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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 2113, Mon Feb 18 08:27:41 2008 UTC
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1    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (subset.ij): utility, as first step to faster
4               M [ <ij-matrix> ] indexing.
5    
6            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
7    
8            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
9            for more efficient symmpart() and skewpart() methods.
10    
11            * src/Mutils.c (equal_string_vectors): utility
12    
13            * src/dense.c (ddense_to_symmetric): new function used in
14    
15            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
16    
17            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
18            order to match the generic (and evade .local(..)).
19    
20            * R/dsCMatrix.R: dgC -> dsC: use C code!
21    
22            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
23            as per TODO
24    
25            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
26    
27            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
28    
29    
30    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
33    
34            * R/Auxiliaries.R (non0.i): take out of non0ind
35    
36            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
37            make tril(), triu(), band() work for "matrix" and all "dense*"
38    
39            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
40            * tests/simple.R: test the fix above
41    
42            * R/sparseMatrix.R ([): simplification: no coerce to <general>
43                    before we use as(., <Tsparse>)[...] anyway
44    
45            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
46    
47            * R/triangularMatrix.R (isTriangular): methods for all subclasses
48            instead of "triangularMatrix" -- just to disambiguate
49    
50    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
53            * tests/indexing.R: example that fails above
54    
55    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
58            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
59                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
60    
61            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
62            * src/Tsparse.h, init.c: ditto
63            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
64                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
65            * R/sparseMatrix.R (isTriangular): hence simplified
66    
67    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Ops.R (.Arith.Csparse): new utility factored out of former
70              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
71    
72    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
75    
76            * inst/test-tools.R (isOrthogonal): new function; also file restructured
77    
78    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
81            coercion to "nMatrix" and "pMatrix"
82    
83            * R/AllClass.R: "Schur" class;  "number" class union
84            * man/number-class.Rd:
85            * man/Schur-class.Rd:
86    
87            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
88            (.simpleSchur): Schur() method for diagonal matrices
89            (.triSchur):    Schur() method for triangular matrices
90            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
91    
92    
93    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
96    
97    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
100                    in order to ensure 'system = *' is not lost;
101                    formals()$system instead of cut&paste.
102            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
103    
104    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * DESCRIPTION (Date): make ready for release --> 0.999375-4
107    
108            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
109    
110    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
113                    and hence does as.vector(.).
114            * man/pMatrix-class.Rd: docs
115            * R/sparseMatrix.R: fix for printing "integer sparse"
116    
117            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
118    
119            * R/Matrix.R and others: use "exact" function argument list for
120                    both "["   : (x, i,j, ..., drop)
121                    and  "[<-" : (x, i,j, ..., value)
122    
123            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
124            * R/Tsparse.R (replTmat):    ditto
125            * R/diagMatrix.R (replDiag): ditto
126            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
127            * tests/indexing.R: testing the above
128    
129    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/sparseMatrix.R (cov2cor): method for sparse matrices
132    
133            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
134    
135            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
136    
137            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
138    
139    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Matrix.R: "generic" cov2cor() method
142    
143            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
144                    speed up Q %*% D %*% t(Q)
145            * tests/dpoMatrix.R: test nearPD()
146    
147    2007-12-05  Doug Bates and Martin Maechler
148    
149            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
150            stats::xtabs() allowing to create sparse matrices.
151    
152    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
155    
156    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
159    
160    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/LU.R: solve() method for "denseLU"
163    
164    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * DESCRIPTION (Version): 0.999375-3 preparing for release
167    
168            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
169    
170            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
171    
172    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
175              thanks to Kasper Kristensen.
176            * tests/matprod.R: regression test for that.
177    
178    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
179    
180            * [r4778] R/AllGeneric.R: Check R version before defining generics for
181              primitives
182    
183    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/denseMatrix.R (rcond): method
186            * R/sparseQR.R (rcond): method, use x or t(x)
187    
188    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
191            matrices.
192            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
193    
194            * man/rcond.Rd: mention the more general definition, and add
195            example for non-square matrices.
196    
197            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
198    
199    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
202    
203    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
206            * tests/indexing.R: add new regression for the above cases.
207    
208    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * src/Mutils.h (__sun): clause for alloca.h on Solaris
211    
212    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * DESCRIPTION (Date, Version): 0.999375-2
215    
216    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/HBMM.R (readMM): make work for pattern matrices as well
219    
220    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
221    
222            * [r4730] src/Mutils.h: declare alloca
223            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
224              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
225              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
226              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
227              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
228              methods; switch writeMM to use CHOLMOD code; repair readMM
229    
230    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
233            Oehlschlaegel's ... result type still to be discussed!
234    
235    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * man/image-methods.Rd: new, combining all image() methods
238    
239    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
242            to work via dgC...
243    
244            * R/Matrix.R (Matrix): special treatment for "table" (S3)
245    
246    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgTMatrix.R (image): change defaults to
249                    aspect = "iso", colorkey = FALSE
250    
251    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
254            must copy its *expanded* x slot before LAPACK call.
255    
256            * tests/matprod.R: test the last days' changes.
257    
258    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
259    
260            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
261              as well as in sources
262            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
263              Lapack call
264    
265    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
268                    ("Matrix", "matrix") which is needed in some cases.
269            Ditto for solve().
270    
271            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
272            infinite recursion in dispatch for some cases.
273    
274    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
275    
276            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
277              so pointers match
278    
279    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * DESCRIPTION (Date): set ready for release -- 0.999375-1
282    
283    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
284    
285            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
286              src/chm_common.c, src/chm_common.h: Change API for
287              numeric_as_chm_dense and N_AS_CHM_DN
288    
289    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
292            * tests/matprod.R: regr.test for it
293    
294    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
297            * tests/group-methods.R: and regression-test it
298    
299    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
300    
301            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
302              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
303              triplet_to_sparse, documentation, use typedefs
304    
305    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * man/dpoMatrix-class.Rd: added 'corMatrix' example
308    
309            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
310            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
311            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
312    
313            * R/lsparseMatrix.R: bug fix in "all" method
314            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
315    
316            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
317            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
318                    + matrix |-> nMatrix coercion
319            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
320            * man/pMatrix-class.Rd: ditto
321    
322            * R/Matrix.R (Summary): method for non-dMatrix
323    
324            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
325            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
326                    test all Summary methods.
327    
328    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
331    
332    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
335    
336            * R/pMatrix.R (t?crossprod): methods for pMatrix
337    
338    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
339    
340            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
341    
342    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
343    
344            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
345              trying to fix a subtle bug - which has been somewhere else.
346    
347    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
348    
349            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
350              solve the bug
351    
352    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * src/dgCMatrix.c (compressed_to_TMatrix):
355    
356    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/Csparse.c (Rsparse_validate): new, to have some validity
359            checking for RsparseMatrix
360            * src/dgCMatrix.c (xRMatrix_validate): ditto
361            * src/dtCMatrix.c (tRMatrix_validate): ditto
362    
363    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
364    
365            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
366              lgRMatrix
367            * [r4568] DESCRIPTION: Prepare for bug-fix release
368            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
369              for declaration of cholmod_symmetry
370    
371    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
374            release.
375    
376    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
377    
378            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
379              functions - no longer used
380            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
381              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
382              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
383              Alloca
384    
385    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
386    
387            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
388              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
389              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
390              src/t_gCMatrix_colSums.c: more R_CheckStack()s
391    
392    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
393    
394            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
395              the required amount of memory then call M_numeric_as_chm_dense.
396            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
397              (like Calloc but calling alloca)
398    
399    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
402            and extended with more sophisticated 'col.names' option.
403            * NAMESPACE: export  printSparseMatrix()
404            * man/printSpMatrix.Rd: document, incl. examples
405    
406    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
407    
408            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
409              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
410              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
411    
412    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * DESCRIPTION (Version): 0.99875-4
415    
416            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
417            some dimnames perservation.
418    
419            * R/dsTMatrix.R (t-method): keep dimnames
420            * R/dtTMatrix.R:  ditto
421    
422            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
423            and ncol(.) < 10
424    
425            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
426            from Mutils.h
427    
428            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
429            e.g. in as(<ngCMatrix>, "matrix")
430    
431    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
432    
433            * [r4529] .: Create a branch for the API changes from the 0.99875
434              series to the 0.999375 series
435            * [r4530] DESCRIPTION, inst/include/Matrix.h,
436              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
437              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
438              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
439              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
440              as_cholmod_x functions
441    
442    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
443    
444            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
445              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
446              to Comparisons
447    
448    >>>>>>> .merge-right.r4561
449    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * DESCRIPTION (Version): 0.99875-3 ready to be released.
452    
453            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
454    
455            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
456            that should also work in a future version of R.
457    
458    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
461    
462            * R/sparseVector.R: more *sparseVector coercions, notably for
463            non - double ones.
464    
465    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
468              notably the new ones building on the new .Call(.)s:
469    
470            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
471            all 4 of [dlin]gCMatrix_colSums().
472    
473    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
474    
475            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
476            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
477              result
478    
479    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/kronecker.R: fix typo (could lead to inf.recursion)
482            * test/simple.R: testing that
483    
484            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
485            method as well (which can have arguments, show() can't).
486    
487    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
488    
489            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
490              added dgCMatrix_colSums for [col,row][Sums,Means]
491    
492    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
493    
494            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
495              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
496              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
497            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
498              class
499            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
500              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
501              row names to store the levels - duh!  Added an example.
502    
503    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * src/Csparse.c (Csparse_validate): check for *repeated* entries
506            thanks to example from Christian Buchta; with a test here:
507            * tests/simple.R:
508    
509    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
512            of colSums(*, sparseResult = TRUE)
513    
514    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
517            'na.rm = FALSE' as "everywhere" else in R.
518    
519    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
520    
521            * [r4421] src/CSparse_install.sh: Modify for new organization of
522              CSparse package
523            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
524              SuiteSparse
525            * [r4426] src/Makefile: add ./UFconfig to the include path for
526              compilation
527            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
528            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
529              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
530    
531    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
534            * R/sparseMatrix.R (prSpMatrix): now gives a message about
535            suppressed column names.
536    
537    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
538    
539            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
540              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
541              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
542              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
543              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
544              Remove warnings after change to const char* CHAR
545    
546    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
547    
548            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
549              type of M_cholmod_ssmult
550    
551    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
552    
553            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
554              src/init.c: Yet another cholmod export - cholmod_ssmult
555    
556    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * NAMESPACE: exported drop0(), since
559            * man/drop0.Rd: I have seen several cases, I really wanted to use
560            it, so our users may want too.
561    
562    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * man/colSums.Rd: separately document colSums() etc, since these
565            have the extra argument 'sparseResult'.
566    
567    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
570            * man/spMatrix.Rd: docu., including examples
571    
572            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
573            in order to make colMeans() etc fast *and* correct.
574            * R/sparseVector.R (replSPvec): "[<-" functionality for
575            sparseVectors; tested in
576            * tests/simple.R:
577    
578    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
581            (very) sparse Matrices; output similar to Matlab's print().
582    
583    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
584    
585            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
586            0-based, indices (Jose Quesada <quesada@gmail.com>).
587    
588    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
589    
590            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
591    
592    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Auxiliaries.R (sparsapply): new utility, much faster than
595            tapply1() for large sparse matrices.
596    
597    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Matrix.R (dim<-): reshape now via sparseVector.
600    
601            * R/sparseVector.R: methods and function for
602            * R/AllClass.R: new "sparseVector" class and daughters.
603            * NAMESPACE: export new classes
604    
605    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * DESCRIPTION (Version): 0.99875-1
608            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
609    
610    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
613            indexing
614            * tests/indexing.R: test set for that.
615    
616    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
619            entries.
620            * tests/indexing.R(out): add regression test for it
621    
622    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
625            name for "!" method definitions.
626    
627    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/Tsparse.R (intI): new utility, used for "[" :
630                    Cleanup up there, and fixes for duplicated indices - more TODO!
631    
632            * tests/indexing.R(out): more tests
633    
634    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
637            code that is now part of the R Lapack library.
638    
639            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
640            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
641    
642    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
645    
646    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
649            up with extraneous names '0'...'<n-1>'
650    
651    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/dgTMatrix.R (mat2dgT): care about NAs
654    
655    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/kronecker.R: triangularity preserving methods
658    
659    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * R/kronecker.R: new file collecting kronecker() methods in one
662                    place.  Goal: become much faster!
663    
664    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
667            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
668            can be much faster.
669    
670            * tests/matprod.R: add regression tests for these (upper & lower).
671    
672    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Matrix.R (diff): method for our Matrices.
675    
676            * R/sparseMatrix.R (isDiagonal): check dim()!
677    
678    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R (dim<-): new method for "reshape()" built on a
681            proposal from Tamas Papp.
682    
683    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
686    
687            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
688            rather define and export  cBind() and rBind() only.
689            --> useRs *must* change code that used to have cbind()/rbind() !!
690    
691            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
692            * R/bind.Rout.save: ditto
693    
694    2007-02-16  Douglas Bates  <bates@r-project.org>
695    
696            * DESCRIPTION (Date, Version): 0.9975-11 with new date
697            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
698            const modifier on declaration of the array 'valid'
699    
700    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
701    
702            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
703    
704    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
707    
708            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
709            * tests/simple.R: test the above and some of these coercions:
710    
711            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
712                    be careful to avoid infinite recursion, using new coercions in
713            * R/ngCMatrix.R and nsC... and ntC...
714            * R/lsparseMatrix.R: ditto
715    
716            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
717    
718            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
719            * R/Rsparse.R: reactivate .Call()s
720    
721            * tests/Class+Meth.R: a bit more on actual classes
722    
723    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
724    
725            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
726    
727    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * DESCRIPTION (Version): 0.9975-10 to upload
730    
731            * tests/Class+Meth.R (tstMatrixClass): require coercions to
732            specific classes less unconditionally.
733    
734            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
735    
736            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
737    
738            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
739            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
740            R_to_CMatrix segfaults on one platform.
741            Eliminate most coercion method to *specific* classes, and replace
742            with virtual classes coercions.
743    
744    
745    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
746    
747            * src/init.c: export the CHM...._validate() placeholders, since
748            they *are* called.
749    
750            * tests/Class+Meth.R (classCanCoerce): and starting to test
751            all as(<from>, <to>)
752    
753    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
756            * tests/indexing.R: tested now
757            * tests/indexing.Rout.save: updated
758    
759            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
760            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
761            appropriate.
762    
763            * NAMESPACE: export a trivial
764            * R/Matrix.R: drop() Matrix-method
765    
766            * R/AllClass.R: moved all prototypes to virtual super classes.
767    
768            * R/Rsparse.R: many more coercions to have less exceptions in
769            * tests/Class+Meth.R:
770    
771            * R/Ops.R (Compare): tweak for case with NA
772            * tests/simpl.R: hence another 'FIXME' eliminated
773    
774    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
777            objects.
778    
779            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
780              and more of "!", "&", "|", all, any; coercions
781    
782            * R/Rsparse.R: many coercions (which enable quite a few other
783            methods), thanks to enhancements in
784            * src/dgCMatrix.c (R_to_CMatrix): new, and
785            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
786            symmetric & triangular and ..RMatrix objects.
787    
788            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
789            renamed file from src/dsTMatrix.c;
790            now dealing with symmetric and triangular Tsparse coercions, both
791            to dense and general.
792    
793    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
796    
797            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
798            where sensible when the <numeric> is of length > 1.
799    
800    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * R/Matrix.R ([<-): for M[] <- value: fix length
803    
804    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
807            * R/ndenseMatrix.R: new coercions n* -> l*
808    
809    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
810    
811            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
812    
813            * R/Ops.R ("Logic"): and other "Ops", many updates
814    
815    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * src/Mutils.h (SET_DimNames): new utility
818    
819            * R/Auxiliaries.R (nnzero): improved and now exported via
820    
821            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
822    
823    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * R/diagMatrix.R (!): fix typo.
826    
827    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/Auxiliaries.R (as_Csparse): and quite a few others:
830                    allow to pass class definition --> speedup
831            * R/sparseMatrix.R: apply the above
832    
833            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
834    
835            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
836            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
837            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
838    
839            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
840    
841            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
842            and use it for "sparse*" as well, since it's faster than the
843            as_Csparse(.) way.
844    
845    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
848    
849    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
852            as method for   M[ ij ] <- v
853            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
854    
855            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
856            FALSE answer
857    
858            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
859            * tests/indexing.R: test it, and some of the above
860    
861    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/Auxiliaries.R (is_duplicatedT): new utility
864    
865    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
866    
867            * src/init.c (R_init_Matrix): export cholmod_scale
868    
869    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
872            base::as.matrix to (x, ...)
873    
874    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
877            file; start using "Logic", hence
878    
879            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
880            * NAMESPACE: import and export "Logic"
881    
882    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
885            only needed previously to R version 2.5.0.
886    
887    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
890    
891            * R/Tsparse.R (replTmat): fix subassignment of triangular
892            * R/Csparse.R (replCmat): ditto
893            * tests/indexing.R: more tests, incl the above fix
894    
895    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * R/Auxiliaries.R (drop0): extend for non CSparse
898            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
899    
900            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
901                    use uplo correctly (!); other places: use uplo_P() macro
902    
903            * R/Csparse.R (replCmat): call diagU2N() when needed
904            * R/Tsparse.R (replTmat): ditto
905    
906            * src/dtCMatrix.c (tCMatrix_validate): new
907            * src/dtTMatrix.c (tTMatrix_validate): new, used in
908            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
909    
910            * R/diagMatrix.R (replDiag): to use in [<-
911    
912    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
913    
914            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
915                    also more general diagU2N().
916    
917    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
920            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
921    
922    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
923    
924            * tests/bind.R: a few more cases
925            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
926    
927            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
928            * R/ddenseMatrix.R (cbind2/rbind2)
929            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
930            * tests/indexing.R
931            * tests/indexing.Rout.save: updated
932    
933    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
934    
935            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
936            * tests/indexing.R
937    
938    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
941            align with proper position of "0", i.e., right for integers.
942            argument 'align' by default is "fancy".
943    
944    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
947            * R/Csparse.R: and fix "Compare" for more cases.
948            * tests/Class+Meth.R: test some of these (m == m, m != m)
949    
950    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/lsparseMatrix.R: all() and any() methods
953            * R/ldenseMatrix.R:      ditto
954            * NAMESPACE, R/Matrix.R: ditto
955    
956            * man/all-methods.Rd: document them minimally
957    
958            * tests/simple.R: add a few examples for these
959    
960    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * R/Tsparse.R ([): fix long standing typo in symmetric case
963            * man/dsCMatrix-class.Rd: add example exhibiting the above case
964    
965    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
966    
967            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
968            to LL before converting to a sparse matrix. (The LDL form can be
969            converted to a sparse matrix but it is implicitly a unit
970            triangular matrix and a diagonal matrix overwritten on the diagonal.)
971    
972    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
973    
974            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
975    
976    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
977    
978            * DESCRIPTION (Version): updated -> release 0.9975-7
979            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
980    
981    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
982    
983            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
984    
985    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
986    
987            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
988            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
989            is exactly singular.
990    
991    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * DESCRIPTION (Date): updated -> release 0.9975-6
994    
995    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
998            now returns symmetric.
999    
1000            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1001    
1002            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1003            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1004    
1005            * R/Auxiliaries.R (.type.kind): added
1006    
1007    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1010            running src/CSparse_install.sh
1011    
1012            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1013    
1014    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1017            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1018    
1019            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1020    
1021            * tests/Class+Meth.R (tstMatrixClass): now assure
1022            the (important in method programming) property :
1023    
1024                    ###>>  Every "Matrix" is either
1025                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1026    
1027                    (where "*" stands for "Matrix")
1028    
1029            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1030    
1031            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1032            * tests/validObj.R: checks for "comparison"
1033    
1034            * R/sparseMatrix.R ([): improved indexing for sparse;
1035                    trying to keep <symmetric>[ n, n] symmmetric
1036    
1037            * tests/indexing.R: indexing for logical sparse now ok
1038    
1039    
1040    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1043    
1044            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1045    
1046    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1049    
1050            * tests/simple.R: validObject() checking the above.
1051    
1052            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1053            replacing both dgCMatrix_validate and lgCM*.
1054    
1055            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1056            fix dimnames setting in other places.
1057            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1058    
1059    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1060    
1061            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1062    
1063            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1064            symmetry test, via
1065            * R/Auxiliaries.R (.as.dgC.0.factors):
1066    
1067    2006-11-01  Douglas Bates  <bates@r-project.org>
1068    
1069            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1070            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1071            <CsparseMatrix>) added
1072    
1073    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1074    
1075            * tests/matprod.R: add a variation of Harri's example
1076    
1077            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1078            recursive infinitely.
1079    
1080            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1081    
1082            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1083    
1084    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1087            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1088            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1089            satisfy the above test.
1090    
1091    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1092    
1093            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1094    
1095            * R/dgCMatrix.R: solve(a, b="missing") based on
1096            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1097            RHS = NULL.
1098    
1099            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1100            add more (needed) [t]crossprod() methods.
1101    
1102            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1103    
1104            * R/Auxiliaries.R (as_CspClass): cleanup
1105            (drop0): internal utility for "Csparse_drop(*, 0)"
1106            (.bail.out.2): encourage active feedback
1107    
1108    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1109    
1110            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1111    
1112            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1113            non-valid or 'sorted' case).
1114    
1115            * R/dsparseMatrix.R: add "chol" method.
1116            * R/ddenseMatrix.R: ditto
1117    
1118            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1119            * NAMESPACE (Ops)
1120            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1121            coercion; deprecating direct lower level coercions.
1122    
1123            * R/*.R (seq): use seq_len() and seq_along() where possible.
1124    
1125    
1126    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1127    
1128            * DESCRIPTION (Version): 0.9975-5 ready for release
1129    
1130    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1131    
1132            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1133    
1134    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * R/AllClass.R (corMatrix): add 'validity' check;
1137                    comment out unused "LDL" class definition
1138            * NAMESPACE: mention, but do not export "LDL" class
1139            * R/corMatrix.R: new (simple), needed for R-devel with
1140            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1141              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1142    
1143    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1144    
1145            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1146            use Rprintf and R's error handling.
1147    
1148    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1149    
1150            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1151            * tests/matprod.R: add tests for the bug fixed.
1152    
1153    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1154    
1155            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1156            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1157    
1158    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1159    
1160            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1161    
1162    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * DESCRIPTION (Version): 0.9975-3
1165    
1166            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1167            (sparse) matrices.
1168            * man/bdiag.Rd: docu + examples
1169    
1170            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1171    
1172            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1173            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1174    
1175            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1176            that result is sparse or diagonal (and not dense).
1177    
1178            * man/Subassign-methods.Rd: fix examples
1179    
1180            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1181            should always return a sparse (and not sometimes a diagonal) matrix.
1182    
1183    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1186    
1187    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1188    
1189            * DESCRIPTION (Version): 0.9975-2
1190    
1191            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1192    
1193    2006-10-02  Douglas Bates  <bates@R-project.org>
1194    
1195            * tests/dg_Matrix.R: Simplify test taking into account new code.
1196    
1197    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1200    
1201            * R/lsTMatrix.R: new files w/ missing methods
1202            * R/nsTMatrix.R:  "  'for completeness'
1203    
1204            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1205    
1206            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1207    
1208    
1209    2006-09-28  Douglas Bates  <bates@R-project.org>
1210    
1211            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1212            included.
1213    
1214            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1215            Export C-callable functions used in Zt_create in lme4.
1216    
1217    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1218    
1219            * DESCRIPTION (Version): 0.9975-1
1220    
1221            * tests/simple.R: less checks fail; using NA, found that our
1222                    kronecker() is not base-compatible with NA's.
1223    
1224            * R/dMatrix.R: "Compare" method now implemented for all cases
1225    
1226            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1227    
1228            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1229    
1230            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1231            * src/dspMatrix.c (dspMatrix_validate): ditto
1232    
1233            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1234              including coercion to [nl]tTMatrix.
1235    
1236            * R/diagMatrix.R (show): print a header line as for other classes.
1237    
1238    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1239    
1240            * src/Makefile.win (SUBDIRS): fix typo
1241    
1242    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1245    
1246    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1247    
1248            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1249            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1250            accept a symmetric matrix).
1251            * tests/group-methods.R: Uncomment test of crossprod applied to
1252            lsCMatrix objects.
1253    
1254    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1255    
1256            * R/AllClass.R (symmetricMatrix): add validity method (available
1257            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1258    
1259            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1260    
1261            * tests/indexing.Rout.save:
1262            * tests/indexing.R: additions, mainly for 'lsparse'
1263    
1264            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1265            case.
1266    
1267            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1268    
1269    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1272                    as 'N' (1-letter - Ok?)
1273    
1274            * tests/group-methods.R: add test for logical + NAs
1275    
1276            * R/dMatrix.R ("Compare"): fix to work with NA's
1277    
1278            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1279    
1280            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1281                    which is implemented.
1282    
1283    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1284    
1285            * src/chm_common.c: coerce logical <-> double instead of
1286            typecasting;  needed for "l" matrix handling in cholmod.
1287    
1288            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1289    
1290            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1291            (Tsp2grNEL): other fixes needed
1292    
1293    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1294    
1295            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1296                    Matrices, since "lMatrix", also "lsparseM" can have NA
1297            * R/ndenseMatrix.R, etc: new source files
1298            * man/nsparseMatrix-classes.Rd, etc: new help files
1299            * tests/: adaptions
1300            * src/chm_common.c (chm_dense_to_SEXP): and others:
1301                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1302            * src/Csparse.c, etc: ditto
1303    
1304    2006-09-11  Douglas Bates  <bates@R-project.org>
1305    
1306            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1307            alloc_d**Matrix functions to the lme4 package.
1308    
1309    2006-09-09  Douglas Bates  <bates@R-project.org>
1310    
1311            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1312            fixed
1313    
1314    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1315    
1316            * R/lMatrix.R: new
1317    
1318            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1319    
1320            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1321            * man/tcrossprod.Rd: ditto
1322    
1323    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1324    
1325            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1326            for exported functions
1327            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1328            Remove partitioning algorithms for sparse matrix reordering.  The
1329            copyright on the Metis code was problematic and the methods were
1330            rarely used.
1331            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1332            operations are now done entirely in CHOLMOD code.
1333    
1334    2006-09-06  Douglas Bates  <bates@R-project.org>
1335    
1336            * src/Mutils.h: Remove functions that are no longer used.
1337    
1338  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
1339    
1340          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 1361 
1361    
1362          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1363          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1364          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1365          * R/Csparse.R: dito          * R/Csparse.R: ditto
1366    
1367  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1368    
# Line 41  Line 1378 
1378    
1379          * 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
1380          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1381          (.is.diagonal): dito          (.is.diagonal): ditto
1382    
1383          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1384    

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