504    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
507    
508    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
511            as method for   M[ ij ] <- v
512            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
513    
514            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
515            FALSE answer
516    
517            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
518            * tests/indexing.R: test it, and some of the above
519    
520    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * R/Auxiliaries.R (is_duplicatedT): new utility
523    
524    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
525    
526            * src/init.c (R_init_Matrix): export cholmod_scale
527    
528    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
531            base::as.matrix to (x, ...)
532    
533    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
536            file; start using "Logic", hence
537    
538            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
539            * NAMESPACE: import and export "Logic"
540    
541    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
542    
543            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
544            only needed previously to R version 2.5.0.
545    
546    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
549    
550            * R/Tsparse.R (replTmat): fix subassignment of triangular
551            * R/Csparse.R (replCmat): ditto
552            * tests/indexing.R: more tests, incl the above fix
553    
554    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * R/Auxiliaries.R (drop0): extend for non CSparse
557            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
558    
559            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
560                    use uplo correctly (!); other places: use uplo_P() macro
561    
562            * R/Csparse.R (replCmat): call diagU2N() when needed
563            * R/Tsparse.R (replTmat): ditto
564    
565            * src/dtCMatrix.c (tCMatrix_validate): new
566            * src/dtTMatrix.c (tTMatrix_validate): new, used in
567            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
568    
569            * R/diagMatrix.R (replDiag): to use in [<-
570    
571    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
574                    also more general diagU2N().
575    
576    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
579            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
580    
581    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * tests/bind.R: a few more cases
584            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
585    
586            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
587            * R/ddenseMatrix.R (cbind2/rbind2)
588            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
589            * tests/indexing.R
590            * tests/indexing.Rout.save: updated
591    
592    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
595            * tests/indexing.R
596    
597    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
600            align with proper position of "0", i.e., right for integers.
601            argument 'align' by default is "fancy".
602    
603    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
606            * R/Csparse.R: and fix "Compare" for more cases.
607            * tests/Class+Meth.R: test some of these (m == m, m != m)
608    
609    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/lsparseMatrix.R: all() and any() methods
612            * R/ldenseMatrix.R:      ditto
613            * NAMESPACE, R/Matrix.R: ditto
614    
615            * man/all-methods.Rd: document them minimally
616    
617            * tests/simple.R: add a few examples for these
618    
619    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/Tsparse.R ([): fix long standing typo in symmetric case
622            * man/dsCMatrix-class.Rd: add example exhibiting the above case
623    
624    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
625    
626            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
627            to LL before converting to a sparse matrix. (The LDL form can be
628            converted to a sparse matrix but it is implicitly a unit
629            triangular matrix and a diagonal matrix overwritten on the diagonal.)
630    
631    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
632    
633            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
634    
635    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
636    
637            * DESCRIPTION (Version): updated -> release 0.9975-7
638            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
639    
640    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
643    
644    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
645    
646            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
647            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
648            is exactly singular.
649    
650    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * DESCRIPTION (Date): updated -> release 0.9975-6
653    
654    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
657            now returns symmetric.
658    
659            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
660    
661            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
662            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
663    
664            * R/Auxiliaries.R (.type.kind): added
665    
666    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
669            running src/CSparse_install.sh
670    
671            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
672    
673    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
674    
675            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
676            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
677    
678            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
679    
680            * tests/Class+Meth.R (tstMatrixClass): now assure
681            the (important in method programming) property :
682    
683                    ###>>  Every "Matrix" is either
684                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
685    
686                    (where "*" stands for "Matrix")
687    
688            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
689    
690            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
691            * tests/validObj.R: checks for "comparison"
692    
693            * R/sparseMatrix.R ([): improved indexing for sparse;
694                    trying to keep <symmetric>[ n, n] symmmetric
695    
696            * tests/indexing.R: indexing for logical sparse now ok
697    
698    
699    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * src/Tsparse.c: use xTsparse_validate() , and hence remove
702    
703            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
704    
705    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
708    
709            * tests/simple.R: validObject() checking the above.
710    
711            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
712            replacing both dgCMatrix_validate and lgCM*.
713    
714            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
715            fix dimnames setting in other places.
716            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
717    
718    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
721    
722            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
723            symmetry test, via
724            * R/Auxiliaries.R (.as.dgC.0.factors):
725    
726    2006-11-01  Douglas Bates  <bates@r-project.org>
727    
728            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
729            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
730            <CsparseMatrix>) added
731    
732    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * tests/matprod.R: add a variation of Harri's example
735    
736            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
737            recursive infinitely.
738    
739            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
740    
741            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
742    
743    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
746            matrix if possible; test m+m == 2*m; now test dgRMatrix.
747            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
748            satisfy the above test.
749    
750    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
753    
754            * R/dgCMatrix.R: solve(a, b="missing") based on
755            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
756            RHS = NULL.
757    
758            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
759            add more (needed) [t]crossprod() methods.
760    
761            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
762    
763            * R/Auxiliaries.R (as_CspClass): cleanup
764            (drop0): internal utility for "Csparse_drop(*, 0)"
765            (.bail.out.2): encourage active feedback
766    
767    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/dMatrix.R(Compare): new(), then slots [no validity check]
770    
771            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
772            non-valid or 'sorted' case).
773    
774            * R/dsparseMatrix.R: add "chol" method.
775            * R/ddenseMatrix.R: ditto
776    
777            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
778            * NAMESPACE (Ops)
779            * R/diagMatrix.R (diag2T): simple utility used "higher level"
780            coercion; deprecating direct lower level coercions.
781    
782            * R/*.R (seq): use seq_len() and seq_along() where possible.
783    
784    
785    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * DESCRIPTION (Version): 0.9975-5 ready for release
788    
789    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
790    
791            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
792    
793    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/AllClass.R (corMatrix): add 'validity' check;
796                    comment out unused "LDL" class definition
797            * NAMESPACE: mention, but do not export "LDL" class
798            * R/corMatrix.R: new (simple), needed for R-devel with
799            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
800              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
801    
802    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
803    
804            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
805            use Rprintf and R's error handling.
806    
807    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
810            * tests/matprod.R: add tests for the bug fixed.
811    
812    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
813    
814            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
815            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
816    
817    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
818    
819            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
820    
821    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * DESCRIPTION (Version): 0.9975-3
824    
825            * R/diagMatrix.R (bdiag): new function constructing block diagonal
826            (sparse) matrices.
827            * man/bdiag.Rd: docu + examples
828    
829            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
830    
831            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
832            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
833    
834            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
835            that result is sparse or diagonal (and not dense).
836    
837            * man/Subassign-methods.Rd: fix examples
838    
839            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
840            should always return a sparse (and not sometimes a diagonal) matrix.
841    
842    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
845    
846    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
847    
848            * DESCRIPTION (Version): 0.9975-2
849    
850            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
851    
852    2006-10-02  Douglas Bates  <bates@R-project.org>
853    
854            * tests/dg_Matrix.R: Simplify test taking into account new code.
855    
856    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
857    
858            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
859    
860            * R/lsTMatrix.R: new files w/ missing methods
861            * R/nsTMatrix.R:  "  'for completeness'
862    
863            * tests/Class+Meth.R: a bit less 'not.ok.classes'
864    
865            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
866    
867    
868    2006-09-28  Douglas Bates  <bates@R-project.org>
869    
870            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
871            included.
872    
873            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
874            Export C-callable functions used in Zt_create in lme4.
875    
876    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
877    
878            * DESCRIPTION (Version): 0.9975-1
879    
880            * tests/simple.R: less checks fail; using NA, found that our
881                    kronecker() is not base-compatible with NA's.
882    
883            * R/dMatrix.R: "Compare" method now implemented for all cases
884    
885            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
886    
887            * man/dtpMatrix-class.Rd: mention length of 'x' slot
888    
889            * src/dtpMatrix.c (dtpMatrix_validate): fix check
890            * src/dspMatrix.c (dspMatrix_validate): ditto
891    
892            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
893              including coercion to [nl]tTMatrix.
894    
895            * R/diagMatrix.R (show): print a header line as for other classes.
896    
897    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * src/Makefile.win (SUBDIRS): fix typo
900    
901    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
904    
905    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
906    
907            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
908            symmetric and y missing in R code using %*% (cholmod_aat doesn't
909            accept a symmetric matrix).
910            * tests/group-methods.R: Uncomment test of crossprod applied to
911            lsCMatrix objects.
912    
913    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * R/AllClass.R (symmetricMatrix): add validity method (available
916            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
917    
918            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
919    
920            * tests/indexing.Rout.save:
921            * tests/indexing.R: additions, mainly for 'lsparse'
922    
923            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
924            case.
925    
926            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
927    
928    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
931                    as 'N' (1-letter - Ok?)
932    
933            * tests/group-methods.R: add test for logical + NAs
934    
935            * R/dMatrix.R ("Compare"): fix to work with NA's
936    
937            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
938    
939            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
940                    which is implemented.
941    
942    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * src/chm_common.c: coerce logical <-> double instead of
945            typecasting;  needed for "l" matrix handling in cholmod.
946    
947            * tests/other-pkgs.R (graph): small extension in "graph" checks.
948    
949            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
950            (Tsp2grNEL): other fixes needed
951    
952    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
955                    Matrices, since "lMatrix", also "lsparseM" can have NA
956            * R/ndenseMatrix.R, etc: new source files
957            * man/nsparseMatrix-classes.Rd, etc: new help files
958            * tests/: adaptions
959            * src/chm_common.c (chm_dense_to_SEXP): and others:
960                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
961            * src/Csparse.c, etc: ditto
962    
963    2006-09-11  Douglas Bates  <bates@R-project.org>
964    
965            * src/Mutils.[ch],init.c inst/include/*.h: Move the
966            alloc_d**Matrix functions to the lme4 package.
967    
968    2006-09-09  Douglas Bates  <bates@R-project.org>
969    
970            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
971            fixed
972    
973    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * R/lMatrix.R: new
976    
977            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
978    
979            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
980            * man/tcrossprod.Rd: ditto
981    
982    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
983    
984            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
985            for exported functions
986            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
987            Remove partitioning algorithms for sparse matrix reordering.  The
988            copyright on the Metis code was problematic and the methods were
989            rarely used.
990            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
991            operations are now done entirely in CHOLMOD code.
992    
993    2006-09-06  Douglas Bates  <bates@R-project.org>
994    
995            * src/Mutils.h: Remove functions that are no longer used.
996    
997  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
998    
999          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 1020 
1020    
1021          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1022          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1023          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1024          * R/Csparse.R: dito          * R/Csparse.R: ditto
1025    
1026  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
# Line 41  Line 1037 
1037    
1038          * 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
1039          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1040          (.is.diagonal): dito          (.is.diagonal): ditto
1041    
1042          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1043    

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