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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 2008, Thu Jul 19 19:47:59 2007 UTC
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1    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
4              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
5              triplet_to_sparse, documentation, use typedefs
6    
7    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * man/dpoMatrix-class.Rd: added 'corMatrix' example
10    
11            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
12            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
13            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
14    
15            * R/lsparseMatrix.R: bug fix in "all" method
16            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
17    
18            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
19            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
20                    + matrix |-> nMatrix coercion
21            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
22            * man/pMatrix-class.Rd: ditto
23    
24            * R/Matrix.R (Summary): method for non-dMatrix
25    
26            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
27            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
28                    test all Summary methods.
29    
30    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
33    
34    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
37    
38            * R/pMatrix.R (t?crossprod): methods for pMatrix
39    
40    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
41    
42            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
43    
44    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
45    
46            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
47              trying to fix a subtle bug - which has been somewhere else.
48    
49    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
50    
51            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
52              solve the bug
53    
54    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * src/dgCMatrix.c (compressed_to_TMatrix):
57    
58    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * src/Csparse.c (Rsparse_validate): new, to have some validity
61            checking for RsparseMatrix
62            * src/dgCMatrix.c (xRMatrix_validate): ditto
63            * src/dtCMatrix.c (tRMatrix_validate): ditto
64    
65    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
68              lgRMatrix
69            * [r4568] DESCRIPTION: Prepare for bug-fix release
70            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
71              for declaration of cholmod_symmetry
72    
73    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
76            release.
77    
78    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
79    
80            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
81              functions - no longer used
82            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
83              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
84              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
85              Alloca
86    
87    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
88    
89            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
90              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
91              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
92              src/t_gCMatrix_colSums.c: more R_CheckStack()s
93    
94    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
95    
96            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
97              the required amount of memory then call M_numeric_as_chm_dense.
98            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
99              (like Calloc but calling alloca)
100    
101    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
104            and extended with more sophisticated 'col.names' option.
105            * NAMESPACE: export  printSparseMatrix()
106            * man/printSpMatrix.Rd: document, incl. examples
107    
108    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
109    
110            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
111              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
112              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
113    
114    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.99875-4
117    
118            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
119            some dimnames perservation.
120    
121            * R/dsTMatrix.R (t-method): keep dimnames
122            * R/dtTMatrix.R:  ditto
123    
124            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
125            and ncol(.) < 10
126    
127            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
128            from Mutils.h
129    
130            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
131            e.g. in as(<ngCMatrix>, "matrix")
132    
133    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
134    
135            * [r4529] .: Create a branch for the API changes from the 0.99875
136              series to the 0.999375 series
137            * [r4530] DESCRIPTION, inst/include/Matrix.h,
138              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
139              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
140              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
141              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
142              as_cholmod_x functions
143    
144    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
145    
146            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
147              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
148              to Comparisons
149    
150    >>>>>>> .merge-right.r4561
151    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * DESCRIPTION (Version): 0.99875-3 ready to be released.
154    
155            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
156    
157            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
158            that should also work in a future version of R.
159    
160    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
163    
164            * R/sparseVector.R: more *sparseVector coercions, notably for
165            non - double ones.
166    
167    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
170              notably the new ones building on the new .Call(.)s:
171    
172            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
173            all 4 of [dlin]gCMatrix_colSums().
174    
175    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
176    
177            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
178            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
179              result
180    
181    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/kronecker.R: fix typo (could lead to inf.recursion)
184            * test/simple.R: testing that
185    
186            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
187            method as well (which can have arguments, show() can't).
188    
189    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
190    
191            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
192              added dgCMatrix_colSums for [col,row][Sums,Means]
193    
194    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
195    
196            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
197              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
198              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
199            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
200              class
201            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
202              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
203              row names to store the levels - duh!  Added an example.
204    
205    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * src/Csparse.c (Csparse_validate): check for *repeated* entries
208            thanks to example from Christian Buchta; with a test here:
209            * tests/simple.R:
210    
211    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
214            of colSums(*, sparseResult = TRUE)
215    
216    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
219            'na.rm = FALSE' as "everywhere" else in R.
220    
221    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
222    
223            * [r4421] src/CSparse_install.sh: Modify for new organization of
224              CSparse package
225            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
226              SuiteSparse
227            * [r4426] src/Makefile: add ./UFconfig to the include path for
228              compilation
229            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
230            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
231              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
232    
233    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
236            * R/sparseMatrix.R (prSpMatrix): now gives a message about
237            suppressed column names.
238    
239    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
240    
241            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
242              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
243              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
244              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
245              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
246              Remove warnings after change to const char* CHAR
247    
248    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
249    
250            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
251              type of M_cholmod_ssmult
252    
253    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
254    
255            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
256              src/init.c: Yet another cholmod export - cholmod_ssmult
257    
258    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * NAMESPACE: exported drop0(), since
261            * man/drop0.Rd: I have seen several cases, I really wanted to use
262            it, so our users may want too.
263    
264    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * man/colSums.Rd: separately document colSums() etc, since these
267            have the extra argument 'sparseResult'.
268    
269    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
272            * man/spMatrix.Rd: docu., including examples
273    
274            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
275            in order to make colMeans() etc fast *and* correct.
276            * R/sparseVector.R (replSPvec): "[<-" functionality for
277            sparseVectors; tested in
278            * tests/simple.R:
279    
280    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
283            (very) sparse Matrices; output similar to Matlab's print().
284    
285    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
286    
287            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
288            0-based, indices (Jose Quesada <quesada@gmail.com>).
289    
290    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
291    
292            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
293    
294    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/Auxiliaries.R (sparsapply): new utility, much faster than
297            tapply1() for large sparse matrices.
298    
299    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/Matrix.R (dim<-): reshape now via sparseVector.
302    
303            * R/sparseVector.R: methods and function for
304            * R/AllClass.R: new "sparseVector" class and daughters.
305            * NAMESPACE: export new classes
306    
307    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * DESCRIPTION (Version): 0.99875-1
310            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
311    
312    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
315            indexing
316            * tests/indexing.R: test set for that.
317    
318    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
321            entries.
322            * tests/indexing.R(out): add regression test for it
323    
324    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
327            name for "!" method definitions.
328    
329    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Tsparse.R (intI): new utility, used for "[" :
332                    Cleanup up there, and fixes for duplicated indices - more TODO!
333    
334            * tests/indexing.R(out): more tests
335    
336    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
339            code that is now part of the R Lapack library.
340    
341            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
342            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
343    
344    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
347    
348    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
351            up with extraneous names '0'...'<n-1>'
352    
353    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * R/dgTMatrix.R (mat2dgT): care about NAs
356    
357    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/kronecker.R: triangularity preserving methods
360    
361    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/kronecker.R: new file collecting kronecker() methods in one
364                    place.  Goal: become much faster!
365    
366    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
369            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
370            can be much faster.
371    
372            * tests/matprod.R: add regression tests for these (upper & lower).
373    
374    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/Matrix.R (diff): method for our Matrices.
377    
378            * R/sparseMatrix.R (isDiagonal): check dim()!
379    
380    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Matrix.R (dim<-): new method for "reshape()" built on a
383            proposal from Tamas Papp.
384    
385    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
388    
389            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
390            rather define and export  cBind() and rBind() only.
391            --> useRs *must* change code that used to have cbind()/rbind() !!
392    
393            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
394            * R/bind.Rout.save: ditto
395    
396    2007-02-16  Douglas Bates  <bates@r-project.org>
397    
398            * DESCRIPTION (Date, Version): 0.9975-11 with new date
399            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
400            const modifier on declaration of the array 'valid'
401    
402    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
403    
404            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
405    
406    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
409    
410            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
411            * tests/simple.R: test the above and some of these coercions:
412    
413            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
414                    be careful to avoid infinite recursion, using new coercions in
415            * R/ngCMatrix.R and nsC... and ntC...
416            * R/lsparseMatrix.R: ditto
417    
418            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
419    
420            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
421            * R/Rsparse.R: reactivate .Call()s
422    
423            * tests/Class+Meth.R: a bit more on actual classes
424    
425    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
426    
427            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
428    
429    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * DESCRIPTION (Version): 0.9975-10 to upload
432    
433            * tests/Class+Meth.R (tstMatrixClass): require coercions to
434            specific classes less unconditionally.
435    
436            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
437    
438            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
439    
440            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
441            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
442            R_to_CMatrix segfaults on one platform.
443            Eliminate most coercion method to *specific* classes, and replace
444            with virtual classes coercions.
445    
446    
447    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
448    
449            * src/init.c: export the CHM...._validate() placeholders, since
450            they *are* called.
451    
452            * tests/Class+Meth.R (classCanCoerce): and starting to test
453            all as(<from>, <to>)
454    
455    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
458            * tests/indexing.R: tested now
459            * tests/indexing.Rout.save: updated
460    
461            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
462            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
463            appropriate.
464    
465            * NAMESPACE: export a trivial
466            * R/Matrix.R: drop() Matrix-method
467    
468            * R/AllClass.R: moved all prototypes to virtual super classes.
469    
470            * R/Rsparse.R: many more coercions to have less exceptions in
471            * tests/Class+Meth.R:
472    
473            * R/Ops.R (Compare): tweak for case with NA
474            * tests/simpl.R: hence another 'FIXME' eliminated
475    
476    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
479            objects.
480    
481            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
482              and more of "!", "&", "|", all, any; coercions
483    
484            * R/Rsparse.R: many coercions (which enable quite a few other
485            methods), thanks to enhancements in
486            * src/dgCMatrix.c (R_to_CMatrix): new, and
487            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
488            symmetric & triangular and ..RMatrix objects.
489    
490            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
491            renamed file from src/dsTMatrix.c;
492            now dealing with symmetric and triangular Tsparse coercions, both
493            to dense and general.
494    
495    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
498    
499            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
500            where sensible when the <numeric> is of length > 1.
501    
502    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/Matrix.R ([<-): for M[] <- value: fix length
505    
506    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
509            * R/ndenseMatrix.R: new coercions n* -> l*
510    
511    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
512    
513            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
514    
515            * R/Ops.R ("Logic"): and other "Ops", many updates
516    
517    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
518    
519            * src/Mutils.h (SET_DimNames): new utility
520    
521            * R/Auxiliaries.R (nnzero): improved and now exported via
522    
523            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
524    
525    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/diagMatrix.R (!): fix typo.
528    
529    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/Auxiliaries.R (as_Csparse): and quite a few others:
532                    allow to pass class definition --> speedup
533            * R/sparseMatrix.R: apply the above
534    
535            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
536    
537            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
538            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
539            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
540    
541            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
542    
543            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
544            and use it for "sparse*" as well, since it's faster than the
545            as_Csparse(.) way.
546    
547    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
550    
551    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
554            as method for   M[ ij ] <- v
555            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
556    
557            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
558            FALSE answer
559    
560            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
561            * tests/indexing.R: test it, and some of the above
562    
563    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/Auxiliaries.R (is_duplicatedT): new utility
566    
567    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
568    
569            * src/init.c (R_init_Matrix): export cholmod_scale
570    
571    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
574            base::as.matrix to (x, ...)
575    
576    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
579            file; start using "Logic", hence
580    
581            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
582            * NAMESPACE: import and export "Logic"
583    
584    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
587            only needed previously to R version 2.5.0.
588    
589    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
592    
593            * R/Tsparse.R (replTmat): fix subassignment of triangular
594            * R/Csparse.R (replCmat): ditto
595            * tests/indexing.R: more tests, incl the above fix
596    
597    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Auxiliaries.R (drop0): extend for non CSparse
600            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
601    
602            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
603                    use uplo correctly (!); other places: use uplo_P() macro
604    
605            * R/Csparse.R (replCmat): call diagU2N() when needed
606            * R/Tsparse.R (replTmat): ditto
607    
608            * src/dtCMatrix.c (tCMatrix_validate): new
609            * src/dtTMatrix.c (tTMatrix_validate): new, used in
610            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
611    
612            * R/diagMatrix.R (replDiag): to use in [<-
613    
614    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
617                    also more general diagU2N().
618    
619    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
622            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
623    
624    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * tests/bind.R: a few more cases
627            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
628    
629            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
630            * R/ddenseMatrix.R (cbind2/rbind2)
631            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
632            * tests/indexing.R
633            * tests/indexing.Rout.save: updated
634    
635    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
636    
637            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
638            * tests/indexing.R
639    
640    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
643            align with proper position of "0", i.e., right for integers.
644            argument 'align' by default is "fancy".
645    
646    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
649            * R/Csparse.R: and fix "Compare" for more cases.
650            * tests/Class+Meth.R: test some of these (m == m, m != m)
651    
652    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/lsparseMatrix.R: all() and any() methods
655            * R/ldenseMatrix.R:      ditto
656            * NAMESPACE, R/Matrix.R: ditto
657    
658            * man/all-methods.Rd: document them minimally
659    
660            * tests/simple.R: add a few examples for these
661    
662    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/Tsparse.R ([): fix long standing typo in symmetric case
665            * man/dsCMatrix-class.Rd: add example exhibiting the above case
666    
667    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
668    
669            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
670            to LL before converting to a sparse matrix. (The LDL form can be
671            converted to a sparse matrix but it is implicitly a unit
672            triangular matrix and a diagonal matrix overwritten on the diagonal.)
673    
674    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
675    
676            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
677    
678    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
679    
680            * DESCRIPTION (Version): updated -> release 0.9975-7
681            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
682    
683    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
686    
687    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
688    
689            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
690            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
691            is exactly singular.
692    
693    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * DESCRIPTION (Date): updated -> release 0.9975-6
696    
697    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
700            now returns symmetric.
701    
702            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
703    
704            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
705            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
706    
707            * R/Auxiliaries.R (.type.kind): added
708    
709    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
712            running src/CSparse_install.sh
713    
714            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
715    
716    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
719            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
720    
721            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
722    
723            * tests/Class+Meth.R (tstMatrixClass): now assure
724            the (important in method programming) property :
725    
726                    ###>>  Every "Matrix" is either
727                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
728    
729                    (where "*" stands for "Matrix")
730    
731            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
732    
733            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
734            * tests/validObj.R: checks for "comparison"
735    
736            * R/sparseMatrix.R ([): improved indexing for sparse;
737                    trying to keep <symmetric>[ n, n] symmmetric
738    
739            * tests/indexing.R: indexing for logical sparse now ok
740    
741    
742    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * src/Tsparse.c: use xTsparse_validate() , and hence remove
745    
746            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
747    
748    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
751    
752            * tests/simple.R: validObject() checking the above.
753    
754            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
755            replacing both dgCMatrix_validate and lgCM*.
756    
757            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
758            fix dimnames setting in other places.
759            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
760    
761    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
764    
765            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
766            symmetry test, via
767            * R/Auxiliaries.R (.as.dgC.0.factors):
768    
769    2006-11-01  Douglas Bates  <bates@r-project.org>
770    
771            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
772            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
773            <CsparseMatrix>) added
774    
775    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * tests/matprod.R: add a variation of Harri's example
778    
779            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
780            recursive infinitely.
781    
782            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
783    
784            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
785    
786    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
789            matrix if possible; test m+m == 2*m; now test dgRMatrix.
790            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
791            satisfy the above test.
792    
793    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
796    
797            * R/dgCMatrix.R: solve(a, b="missing") based on
798            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
799            RHS = NULL.
800    
801            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
802            add more (needed) [t]crossprod() methods.
803    
804            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
805    
806            * R/Auxiliaries.R (as_CspClass): cleanup
807            (drop0): internal utility for "Csparse_drop(*, 0)"
808            (.bail.out.2): encourage active feedback
809    
810    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * R/dMatrix.R(Compare): new(), then slots [no validity check]
813    
814            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
815            non-valid or 'sorted' case).
816    
817            * R/dsparseMatrix.R: add "chol" method.
818            * R/ddenseMatrix.R: ditto
819    
820            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
821            * NAMESPACE (Ops)
822            * R/diagMatrix.R (diag2T): simple utility used "higher level"
823            coercion; deprecating direct lower level coercions.
824    
825            * R/*.R (seq): use seq_len() and seq_along() where possible.
826    
827    
828    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * DESCRIPTION (Version): 0.9975-5 ready for release
831    
832  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
833    
834          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.

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