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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 2126, Fri Mar 7 07:59:46 2008 UTC
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1    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Date,Version): ready to release 0.999375-5
4    
5            * tests/simple.R: testing diagN2U
6    
7    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/Auxiliaries.R (diagN2U): interface to
10    
11            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
12    
13            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
14    
15    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/chm_common.c (chm_diagN2U): new utility.
18    
19            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
20            make use of chm_diagN2U() and hence now preserve triangularity and
21            unit-triangularity.
22    
23            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
24    
25    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
28    
29            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
30            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
31    
32            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
33    
34            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
35    
36            * src/chm_common.c (AS_CHM_FINISH): add note about problem
37            for triangular (diag = "U").
38    
39    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
42            * R/bind.R:  .Call(dense_to_Csparse, *)
43    
44    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/Matrix.R (Matrix): no longer use coercions to specific classes
47                    (since we are discouraging them in user code).
48    
49            * tests/*.R: also replaces coercions to specific classes by
50            coercions to super classes.
51    
52            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
53    
54    
55    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
58    
59            * src/dense.c (dense_band): generalized from ddense_band
60    
61            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
62              now for "denseMatrix" (instead of just "ddense*"); much
63              simplified setMethod()s for these.
64    
65            * src/dense.c (dense_to_symmetric): generalized from ddense_*
66    
67    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
70            version of as(*, "symmetricMatric").
71    
72            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
73            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
74    
75    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/Matrix.R (subset.ij): utility, as first step to faster
78               M [ <ij-matrix> ] indexing.
79    
80            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
81    
82            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
83            for more efficient symmpart() and skewpart() methods.
84    
85            * src/Mutils.c (equal_string_vectors): utility
86    
87            * src/dense.c (ddense_to_symmetric): new function used in
88    
89            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
90    
91            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
92            order to match the generic (and evade .local(..)).
93    
94            * R/dsCMatrix.R: dgC -> dsC: use C code!
95    
96            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
97            as per TODO
98    
99            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
100    
101            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
102    
103    
104    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
107    
108            * R/Auxiliaries.R (non0.i): take out of non0ind
109    
110            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
111            make tril(), triu(), band() work for "matrix" and all "dense*"
112    
113            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
114            * tests/simple.R: test the fix above
115    
116            * R/sparseMatrix.R ([): simplification: no coerce to <general>
117                    before we use as(., <Tsparse>)[...] anyway
118    
119            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
120    
121            * R/triangularMatrix.R (isTriangular): methods for all subclasses
122            instead of "triangularMatrix" -- just to disambiguate
123    
124    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
127            * tests/indexing.R: example that fails above
128    
129    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
132            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
133                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
134    
135            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
136            * src/Tsparse.h, init.c: ditto
137            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
138                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
139            * R/sparseMatrix.R (isTriangular): hence simplified
140    
141    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Ops.R (.Arith.Csparse): new utility factored out of former
144              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
145    
146    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
149    
150            * inst/test-tools.R (isOrthogonal): new function; also file restructured
151    
152    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
155            coercion to "nMatrix" and "pMatrix"
156    
157            * R/AllClass.R: "Schur" class;  "number" class union
158            * man/number-class.Rd:
159            * man/Schur-class.Rd:
160    
161            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
162            (.simpleSchur): Schur() method for diagonal matrices
163            (.triSchur):    Schur() method for triangular matrices
164            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
165    
166    
167    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
170    
171    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
174                    in order to ensure 'system = *' is not lost;
175                    formals()$system instead of cut&paste.
176            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
177    
178    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * DESCRIPTION (Date): make ready for release --> 0.999375-4
181    
182            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
183    
184    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
187                    and hence does as.vector(.).
188            * man/pMatrix-class.Rd: docs
189            * R/sparseMatrix.R: fix for printing "integer sparse"
190    
191            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
192    
193            * R/Matrix.R and others: use "exact" function argument list for
194                    both "["   : (x, i,j, ..., drop)
195                    and  "[<-" : (x, i,j, ..., value)
196    
197            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
198            * R/Tsparse.R (replTmat):    ditto
199            * R/diagMatrix.R (replDiag): ditto
200            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
201            * tests/indexing.R: testing the above
202    
203    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (cov2cor): method for sparse matrices
206    
207            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
208    
209            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
210    
211            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
212    
213    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Matrix.R: "generic" cov2cor() method
216    
217            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
218                    speed up Q %*% D %*% t(Q)
219            * tests/dpoMatrix.R: test nearPD()
220    
221    2007-12-05  Doug Bates and Martin Maechler
222    
223            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
224            stats::xtabs() allowing to create sparse matrices.
225    
226    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
229    
230    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
233    
234    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/LU.R: solve() method for "denseLU"
237    
238    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * DESCRIPTION (Version): 0.999375-3 preparing for release
241    
242            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
243    
244            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
245    
246    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
249              thanks to Kasper Kristensen.
250            * tests/matprod.R: regression test for that.
251    
252    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
253    
254            * [r4778] R/AllGeneric.R: Check R version before defining generics for
255              primitives
256    
257    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/denseMatrix.R (rcond): method
260            * R/sparseQR.R (rcond): method, use x or t(x)
261    
262    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
265            matrices.
266            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
267    
268            * man/rcond.Rd: mention the more general definition, and add
269            example for non-square matrices.
270    
271            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
272    
273    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
276    
277    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
280            * tests/indexing.R: add new regression for the above cases.
281    
282    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * src/Mutils.h (__sun): clause for alloca.h on Solaris
285    
286    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * DESCRIPTION (Date, Version): 0.999375-2
289    
290    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/HBMM.R (readMM): make work for pattern matrices as well
293    
294    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
295    
296            * [r4730] src/Mutils.h: declare alloca
297            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
298              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
299              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
300              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
301              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
302              methods; switch writeMM to use CHOLMOD code; repair readMM
303    
304    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
307            Oehlschlaegel's ... result type still to be discussed!
308    
309    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * man/image-methods.Rd: new, combining all image() methods
312    
313    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
316            to work via dgC...
317    
318            * R/Matrix.R (Matrix): special treatment for "table" (S3)
319    
320    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/dgTMatrix.R (image): change defaults to
323                    aspect = "iso", colorkey = FALSE
324    
325    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
328            must copy its *expanded* x slot before LAPACK call.
329    
330            * tests/matprod.R: test the last days' changes.
331    
332    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
333    
334            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
335              as well as in sources
336            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
337              Lapack call
338    
339    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
342                    ("Matrix", "matrix") which is needed in some cases.
343            Ditto for solve().
344    
345            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
346            infinite recursion in dispatch for some cases.
347    
348    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
349    
350            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
351              so pointers match
352    
353    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Date): set ready for release -- 0.999375-1
356    
357    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
358    
359            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
360              src/chm_common.c, src/chm_common.h: Change API for
361              numeric_as_chm_dense and N_AS_CHM_DN
362    
363    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
366            * tests/matprod.R: regr.test for it
367    
368    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
371            * tests/group-methods.R: and regression-test it
372    
373    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
374    
375            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
376              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
377              triplet_to_sparse, documentation, use typedefs
378    
379    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * man/dpoMatrix-class.Rd: added 'corMatrix' example
382    
383            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
384            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
385            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
386    
387            * R/lsparseMatrix.R: bug fix in "all" method
388            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
389    
390            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
391            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
392                    + matrix |-> nMatrix coercion
393            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
394            * man/pMatrix-class.Rd: ditto
395    
396            * R/Matrix.R (Summary): method for non-dMatrix
397    
398            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
399            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
400                    test all Summary methods.
401    
402    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
405    
406    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
409    
410            * R/pMatrix.R (t?crossprod): methods for pMatrix
411    
412    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
413    
414            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
415    
416    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
417    
418            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
419              trying to fix a subtle bug - which has been somewhere else.
420    
421    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
422    
423            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
424              solve the bug
425    
426    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * src/dgCMatrix.c (compressed_to_TMatrix):
429    
430    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * src/Csparse.c (Rsparse_validate): new, to have some validity
433            checking for RsparseMatrix
434            * src/dgCMatrix.c (xRMatrix_validate): ditto
435            * src/dtCMatrix.c (tRMatrix_validate): ditto
436    
437    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
438    
439            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
440              lgRMatrix
441            * [r4568] DESCRIPTION: Prepare for bug-fix release
442            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
443              for declaration of cholmod_symmetry
444    
445    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
448            release.
449    
450    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
451    
452            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
453              functions - no longer used
454            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
455              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
456              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
457              Alloca
458    
459    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
460    
461            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
462              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
463              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
464              src/t_gCMatrix_colSums.c: more R_CheckStack()s
465    
466    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
467    
468            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
469              the required amount of memory then call M_numeric_as_chm_dense.
470            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
471              (like Calloc but calling alloca)
472    
473    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
476            and extended with more sophisticated 'col.names' option.
477            * NAMESPACE: export  printSparseMatrix()
478            * man/printSpMatrix.Rd: document, incl. examples
479    
480    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
481    
482            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
483              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
484              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
485    
486    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * DESCRIPTION (Version): 0.99875-4
489    
490            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
491            some dimnames perservation.
492    
493            * R/dsTMatrix.R (t-method): keep dimnames
494            * R/dtTMatrix.R:  ditto
495    
496            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
497            and ncol(.) < 10
498    
499            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
500            from Mutils.h
501    
502            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
503            e.g. in as(<ngCMatrix>, "matrix")
504    
505    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
506    
507            * [r4529] .: Create a branch for the API changes from the 0.99875
508              series to the 0.999375 series
509            * [r4530] DESCRIPTION, inst/include/Matrix.h,
510              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
511              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
512              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
513              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
514              as_cholmod_x functions
515    
516    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
517    
518            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
519              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
520              to Comparisons
521    
522    >>>>>>> .merge-right.r4561
523    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * DESCRIPTION (Version): 0.99875-3 ready to be released.
526    
527            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
528    
529            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
530            that should also work in a future version of R.
531    
532    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
535    
536            * R/sparseVector.R: more *sparseVector coercions, notably for
537            non - double ones.
538    
539    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
542              notably the new ones building on the new .Call(.)s:
543    
544            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
545            all 4 of [dlin]gCMatrix_colSums().
546    
547    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
548    
549            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
550            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
551              result
552    
553    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/kronecker.R: fix typo (could lead to inf.recursion)
556            * test/simple.R: testing that
557    
558            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
559            method as well (which can have arguments, show() can't).
560    
561    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
562    
563            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
564              added dgCMatrix_colSums for [col,row][Sums,Means]
565    
566    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
567    
568            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
569              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
570              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
571            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
572              class
573            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
574              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
575              row names to store the levels - duh!  Added an example.
576    
577    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * src/Csparse.c (Csparse_validate): check for *repeated* entries
580            thanks to example from Christian Buchta; with a test here:
581            * tests/simple.R:
582    
583    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
586            of colSums(*, sparseResult = TRUE)
587    
588    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
591            'na.rm = FALSE' as "everywhere" else in R.
592    
593    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
594    
595            * [r4421] src/CSparse_install.sh: Modify for new organization of
596              CSparse package
597            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
598              SuiteSparse
599            * [r4426] src/Makefile: add ./UFconfig to the include path for
600              compilation
601            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
602            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
603              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
604    
605    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
608            * R/sparseMatrix.R (prSpMatrix): now gives a message about
609            suppressed column names.
610    
611    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
612    
613            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
614              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
615              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
616              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
617              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
618              Remove warnings after change to const char* CHAR
619    
620    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
621    
622            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
623              type of M_cholmod_ssmult
624    
625    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
626    
627            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
628              src/init.c: Yet another cholmod export - cholmod_ssmult
629    
630    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * NAMESPACE: exported drop0(), since
633            * man/drop0.Rd: I have seen several cases, I really wanted to use
634            it, so our users may want too.
635    
636    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * man/colSums.Rd: separately document colSums() etc, since these
639            have the extra argument 'sparseResult'.
640    
641    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
644            * man/spMatrix.Rd: docu., including examples
645    
646            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
647            in order to make colMeans() etc fast *and* correct.
648            * R/sparseVector.R (replSPvec): "[<-" functionality for
649            sparseVectors; tested in
650            * tests/simple.R:
651    
652    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
655            (very) sparse Matrices; output similar to Matlab's print().
656    
657    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
658    
659            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
660            0-based, indices (Jose Quesada <quesada@gmail.com>).
661    
662    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
663    
664            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
665    
666    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/Auxiliaries.R (sparsapply): new utility, much faster than
669            tapply1() for large sparse matrices.
670    
671    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/Matrix.R (dim<-): reshape now via sparseVector.
674    
675            * R/sparseVector.R: methods and function for
676            * R/AllClass.R: new "sparseVector" class and daughters.
677            * NAMESPACE: export new classes
678    
679    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * DESCRIPTION (Version): 0.99875-1
682            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
683    
684    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
685    
686            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
687            indexing
688            * tests/indexing.R: test set for that.
689    
690    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
693            entries.
694            * tests/indexing.R(out): add regression test for it
695    
696    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
699            name for "!" method definitions.
700    
701    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/Tsparse.R (intI): new utility, used for "[" :
704                    Cleanup up there, and fixes for duplicated indices - more TODO!
705    
706            * tests/indexing.R(out): more tests
707    
708    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
709    
710            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
711            code that is now part of the R Lapack library.
712    
713            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
714            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
715    
716    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
719    
720    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
723            up with extraneous names '0'...'<n-1>'
724    
725    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/dgTMatrix.R (mat2dgT): care about NAs
728    
729    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/kronecker.R: triangularity preserving methods
732    
733    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/kronecker.R: new file collecting kronecker() methods in one
736                    place.  Goal: become much faster!
737    
738    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
741            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
742            can be much faster.
743    
744            * tests/matprod.R: add regression tests for these (upper & lower).
745    
746    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * R/Matrix.R (diff): method for our Matrices.
749    
750            * R/sparseMatrix.R (isDiagonal): check dim()!
751    
752    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/Matrix.R (dim<-): new method for "reshape()" built on a
755            proposal from Tamas Papp.
756    
757    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
760    
761            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
762            rather define and export  cBind() and rBind() only.
763            --> useRs *must* change code that used to have cbind()/rbind() !!
764    
765            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
766            * R/bind.Rout.save: ditto
767    
768    2007-02-16  Douglas Bates  <bates@r-project.org>
769    
770            * DESCRIPTION (Date, Version): 0.9975-11 with new date
771            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
772            const modifier on declaration of the array 'valid'
773    
774    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
775    
776            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
777    
778    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
781    
782            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
783            * tests/simple.R: test the above and some of these coercions:
784    
785            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
786                    be careful to avoid infinite recursion, using new coercions in
787            * R/ngCMatrix.R and nsC... and ntC...
788            * R/lsparseMatrix.R: ditto
789    
790            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
791    
792            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
793            * R/Rsparse.R: reactivate .Call()s
794    
795            * tests/Class+Meth.R: a bit more on actual classes
796    
797    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
798    
799            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
800    
801    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * DESCRIPTION (Version): 0.9975-10 to upload
804    
805            * tests/Class+Meth.R (tstMatrixClass): require coercions to
806            specific classes less unconditionally.
807    
808            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
809    
810            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
811    
812            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
813            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
814            R_to_CMatrix segfaults on one platform.
815            Eliminate most coercion method to *specific* classes, and replace
816            with virtual classes coercions.
817    
818    
819    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
820    
821            * src/init.c: export the CHM...._validate() placeholders, since
822            they *are* called.
823    
824            * tests/Class+Meth.R (classCanCoerce): and starting to test
825            all as(<from>, <to>)
826    
827    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
830            * tests/indexing.R: tested now
831            * tests/indexing.Rout.save: updated
832    
833            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
834            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
835            appropriate.
836    
837            * NAMESPACE: export a trivial
838            * R/Matrix.R: drop() Matrix-method
839    
840            * R/AllClass.R: moved all prototypes to virtual super classes.
841    
842            * R/Rsparse.R: many more coercions to have less exceptions in
843            * tests/Class+Meth.R:
844    
845            * R/Ops.R (Compare): tweak for case with NA
846            * tests/simpl.R: hence another 'FIXME' eliminated
847    
848    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
851            objects.
852    
853            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
854              and more of "!", "&", "|", all, any; coercions
855    
856            * R/Rsparse.R: many coercions (which enable quite a few other
857            methods), thanks to enhancements in
858            * src/dgCMatrix.c (R_to_CMatrix): new, and
859            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
860            symmetric & triangular and ..RMatrix objects.
861    
862            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
863            renamed file from src/dsTMatrix.c;
864            now dealing with symmetric and triangular Tsparse coercions, both
865            to dense and general.
866    
867    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
870    
871            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
872            where sensible when the <numeric> is of length > 1.
873    
874    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/Matrix.R ([<-): for M[] <- value: fix length
877    
878    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
881            * R/ndenseMatrix.R: new coercions n* -> l*
882    
883    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
886    
887            * R/Ops.R ("Logic"): and other "Ops", many updates
888    
889    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * src/Mutils.h (SET_DimNames): new utility
892    
893            * R/Auxiliaries.R (nnzero): improved and now exported via
894    
895            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
896    
897    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * R/diagMatrix.R (!): fix typo.
900    
901    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * R/Auxiliaries.R (as_Csparse): and quite a few others:
904                    allow to pass class definition --> speedup
905            * R/sparseMatrix.R: apply the above
906    
907            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
908    
909            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
910            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
911            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
912    
913            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
914    
915            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
916            and use it for "sparse*" as well, since it's faster than the
917            as_Csparse(.) way.
918    
919    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
922    
923    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
926            as method for   M[ ij ] <- v
927            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
928    
929            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
930            FALSE answer
931    
932            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
933            * tests/indexing.R: test it, and some of the above
934    
935    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
936    
937            * R/Auxiliaries.R (is_duplicatedT): new utility
938    
939    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
940    
941            * src/init.c (R_init_Matrix): export cholmod_scale
942    
943    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
946            base::as.matrix to (x, ...)
947    
948    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
951            file; start using "Logic", hence
952    
953            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
954            * NAMESPACE: import and export "Logic"
955    
956    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
957    
958            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
959            only needed previously to R version 2.5.0.
960    
961    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
964    
965            * R/Tsparse.R (replTmat): fix subassignment of triangular
966            * R/Csparse.R (replCmat): ditto
967            * tests/indexing.R: more tests, incl the above fix
968    
969    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/Auxiliaries.R (drop0): extend for non CSparse
972            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
973    
974            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
975                    use uplo correctly (!); other places: use uplo_P() macro
976    
977            * R/Csparse.R (replCmat): call diagU2N() when needed
978            * R/Tsparse.R (replTmat): ditto
979    
980            * src/dtCMatrix.c (tCMatrix_validate): new
981            * src/dtTMatrix.c (tTMatrix_validate): new, used in
982            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
983    
984            * R/diagMatrix.R (replDiag): to use in [<-
985    
986    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
989                    also more general diagU2N().
990    
991    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
994            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
995    
996    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * tests/bind.R: a few more cases
999            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1000    
1001            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1002            * R/ddenseMatrix.R (cbind2/rbind2)
1003            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1004            * tests/indexing.R
1005            * tests/indexing.Rout.save: updated
1006    
1007    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1010            * tests/indexing.R
1011    
1012    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1015            align with proper position of "0", i.e., right for integers.
1016            argument 'align' by default is "fancy".
1017    
1018    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1021            * R/Csparse.R: and fix "Compare" for more cases.
1022            * tests/Class+Meth.R: test some of these (m == m, m != m)
1023    
1024    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1025    
1026            * R/lsparseMatrix.R: all() and any() methods
1027            * R/ldenseMatrix.R:      ditto
1028            * NAMESPACE, R/Matrix.R: ditto
1029    
1030            * man/all-methods.Rd: document them minimally
1031    
1032            * tests/simple.R: add a few examples for these
1033    
1034    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * R/Tsparse.R ([): fix long standing typo in symmetric case
1037            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1038    
1039    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1040    
1041            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1042            to LL before converting to a sparse matrix. (The LDL form can be
1043            converted to a sparse matrix but it is implicitly a unit
1044            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1045    
1046    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1047    
1048            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1049    
1050    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1051    
1052            * DESCRIPTION (Version): updated -> release 0.9975-7
1053            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1054    
1055    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1058    
1059    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1060    
1061            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1062            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1063            is exactly singular.
1064    
1065    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * DESCRIPTION (Date): updated -> release 0.9975-6
1068    
1069    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1072            now returns symmetric.
1073    
1074            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1075    
1076            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1077            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1078    
1079            * R/Auxiliaries.R (.type.kind): added
1080    
1081    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1082    
1083            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1084            running src/CSparse_install.sh
1085    
1086            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1087    
1088    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1091            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1092    
1093            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1094    
1095            * tests/Class+Meth.R (tstMatrixClass): now assure
1096            the (important in method programming) property :
1097    
1098                    ###>>  Every "Matrix" is either
1099                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1100    
1101                    (where "*" stands for "Matrix")
1102    
1103            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1104    
1105            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1106            * tests/validObj.R: checks for "comparison"
1107    
1108            * R/sparseMatrix.R ([): improved indexing for sparse;
1109                    trying to keep <symmetric>[ n, n] symmmetric
1110    
1111            * tests/indexing.R: indexing for logical sparse now ok
1112    
1113    
1114    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1115    
1116            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1117    
1118            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1119    
1120    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1123    
1124            * tests/simple.R: validObject() checking the above.
1125    
1126            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1127            replacing both dgCMatrix_validate and lgCM*.
1128    
1129            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1130            fix dimnames setting in other places.
1131            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1132    
1133    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1134    
1135            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1136    
1137            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1138            symmetry test, via
1139            * R/Auxiliaries.R (.as.dgC.0.factors):
1140    
1141    2006-11-01  Douglas Bates  <bates@r-project.org>
1142    
1143            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1144            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1145            <CsparseMatrix>) added
1146    
1147    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1148    
1149            * tests/matprod.R: add a variation of Harri's example
1150    
1151            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1152            recursive infinitely.
1153    
1154            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1155    
1156            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1157    
1158    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1159    
1160            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1161            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1162            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1163            satisfy the above test.
1164    
1165    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1166    
1167            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1168    
1169            * R/dgCMatrix.R: solve(a, b="missing") based on
1170            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1171            RHS = NULL.
1172    
1173            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1174            add more (needed) [t]crossprod() methods.
1175    
1176            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1177    
1178            * R/Auxiliaries.R (as_CspClass): cleanup
1179            (drop0): internal utility for "Csparse_drop(*, 0)"
1180            (.bail.out.2): encourage active feedback
1181    
1182    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1183    
1184            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1185    
1186            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1187            non-valid or 'sorted' case).
1188    
1189            * R/dsparseMatrix.R: add "chol" method.
1190            * R/ddenseMatrix.R: ditto
1191    
1192            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1193            * NAMESPACE (Ops)
1194            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1195            coercion; deprecating direct lower level coercions.
1196    
1197            * R/*.R (seq): use seq_len() and seq_along() where possible.
1198    
1199    
1200    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * DESCRIPTION (Version): 0.9975-5 ready for release
1203    
1204    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1205    
1206            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1207    
1208    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1209    
1210            * R/AllClass.R (corMatrix): add 'validity' check;
1211                    comment out unused "LDL" class definition
1212            * NAMESPACE: mention, but do not export "LDL" class
1213            * R/corMatrix.R: new (simple), needed for R-devel with
1214            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1215              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1216    
1217    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1218    
1219            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1220            use Rprintf and R's error handling.
1221    
1222    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1223    
1224            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1225            * tests/matprod.R: add tests for the bug fixed.
1226    
1227    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1228    
1229            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1230            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1231    
1232    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1233    
1234            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1235    
1236    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1237    
1238            * DESCRIPTION (Version): 0.9975-3
1239    
1240            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1241            (sparse) matrices.
1242            * man/bdiag.Rd: docu + examples
1243    
1244            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1245    
1246            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1247            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1248    
1249            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1250            that result is sparse or diagonal (and not dense).
1251    
1252            * man/Subassign-methods.Rd: fix examples
1253    
1254            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1255            should always return a sparse (and not sometimes a diagonal) matrix.
1256    
1257    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1258    
1259            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1260    
1261    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1262    
1263            * DESCRIPTION (Version): 0.9975-2
1264    
1265            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1266    
1267    2006-10-02  Douglas Bates  <bates@R-project.org>
1268    
1269            * tests/dg_Matrix.R: Simplify test taking into account new code.
1270    
1271    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1272    
1273            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1274    
1275            * R/lsTMatrix.R: new files w/ missing methods
1276            * R/nsTMatrix.R:  "  'for completeness'
1277    
1278            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1279    
1280            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1281    
1282    
1283    2006-09-28  Douglas Bates  <bates@R-project.org>
1284    
1285            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1286            included.
1287    
1288            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1289            Export C-callable functions used in Zt_create in lme4.
1290    
1291    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * DESCRIPTION (Version): 0.9975-1
1294    
1295            * tests/simple.R: less checks fail; using NA, found that our
1296                    kronecker() is not base-compatible with NA's.
1297    
1298            * R/dMatrix.R: "Compare" method now implemented for all cases
1299    
1300            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1301    
1302            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1303    
1304            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1305            * src/dspMatrix.c (dspMatrix_validate): ditto
1306    
1307            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1308              including coercion to [nl]tTMatrix.
1309    
1310            * R/diagMatrix.R (show): print a header line as for other classes.
1311    
1312    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1313    
1314            * src/Makefile.win (SUBDIRS): fix typo
1315    
1316    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1317    
1318            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1319    
1320    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1321    
1322            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1323            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1324            accept a symmetric matrix).
1325            * tests/group-methods.R: Uncomment test of crossprod applied to
1326            lsCMatrix objects.
1327    
1328    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * R/AllClass.R (symmetricMatrix): add validity method (available
1331            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1332    
1333            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1334    
1335            * tests/indexing.Rout.save:
1336            * tests/indexing.R: additions, mainly for 'lsparse'
1337    
1338            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1339            case.
1340    
1341            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1342    
1343    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1344    
1345            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1346                    as 'N' (1-letter - Ok?)
1347    
1348            * tests/group-methods.R: add test for logical + NAs
1349    
1350            * R/dMatrix.R ("Compare"): fix to work with NA's
1351    
1352            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1353    
1354            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1355                    which is implemented.
1356    
1357    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1358    
1359            * src/chm_common.c: coerce logical <-> double instead of
1360            typecasting;  needed for "l" matrix handling in cholmod.
1361    
1362            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1363    
1364            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1365            (Tsp2grNEL): other fixes needed
1366    
1367    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1368    
1369            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1370                    Matrices, since "lMatrix", also "lsparseM" can have NA
1371            * R/ndenseMatrix.R, etc: new source files
1372            * man/nsparseMatrix-classes.Rd, etc: new help files
1373            * tests/: adaptions
1374            * src/chm_common.c (chm_dense_to_SEXP): and others:
1375                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1376            * src/Csparse.c, etc: ditto
1377    
1378    2006-09-11  Douglas Bates  <bates@R-project.org>
1379    
1380            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1381            alloc_d**Matrix functions to the lme4 package.
1382    
1383    2006-09-09  Douglas Bates  <bates@R-project.org>
1384    
1385            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1386            fixed
1387    
1388    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * R/lMatrix.R: new
1391    
1392            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1393    
1394            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1395            * man/tcrossprod.Rd: ditto
1396    
1397    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1398    
1399            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1400            for exported functions
1401            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1402            Remove partitioning algorithms for sparse matrix reordering.  The
1403            copyright on the Metis code was problematic and the methods were
1404            rarely used.
1405            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1406            operations are now done entirely in CHOLMOD code.
1407    
1408    2006-09-06  Douglas Bates  <bates@R-project.org>
1409    
1410            * src/Mutils.h: Remove functions that are no longer used.
1411    
1412    2006-09-04  Douglas Bates  <bates@R-project.org>
1413    
1414            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1415            * src/DEPS.mkf: update
1416    
1417    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1418    
1419            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1420            * DESCRIPTION (Version): 0.9975-0
1421            (Depends): R (>= 2.4.0)
1422    
1423    2006-09-01  Douglas Bates  <bates@R-project.org>
1424    
1425            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1426    
1427    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1428    
1429            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1430            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1431    
1432            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1433    
1434    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1435    
1436            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1437            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1438            * R/dsparseMatrix.R: ditto
1439            * R/Csparse.R: ditto
1440    
1441    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1442    
1443            * R/dMatrix.R (Compare): improve availability of "<", etc
1444            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1445    
1446    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1447    
1448            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1449            of a 0-index which was used as 1-index (..hmm)
1450    
1451            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1452    
1453            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1454            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1455            (.is.diagonal): ditto
1456    
1457            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1458    
1459            * R/Matrix.R (Matrix): also work for NA data
1460    
1461  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1462    
1463          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting          * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting

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