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revision 1624, Wed Oct 11 15:00:11 2006 UTC revision 2036, Mon Aug 6 12:03:47 2007 UTC
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1    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
4                    ("Matrix", "matrix") whish is needed in some cases.
5    
6            * src/dsyMatrix.c (dsyMatrix_matrix_mm): get @Dim of 'val', not
7            'b' which differs for 'matrix'
8    
9            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
10            infinite recursion in dispatch for some cases.
11    
12            * tests/matprod.R: test all of the above
13    
14    
15    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * DESCRIPTION (Date): set ready for release -- 0.999375-1
18    
19    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
20    
21            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
22              src/chm_common.c, src/chm_common.h: Change API for
23              numeric_as_chm_dense and N_AS_CHM_DN
24    
25    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
28            * tests/matprod.R: regr.test for it
29    
30    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
33            * tests/group-methods.R: and regression-test it
34    
35    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
36    
37            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
38              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
39              triplet_to_sparse, documentation, use typedefs
40    
41    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * man/dpoMatrix-class.Rd: added 'corMatrix' example
44    
45            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
46            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
47            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
48    
49            * R/lsparseMatrix.R: bug fix in "all" method
50            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
51    
52            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
53            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
54                    + matrix |-> nMatrix coercion
55            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
56            * man/pMatrix-class.Rd: ditto
57    
58            * R/Matrix.R (Summary): method for non-dMatrix
59    
60            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
61            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
62                    test all Summary methods.
63    
64    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
67    
68    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
71    
72            * R/pMatrix.R (t?crossprod): methods for pMatrix
73    
74    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
75    
76            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
77    
78    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
79    
80            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
81              trying to fix a subtle bug - which has been somewhere else.
82    
83    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
84    
85            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
86              solve the bug
87    
88    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
89    
90            * src/dgCMatrix.c (compressed_to_TMatrix):
91    
92    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * src/Csparse.c (Rsparse_validate): new, to have some validity
95            checking for RsparseMatrix
96            * src/dgCMatrix.c (xRMatrix_validate): ditto
97            * src/dtCMatrix.c (tRMatrix_validate): ditto
98    
99    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
100    
101            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
102              lgRMatrix
103            * [r4568] DESCRIPTION: Prepare for bug-fix release
104            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
105              for declaration of cholmod_symmetry
106    
107    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
110            release.
111    
112    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
113    
114            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
115              functions - no longer used
116            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
117              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
118              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
119              Alloca
120    
121    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
122    
123            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
124              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
125              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
126              src/t_gCMatrix_colSums.c: more R_CheckStack()s
127    
128    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
131              the required amount of memory then call M_numeric_as_chm_dense.
132            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
133              (like Calloc but calling alloca)
134    
135    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
138            and extended with more sophisticated 'col.names' option.
139            * NAMESPACE: export  printSparseMatrix()
140            * man/printSpMatrix.Rd: document, incl. examples
141    
142    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
143    
144            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
145              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
146              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
147    
148    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * DESCRIPTION (Version): 0.99875-4
151    
152            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
153            some dimnames perservation.
154    
155            * R/dsTMatrix.R (t-method): keep dimnames
156            * R/dtTMatrix.R:  ditto
157    
158            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
159            and ncol(.) < 10
160    
161            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
162            from Mutils.h
163    
164            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
165            e.g. in as(<ngCMatrix>, "matrix")
166    
167    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
168    
169            * [r4529] .: Create a branch for the API changes from the 0.99875
170              series to the 0.999375 series
171            * [r4530] DESCRIPTION, inst/include/Matrix.h,
172              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
173              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
174              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
175              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
176              as_cholmod_x functions
177    
178    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
179    
180            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
181              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
182              to Comparisons
183    
184    >>>>>>> .merge-right.r4561
185    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * DESCRIPTION (Version): 0.99875-3 ready to be released.
188    
189            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
190    
191            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
192            that should also work in a future version of R.
193    
194    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
197    
198            * R/sparseVector.R: more *sparseVector coercions, notably for
199            non - double ones.
200    
201    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
204              notably the new ones building on the new .Call(.)s:
205    
206            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
207            all 4 of [dlin]gCMatrix_colSums().
208    
209    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
210    
211            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
212            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
213              result
214    
215    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/kronecker.R: fix typo (could lead to inf.recursion)
218            * test/simple.R: testing that
219    
220            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
221            method as well (which can have arguments, show() can't).
222    
223    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
224    
225            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
226              added dgCMatrix_colSums for [col,row][Sums,Means]
227    
228    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
229    
230            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
231              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
232              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
233            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
234              class
235            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
236              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
237              row names to store the levels - duh!  Added an example.
238    
239    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * src/Csparse.c (Csparse_validate): check for *repeated* entries
242            thanks to example from Christian Buchta; with a test here:
243            * tests/simple.R:
244    
245    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
248            of colSums(*, sparseResult = TRUE)
249    
250    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
253            'na.rm = FALSE' as "everywhere" else in R.
254    
255    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
256    
257            * [r4421] src/CSparse_install.sh: Modify for new organization of
258              CSparse package
259            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
260              SuiteSparse
261            * [r4426] src/Makefile: add ./UFconfig to the include path for
262              compilation
263            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
264            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
265              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
266    
267    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
270            * R/sparseMatrix.R (prSpMatrix): now gives a message about
271            suppressed column names.
272    
273    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
274    
275            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
276              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
277              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
278              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
279              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
280              Remove warnings after change to const char* CHAR
281    
282    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
283    
284            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
285              type of M_cholmod_ssmult
286    
287    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
288    
289            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
290              src/init.c: Yet another cholmod export - cholmod_ssmult
291    
292    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * NAMESPACE: exported drop0(), since
295            * man/drop0.Rd: I have seen several cases, I really wanted to use
296            it, so our users may want too.
297    
298    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * man/colSums.Rd: separately document colSums() etc, since these
301            have the extra argument 'sparseResult'.
302    
303    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
306            * man/spMatrix.Rd: docu., including examples
307    
308            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
309            in order to make colMeans() etc fast *and* correct.
310            * R/sparseVector.R (replSPvec): "[<-" functionality for
311            sparseVectors; tested in
312            * tests/simple.R:
313    
314    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
317            (very) sparse Matrices; output similar to Matlab's print().
318    
319    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
320    
321            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
322            0-based, indices (Jose Quesada <quesada@gmail.com>).
323    
324    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
325    
326            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
327    
328    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Auxiliaries.R (sparsapply): new utility, much faster than
331            tapply1() for large sparse matrices.
332    
333    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Matrix.R (dim<-): reshape now via sparseVector.
336    
337            * R/sparseVector.R: methods and function for
338            * R/AllClass.R: new "sparseVector" class and daughters.
339            * NAMESPACE: export new classes
340    
341    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * DESCRIPTION (Version): 0.99875-1
344            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
345    
346    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
349            indexing
350            * tests/indexing.R: test set for that.
351    
352    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
355            entries.
356            * tests/indexing.R(out): add regression test for it
357    
358    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
361            name for "!" method definitions.
362    
363    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/Tsparse.R (intI): new utility, used for "[" :
366                    Cleanup up there, and fixes for duplicated indices - more TODO!
367    
368            * tests/indexing.R(out): more tests
369    
370    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
371    
372            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
373            code that is now part of the R Lapack library.
374    
375            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
376            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
377    
378    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
381    
382    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
385            up with extraneous names '0'...'<n-1>'
386    
387    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dgTMatrix.R (mat2dgT): care about NAs
390    
391    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/kronecker.R: triangularity preserving methods
394    
395    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/kronecker.R: new file collecting kronecker() methods in one
398                    place.  Goal: become much faster!
399    
400    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
403            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
404            can be much faster.
405    
406            * tests/matprod.R: add regression tests for these (upper & lower).
407    
408    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Matrix.R (diff): method for our Matrices.
411    
412            * R/sparseMatrix.R (isDiagonal): check dim()!
413    
414    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/Matrix.R (dim<-): new method for "reshape()" built on a
417            proposal from Tamas Papp.
418    
419    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
422    
423            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
424            rather define and export  cBind() and rBind() only.
425            --> useRs *must* change code that used to have cbind()/rbind() !!
426    
427            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
428            * R/bind.Rout.save: ditto
429    
430    2007-02-16  Douglas Bates  <bates@r-project.org>
431    
432            * DESCRIPTION (Date, Version): 0.9975-11 with new date
433            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
434            const modifier on declaration of the array 'valid'
435    
436    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
437    
438            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
439    
440    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
443    
444            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
445            * tests/simple.R: test the above and some of these coercions:
446    
447            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
448                    be careful to avoid infinite recursion, using new coercions in
449            * R/ngCMatrix.R and nsC... and ntC...
450            * R/lsparseMatrix.R: ditto
451    
452            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
453    
454            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
455            * R/Rsparse.R: reactivate .Call()s
456    
457            * tests/Class+Meth.R: a bit more on actual classes
458    
459    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
460    
461            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
462    
463    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * DESCRIPTION (Version): 0.9975-10 to upload
466    
467            * tests/Class+Meth.R (tstMatrixClass): require coercions to
468            specific classes less unconditionally.
469    
470            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
471    
472            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
473    
474            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
475            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
476            R_to_CMatrix segfaults on one platform.
477            Eliminate most coercion method to *specific* classes, and replace
478            with virtual classes coercions.
479    
480    
481    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
482    
483            * src/init.c: export the CHM...._validate() placeholders, since
484            they *are* called.
485    
486            * tests/Class+Meth.R (classCanCoerce): and starting to test
487            all as(<from>, <to>)
488    
489    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
490    
491            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
492            * tests/indexing.R: tested now
493            * tests/indexing.Rout.save: updated
494    
495            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
496            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
497            appropriate.
498    
499            * NAMESPACE: export a trivial
500            * R/Matrix.R: drop() Matrix-method
501    
502            * R/AllClass.R: moved all prototypes to virtual super classes.
503    
504            * R/Rsparse.R: many more coercions to have less exceptions in
505            * tests/Class+Meth.R:
506    
507            * R/Ops.R (Compare): tweak for case with NA
508            * tests/simpl.R: hence another 'FIXME' eliminated
509    
510    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
513            objects.
514    
515            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
516              and more of "!", "&", "|", all, any; coercions
517    
518            * R/Rsparse.R: many coercions (which enable quite a few other
519            methods), thanks to enhancements in
520            * src/dgCMatrix.c (R_to_CMatrix): new, and
521            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
522            symmetric & triangular and ..RMatrix objects.
523    
524            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
525            renamed file from src/dsTMatrix.c;
526            now dealing with symmetric and triangular Tsparse coercions, both
527            to dense and general.
528    
529    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
532    
533            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
534            where sensible when the <numeric> is of length > 1.
535    
536    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/Matrix.R ([<-): for M[] <- value: fix length
539    
540    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
543            * R/ndenseMatrix.R: new coercions n* -> l*
544    
545    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
548    
549            * R/Ops.R ("Logic"): and other "Ops", many updates
550    
551    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * src/Mutils.h (SET_DimNames): new utility
554    
555            * R/Auxiliaries.R (nnzero): improved and now exported via
556    
557            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
558    
559    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/diagMatrix.R (!): fix typo.
562    
563    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/Auxiliaries.R (as_Csparse): and quite a few others:
566                    allow to pass class definition --> speedup
567            * R/sparseMatrix.R: apply the above
568    
569            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
570    
571            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
572            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
573            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
574    
575            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
576    
577            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
578            and use it for "sparse*" as well, since it's faster than the
579            as_Csparse(.) way.
580    
581    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
584    
585    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
588            as method for   M[ ij ] <- v
589            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
590    
591            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
592            FALSE answer
593    
594            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
595            * tests/indexing.R: test it, and some of the above
596    
597    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Auxiliaries.R (is_duplicatedT): new utility
600    
601    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * src/init.c (R_init_Matrix): export cholmod_scale
604    
605    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
608            base::as.matrix to (x, ...)
609    
610    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
613            file; start using "Logic", hence
614    
615            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
616            * NAMESPACE: import and export "Logic"
617    
618    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
621            only needed previously to R version 2.5.0.
622    
623    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
626    
627            * R/Tsparse.R (replTmat): fix subassignment of triangular
628            * R/Csparse.R (replCmat): ditto
629            * tests/indexing.R: more tests, incl the above fix
630    
631    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/Auxiliaries.R (drop0): extend for non CSparse
634            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
635    
636            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
637                    use uplo correctly (!); other places: use uplo_P() macro
638    
639            * R/Csparse.R (replCmat): call diagU2N() when needed
640            * R/Tsparse.R (replTmat): ditto
641    
642            * src/dtCMatrix.c (tCMatrix_validate): new
643            * src/dtTMatrix.c (tTMatrix_validate): new, used in
644            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
645    
646            * R/diagMatrix.R (replDiag): to use in [<-
647    
648    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
651                    also more general diagU2N().
652    
653    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
654    
655            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
656            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
657    
658    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
659    
660            * tests/bind.R: a few more cases
661            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
662    
663            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
664            * R/ddenseMatrix.R (cbind2/rbind2)
665            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
666            * tests/indexing.R
667            * tests/indexing.Rout.save: updated
668    
669    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
672            * tests/indexing.R
673    
674    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
677            align with proper position of "0", i.e., right for integers.
678            argument 'align' by default is "fancy".
679    
680    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
681    
682            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
683            * R/Csparse.R: and fix "Compare" for more cases.
684            * tests/Class+Meth.R: test some of these (m == m, m != m)
685    
686    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/lsparseMatrix.R: all() and any() methods
689            * R/ldenseMatrix.R:      ditto
690            * NAMESPACE, R/Matrix.R: ditto
691    
692            * man/all-methods.Rd: document them minimally
693    
694            * tests/simple.R: add a few examples for these
695    
696    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/Tsparse.R ([): fix long standing typo in symmetric case
699            * man/dsCMatrix-class.Rd: add example exhibiting the above case
700    
701    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
702    
703            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
704            to LL before converting to a sparse matrix. (The LDL form can be
705            converted to a sparse matrix but it is implicitly a unit
706            triangular matrix and a diagonal matrix overwritten on the diagonal.)
707    
708    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
709    
710            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
711    
712    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
713    
714            * DESCRIPTION (Version): updated -> release 0.9975-7
715            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
716    
717    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
720    
721    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
722    
723            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
724            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
725            is exactly singular.
726    
727    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * DESCRIPTION (Date): updated -> release 0.9975-6
730    
731    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
734            now returns symmetric.
735    
736            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
737    
738            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
739            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
740    
741            * R/Auxiliaries.R (.type.kind): added
742    
743    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
746            running src/CSparse_install.sh
747    
748            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
749    
750    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
751    
752            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
753            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
754    
755            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
756    
757            * tests/Class+Meth.R (tstMatrixClass): now assure
758            the (important in method programming) property :
759    
760                    ###>>  Every "Matrix" is either
761                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
762    
763                    (where "*" stands for "Matrix")
764    
765            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
766    
767            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
768            * tests/validObj.R: checks for "comparison"
769    
770            * R/sparseMatrix.R ([): improved indexing for sparse;
771                    trying to keep <symmetric>[ n, n] symmmetric
772    
773            * tests/indexing.R: indexing for logical sparse now ok
774    
775    
776    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * src/Tsparse.c: use xTsparse_validate() , and hence remove
779    
780            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
781    
782    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
785    
786            * tests/simple.R: validObject() checking the above.
787    
788            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
789            replacing both dgCMatrix_validate and lgCM*.
790    
791            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
792            fix dimnames setting in other places.
793            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
794    
795    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
798    
799            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
800            symmetry test, via
801            * R/Auxiliaries.R (.as.dgC.0.factors):
802    
803    2006-11-01  Douglas Bates  <bates@r-project.org>
804    
805            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
806            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
807            <CsparseMatrix>) added
808    
809    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * tests/matprod.R: add a variation of Harri's example
812    
813            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
814            recursive infinitely.
815    
816            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
817    
818            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
819    
820    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
823            matrix if possible; test m+m == 2*m; now test dgRMatrix.
824            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
825            satisfy the above test.
826    
827    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
830    
831            * R/dgCMatrix.R: solve(a, b="missing") based on
832            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
833            RHS = NULL.
834    
835            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
836            add more (needed) [t]crossprod() methods.
837    
838            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
839    
840            * R/Auxiliaries.R (as_CspClass): cleanup
841            (drop0): internal utility for "Csparse_drop(*, 0)"
842            (.bail.out.2): encourage active feedback
843    
844    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * R/dMatrix.R(Compare): new(), then slots [no validity check]
847    
848            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
849            non-valid or 'sorted' case).
850    
851            * R/dsparseMatrix.R: add "chol" method.
852            * R/ddenseMatrix.R: ditto
853    
854            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
855            * NAMESPACE (Ops)
856            * R/diagMatrix.R (diag2T): simple utility used "higher level"
857            coercion; deprecating direct lower level coercions.
858    
859            * R/*.R (seq): use seq_len() and seq_along() where possible.
860    
861    
862    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * DESCRIPTION (Version): 0.9975-5 ready for release
865    
866    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
867    
868            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
869    
870    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * R/AllClass.R (corMatrix): add 'validity' check;
873                    comment out unused "LDL" class definition
874            * NAMESPACE: mention, but do not export "LDL" class
875            * R/corMatrix.R: new (simple), needed for R-devel with
876            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
877              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
878    
879    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
880    
881            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
882            use Rprintf and R's error handling.
883    
884    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
885    
886            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
887            * tests/matprod.R: add tests for the bug fixed.
888    
889  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
890    
891          * src/HBMM.[ch]: remove HarwellBoeing format for writing.          * src/HBMM.[ch]: remove HarwellBoeing format for writing.
# Line 5  Line 893 
893    
894  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
895    
896          * R/dgCMatrix.R: deprecate the writeHB function.  Use writeMM instead.          * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
897    
898  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
899    

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