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revision 1654, Fri Oct 27 16:58:15 2006 UTC revision 2158, Fri Mar 28 17:07:54 2008 UTC
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1    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
4            order to become compatible to new R 2.7.0 base::rcond().
5    
6    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
9    
10            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
11    
12            * inst/test-tools.R (isValid): new utility, used much in
13            * tests/simple.R:
14    
15            * man/BunchKaufman-methods.Rd: added too
16    
17    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/dsyMatrix.R: add BunchKaufman() methods.
20            * R/dspMatrix.R:
21    
22            * src/init.c: add dsyMatrix_trf
23    
24    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
25    
26            * DESCRIPTION (Version): release 0.999375-7
27            * src/CHMfactor.c (CHMfactor_update): fix
28    
29    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
32            internal_chm_factor().
33    
34            * R/AllGeneric.R: do *not* define a "chol" generic
35                    (but rather use the implicit one *without* making pivot
36                    part of the signature)
37            * R/*.R: drop the 'pivot' from chol's signature and make
38                    'pivot=FALSE' a default argument of method definitions.
39    
40            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
41            version of Matrix
42    
43    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
46    
47            * R/sparseMatrix.R (is.na): new simple method
48            * R/denseMatrix.R (is.na): ditto.
49    
50            * R/diagMatrix.R (.symDiagonal): newly exported utility.
51    
52            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
53    
54            * src/UFsparse_download.sh: -->
55            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
56    
57    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
60            functionality; barely tested in
61            * tests/factorizing.R
62    
63            * src/Csparse.c (diag_tC): new functionality to enable faster
64            determinant(<dsCMatrix>, .) in
65            * R/dsCMatrix.R
66    
67    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
68    
69            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
70              src/CHMfactor.c, src/CHMfactor.h,
71              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
72              Log-determinant of the parent matrix from a CHMfactor object as
73              chm_factor_ldetL2; documentation and support
74    
75    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
78    
79    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
82            warning.
83    
84    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
87    
88            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
89              <diagonal> o <sparse_triangular>
90              setAs(., "nMatrix") added.
91    
92            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
93    
94            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
95                    new argument 'checkDense = FALSE'.
96    
97    
98    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
101            back-permutation of the matrix exponential.
102    
103            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
104    
105            * DESCRIPTION (Date,Version): ready to release 0.999375-5
106    
107            * tests/simple.R: testing diagN2U
108    
109    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Auxiliaries.R (diagN2U): interface to
112    
113            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
114    
115            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
116    
117    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * src/chm_common.c (chm_diagN2U): new utility.
120    
121            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
122            make use of chm_diagN2U() and hence now preserve triangularity and
123            unit-triangularity.
124    
125            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
126    
127    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
130    
131            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
132            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
133    
134            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
135    
136            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
137    
138            * src/chm_common.c (AS_CHM_FINISH): add note about problem
139            for triangular (diag = "U").
140    
141    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
144            * R/bind.R:  .Call(dense_to_Csparse, *)
145    
146    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Matrix.R (Matrix): no longer use coercions to specific classes
149                    (since we are discouraging them in user code).
150    
151            * tests/*.R: also replaces coercions to specific classes by
152            coercions to super classes.
153    
154            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
155    
156    
157    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
160    
161            * src/dense.c (dense_band): generalized from ddense_band
162    
163            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
164              now for "denseMatrix" (instead of just "ddense*"); much
165              simplified setMethod()s for these.
166    
167            * src/dense.c (dense_to_symmetric): generalized from ddense_*
168    
169    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
172            version of as(*, "symmetricMatric").
173    
174            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
175            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
176    
177    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Matrix.R (subset.ij): utility, as first step to faster
180               M [ <ij-matrix> ] indexing.
181    
182            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
183    
184            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
185            for more efficient symmpart() and skewpart() methods.
186    
187            * src/Mutils.c (equal_string_vectors): utility
188    
189            * src/dense.c (ddense_to_symmetric): new function used in
190    
191            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
192    
193            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
194            order to match the generic (and evade .local(..)).
195    
196            * R/dsCMatrix.R: dgC -> dsC: use C code!
197    
198            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
199            as per TODO
200    
201            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
202    
203            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
204    
205    
206    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
209    
210            * R/Auxiliaries.R (non0.i): take out of non0ind
211    
212            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
213            make tril(), triu(), band() work for "matrix" and all "dense*"
214    
215            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
216            * tests/simple.R: test the fix above
217    
218            * R/sparseMatrix.R ([): simplification: no coerce to <general>
219                    before we use as(., <Tsparse>)[...] anyway
220    
221            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
222    
223            * R/triangularMatrix.R (isTriangular): methods for all subclasses
224            instead of "triangularMatrix" -- just to disambiguate
225    
226    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
229            * tests/indexing.R: example that fails above
230    
231    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
234            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
235                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
236    
237            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
238            * src/Tsparse.h, init.c: ditto
239            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
240                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
241            * R/sparseMatrix.R (isTriangular): hence simplified
242    
243    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Ops.R (.Arith.Csparse): new utility factored out of former
246              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
247    
248    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
251    
252            * inst/test-tools.R (isOrthogonal): new function; also file restructured
253    
254    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
257            coercion to "nMatrix" and "pMatrix"
258    
259            * R/AllClass.R: "Schur" class;  "number" class union
260            * man/number-class.Rd:
261            * man/Schur-class.Rd:
262    
263            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
264            (.simpleSchur): Schur() method for diagonal matrices
265            (.triSchur):    Schur() method for triangular matrices
266            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
267    
268    
269    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
272    
273    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
276                    in order to ensure 'system = *' is not lost;
277                    formals()$system instead of cut&paste.
278            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
279    
280    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * DESCRIPTION (Date): make ready for release --> 0.999375-4
283    
284            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
285    
286    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
287    
288            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
289                    and hence does as.vector(.).
290            * man/pMatrix-class.Rd: docs
291            * R/sparseMatrix.R: fix for printing "integer sparse"
292    
293            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
294    
295            * R/Matrix.R and others: use "exact" function argument list for
296                    both "["   : (x, i,j, ..., drop)
297                    and  "[<-" : (x, i,j, ..., value)
298    
299            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
300            * R/Tsparse.R (replTmat):    ditto
301            * R/diagMatrix.R (replDiag): ditto
302            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
303            * tests/indexing.R: testing the above
304    
305    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/sparseMatrix.R (cov2cor): method for sparse matrices
308    
309            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
310    
311            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
312    
313            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
314    
315    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R: "generic" cov2cor() method
318    
319            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
320                    speed up Q %*% D %*% t(Q)
321            * tests/dpoMatrix.R: test nearPD()
322    
323    2007-12-05  Doug Bates and Martin Maechler
324    
325            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
326            stats::xtabs() allowing to create sparse matrices.
327    
328    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
331    
332    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
335    
336    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/LU.R: solve() method for "denseLU"
339    
340    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * DESCRIPTION (Version): 0.999375-3 preparing for release
343    
344            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
345    
346            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
347    
348    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
351              thanks to Kasper Kristensen.
352            * tests/matprod.R: regression test for that.
353    
354    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
355    
356            * [r4778] R/AllGeneric.R: Check R version before defining generics for
357              primitives
358    
359    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/denseMatrix.R (rcond): method
362            * R/sparseQR.R (rcond): method, use x or t(x)
363    
364    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
367            matrices.
368            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
369    
370            * man/rcond.Rd: mention the more general definition, and add
371            example for non-square matrices.
372    
373            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
374    
375    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
378    
379    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
382            * tests/indexing.R: add new regression for the above cases.
383    
384    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * src/Mutils.h (__sun): clause for alloca.h on Solaris
387    
388    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * DESCRIPTION (Date, Version): 0.999375-2
391    
392    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * R/HBMM.R (readMM): make work for pattern matrices as well
395    
396    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
397    
398            * [r4730] src/Mutils.h: declare alloca
399            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
400              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
401              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
402              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
403              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
404              methods; switch writeMM to use CHOLMOD code; repair readMM
405    
406    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
409            Oehlschlaegel's ... result type still to be discussed!
410    
411    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * man/image-methods.Rd: new, combining all image() methods
414    
415    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
418            to work via dgC...
419    
420            * R/Matrix.R (Matrix): special treatment for "table" (S3)
421    
422    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * R/dgTMatrix.R (image): change defaults to
425                    aspect = "iso", colorkey = FALSE
426    
427    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
430            must copy its *expanded* x slot before LAPACK call.
431    
432            * tests/matprod.R: test the last days' changes.
433    
434    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
435    
436            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
437              as well as in sources
438            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
439              Lapack call
440    
441    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
444                    ("Matrix", "matrix") which is needed in some cases.
445            Ditto for solve().
446    
447            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
448            infinite recursion in dispatch for some cases.
449    
450    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
451    
452            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
453              so pointers match
454    
455    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * DESCRIPTION (Date): set ready for release -- 0.999375-1
458    
459    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
460    
461            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
462              src/chm_common.c, src/chm_common.h: Change API for
463              numeric_as_chm_dense and N_AS_CHM_DN
464    
465    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
468            * tests/matprod.R: regr.test for it
469    
470    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
471    
472            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
473            * tests/group-methods.R: and regression-test it
474    
475    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
476    
477            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
478              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
479              triplet_to_sparse, documentation, use typedefs
480    
481    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * man/dpoMatrix-class.Rd: added 'corMatrix' example
484    
485            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
486            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
487            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
488    
489            * R/lsparseMatrix.R: bug fix in "all" method
490            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
491    
492            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
493            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
494                    + matrix |-> nMatrix coercion
495            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
496            * man/pMatrix-class.Rd: ditto
497    
498            * R/Matrix.R (Summary): method for non-dMatrix
499    
500            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
501            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
502                    test all Summary methods.
503    
504    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
507    
508    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
511    
512            * R/pMatrix.R (t?crossprod): methods for pMatrix
513    
514    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
515    
516            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
517    
518    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
519    
520            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
521              trying to fix a subtle bug - which has been somewhere else.
522    
523    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
524    
525            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
526              solve the bug
527    
528    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * src/dgCMatrix.c (compressed_to_TMatrix):
531    
532    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * src/Csparse.c (Rsparse_validate): new, to have some validity
535            checking for RsparseMatrix
536            * src/dgCMatrix.c (xRMatrix_validate): ditto
537            * src/dtCMatrix.c (tRMatrix_validate): ditto
538    
539    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
540    
541            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
542              lgRMatrix
543            * [r4568] DESCRIPTION: Prepare for bug-fix release
544            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
545              for declaration of cholmod_symmetry
546    
547    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
550            release.
551    
552    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
553    
554            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
555              functions - no longer used
556            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
557              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
558              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
559              Alloca
560    
561    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
562    
563            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
564              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
565              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
566              src/t_gCMatrix_colSums.c: more R_CheckStack()s
567    
568    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
569    
570            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
571              the required amount of memory then call M_numeric_as_chm_dense.
572            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
573              (like Calloc but calling alloca)
574    
575    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
578            and extended with more sophisticated 'col.names' option.
579            * NAMESPACE: export  printSparseMatrix()
580            * man/printSpMatrix.Rd: document, incl. examples
581    
582    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
583    
584            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
585              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
586              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
587    
588    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * DESCRIPTION (Version): 0.99875-4
591    
592            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
593            some dimnames perservation.
594    
595            * R/dsTMatrix.R (t-method): keep dimnames
596            * R/dtTMatrix.R:  ditto
597    
598            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
599            and ncol(.) < 10
600    
601            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
602            from Mutils.h
603    
604            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
605            e.g. in as(<ngCMatrix>, "matrix")
606    
607    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
608    
609            * [r4529] .: Create a branch for the API changes from the 0.99875
610              series to the 0.999375 series
611            * [r4530] DESCRIPTION, inst/include/Matrix.h,
612              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
613              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
614              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
615              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
616              as_cholmod_x functions
617    
618    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
619    
620            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
621              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
622              to Comparisons
623    
624    >>>>>>> .merge-right.r4561
625    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * DESCRIPTION (Version): 0.99875-3 ready to be released.
628    
629            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
630    
631            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
632            that should also work in a future version of R.
633    
634    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
637    
638            * R/sparseVector.R: more *sparseVector coercions, notably for
639            non - double ones.
640    
641    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
644              notably the new ones building on the new .Call(.)s:
645    
646            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
647            all 4 of [dlin]gCMatrix_colSums().
648    
649    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
650    
651            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
652            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
653              result
654    
655    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/kronecker.R: fix typo (could lead to inf.recursion)
658            * test/simple.R: testing that
659    
660            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
661            method as well (which can have arguments, show() can't).
662    
663    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
664    
665            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
666              added dgCMatrix_colSums for [col,row][Sums,Means]
667    
668    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
669    
670            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
671              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
672              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
673            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
674              class
675            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
676              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
677              row names to store the levels - duh!  Added an example.
678    
679    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * src/Csparse.c (Csparse_validate): check for *repeated* entries
682            thanks to example from Christian Buchta; with a test here:
683            * tests/simple.R:
684    
685    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
688            of colSums(*, sparseResult = TRUE)
689    
690    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
693            'na.rm = FALSE' as "everywhere" else in R.
694    
695    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
696    
697            * [r4421] src/CSparse_install.sh: Modify for new organization of
698              CSparse package
699            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
700              SuiteSparse
701            * [r4426] src/Makefile: add ./UFconfig to the include path for
702              compilation
703            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
704            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
705              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
706    
707    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
710            * R/sparseMatrix.R (prSpMatrix): now gives a message about
711            suppressed column names.
712    
713    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
714    
715            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
716              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
717              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
718              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
719              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
720              Remove warnings after change to const char* CHAR
721    
722    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
723    
724            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
725              type of M_cholmod_ssmult
726    
727    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
728    
729            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
730              src/init.c: Yet another cholmod export - cholmod_ssmult
731    
732    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * NAMESPACE: exported drop0(), since
735            * man/drop0.Rd: I have seen several cases, I really wanted to use
736            it, so our users may want too.
737    
738    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * man/colSums.Rd: separately document colSums() etc, since these
741            have the extra argument 'sparseResult'.
742    
743    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
744    
745            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
746            * man/spMatrix.Rd: docu., including examples
747    
748            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
749            in order to make colMeans() etc fast *and* correct.
750            * R/sparseVector.R (replSPvec): "[<-" functionality for
751            sparseVectors; tested in
752            * tests/simple.R:
753    
754    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
757            (very) sparse Matrices; output similar to Matlab's print().
758    
759    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
760    
761            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
762            0-based, indices (Jose Quesada <quesada@gmail.com>).
763    
764    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
765    
766            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
767    
768    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/Auxiliaries.R (sparsapply): new utility, much faster than
771            tapply1() for large sparse matrices.
772    
773    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
774    
775            * R/Matrix.R (dim<-): reshape now via sparseVector.
776    
777            * R/sparseVector.R: methods and function for
778            * R/AllClass.R: new "sparseVector" class and daughters.
779            * NAMESPACE: export new classes
780    
781    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * DESCRIPTION (Version): 0.99875-1
784            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
785    
786    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
789            indexing
790            * tests/indexing.R: test set for that.
791    
792    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
793    
794            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
795            entries.
796            * tests/indexing.R(out): add regression test for it
797    
798    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
801            name for "!" method definitions.
802    
803    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/Tsparse.R (intI): new utility, used for "[" :
806                    Cleanup up there, and fixes for duplicated indices - more TODO!
807    
808            * tests/indexing.R(out): more tests
809    
810    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
811    
812            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
813            code that is now part of the R Lapack library.
814    
815            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
816            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
817    
818    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
821    
822    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
825            up with extraneous names '0'...'<n-1>'
826    
827    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/dgTMatrix.R (mat2dgT): care about NAs
830    
831    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/kronecker.R: triangularity preserving methods
834    
835    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * R/kronecker.R: new file collecting kronecker() methods in one
838                    place.  Goal: become much faster!
839    
840    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
843            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
844            can be much faster.
845    
846            * tests/matprod.R: add regression tests for these (upper & lower).
847    
848    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
849    
850            * R/Matrix.R (diff): method for our Matrices.
851    
852            * R/sparseMatrix.R (isDiagonal): check dim()!
853    
854    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/Matrix.R (dim<-): new method for "reshape()" built on a
857            proposal from Tamas Papp.
858    
859    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
862    
863            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
864            rather define and export  cBind() and rBind() only.
865            --> useRs *must* change code that used to have cbind()/rbind() !!
866    
867            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
868            * R/bind.Rout.save: ditto
869    
870    2007-02-16  Douglas Bates  <bates@r-project.org>
871    
872            * DESCRIPTION (Date, Version): 0.9975-11 with new date
873            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
874            const modifier on declaration of the array 'valid'
875    
876    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
877    
878            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
879    
880    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
881    
882            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
883    
884            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
885            * tests/simple.R: test the above and some of these coercions:
886    
887            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
888                    be careful to avoid infinite recursion, using new coercions in
889            * R/ngCMatrix.R and nsC... and ntC...
890            * R/lsparseMatrix.R: ditto
891    
892            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
893    
894            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
895            * R/Rsparse.R: reactivate .Call()s
896    
897            * tests/Class+Meth.R: a bit more on actual classes
898    
899    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
900    
901            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
902    
903    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * DESCRIPTION (Version): 0.9975-10 to upload
906    
907            * tests/Class+Meth.R (tstMatrixClass): require coercions to
908            specific classes less unconditionally.
909    
910            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
911    
912            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
913    
914            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
915            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
916            R_to_CMatrix segfaults on one platform.
917            Eliminate most coercion method to *specific* classes, and replace
918            with virtual classes coercions.
919    
920    
921    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
922    
923            * src/init.c: export the CHM...._validate() placeholders, since
924            they *are* called.
925    
926            * tests/Class+Meth.R (classCanCoerce): and starting to test
927            all as(<from>, <to>)
928    
929    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
932            * tests/indexing.R: tested now
933            * tests/indexing.Rout.save: updated
934    
935            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
936            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
937            appropriate.
938    
939            * NAMESPACE: export a trivial
940            * R/Matrix.R: drop() Matrix-method
941    
942            * R/AllClass.R: moved all prototypes to virtual super classes.
943    
944            * R/Rsparse.R: many more coercions to have less exceptions in
945            * tests/Class+Meth.R:
946    
947            * R/Ops.R (Compare): tweak for case with NA
948            * tests/simpl.R: hence another 'FIXME' eliminated
949    
950    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
953            objects.
954    
955            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
956              and more of "!", "&", "|", all, any; coercions
957    
958            * R/Rsparse.R: many coercions (which enable quite a few other
959            methods), thanks to enhancements in
960            * src/dgCMatrix.c (R_to_CMatrix): new, and
961            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
962            symmetric & triangular and ..RMatrix objects.
963    
964            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
965            renamed file from src/dsTMatrix.c;
966            now dealing with symmetric and triangular Tsparse coercions, both
967            to dense and general.
968    
969    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
972    
973            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
974            where sensible when the <numeric> is of length > 1.
975    
976    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * R/Matrix.R ([<-): for M[] <- value: fix length
979    
980    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
983            * R/ndenseMatrix.R: new coercions n* -> l*
984    
985    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
986    
987            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
988    
989            * R/Ops.R ("Logic"): and other "Ops", many updates
990    
991    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * src/Mutils.h (SET_DimNames): new utility
994    
995            * R/Auxiliaries.R (nnzero): improved and now exported via
996    
997            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
998    
999    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * R/diagMatrix.R (!): fix typo.
1002    
1003    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1006                    allow to pass class definition --> speedup
1007            * R/sparseMatrix.R: apply the above
1008    
1009            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1010    
1011            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1012            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1013            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1014    
1015            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1016    
1017            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1018            and use it for "sparse*" as well, since it's faster than the
1019            as_Csparse(.) way.
1020    
1021    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1022    
1023            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1024    
1025    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1028            as method for   M[ ij ] <- v
1029            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1030    
1031            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1032            FALSE answer
1033    
1034            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1035            * tests/indexing.R: test it, and some of the above
1036    
1037    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1038    
1039            * R/Auxiliaries.R (is_duplicatedT): new utility
1040    
1041    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1042    
1043            * src/init.c (R_init_Matrix): export cholmod_scale
1044    
1045    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1046    
1047            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1048            base::as.matrix to (x, ...)
1049    
1050    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1053            file; start using "Logic", hence
1054    
1055            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1056            * NAMESPACE: import and export "Logic"
1057    
1058    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1059    
1060            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1061            only needed previously to R version 2.5.0.
1062    
1063    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1066    
1067            * R/Tsparse.R (replTmat): fix subassignment of triangular
1068            * R/Csparse.R (replCmat): ditto
1069            * tests/indexing.R: more tests, incl the above fix
1070    
1071    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1072    
1073            * R/Auxiliaries.R (drop0): extend for non CSparse
1074            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1075    
1076            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1077                    use uplo correctly (!); other places: use uplo_P() macro
1078    
1079            * R/Csparse.R (replCmat): call diagU2N() when needed
1080            * R/Tsparse.R (replTmat): ditto
1081    
1082            * src/dtCMatrix.c (tCMatrix_validate): new
1083            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1084            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1085    
1086            * R/diagMatrix.R (replDiag): to use in [<-
1087    
1088    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1091                    also more general diagU2N().
1092    
1093    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1096            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1097    
1098    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1099    
1100            * tests/bind.R: a few more cases
1101            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1102    
1103            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1104            * R/ddenseMatrix.R (cbind2/rbind2)
1105            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1106            * tests/indexing.R
1107            * tests/indexing.Rout.save: updated
1108    
1109    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1112            * tests/indexing.R
1113    
1114    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1115    
1116            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1117            align with proper position of "0", i.e., right for integers.
1118            argument 'align' by default is "fancy".
1119    
1120    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1123            * R/Csparse.R: and fix "Compare" for more cases.
1124            * tests/Class+Meth.R: test some of these (m == m, m != m)
1125    
1126    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1127    
1128            * R/lsparseMatrix.R: all() and any() methods
1129            * R/ldenseMatrix.R:      ditto
1130            * NAMESPACE, R/Matrix.R: ditto
1131    
1132            * man/all-methods.Rd: document them minimally
1133    
1134            * tests/simple.R: add a few examples for these
1135    
1136    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1137    
1138            * R/Tsparse.R ([): fix long standing typo in symmetric case
1139            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1140    
1141    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1142    
1143            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1144            to LL before converting to a sparse matrix. (The LDL form can be
1145            converted to a sparse matrix but it is implicitly a unit
1146            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1147    
1148    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1149    
1150            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1151    
1152    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1153    
1154            * DESCRIPTION (Version): updated -> release 0.9975-7
1155            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1156    
1157    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1158    
1159            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1160    
1161    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1162    
1163            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1164            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1165            is exactly singular.
1166    
1167    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1168    
1169            * DESCRIPTION (Date): updated -> release 0.9975-6
1170    
1171    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1172    
1173            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1174            now returns symmetric.
1175    
1176            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1177    
1178            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1179            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1180    
1181            * R/Auxiliaries.R (.type.kind): added
1182    
1183    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1186            running src/CSparse_install.sh
1187    
1188            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1189    
1190    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1193            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1194    
1195            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1196    
1197            * tests/Class+Meth.R (tstMatrixClass): now assure
1198            the (important in method programming) property :
1199    
1200                    ###>>  Every "Matrix" is either
1201                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1202    
1203                    (where "*" stands for "Matrix")
1204    
1205            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1206    
1207            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1208            * tests/validObj.R: checks for "comparison"
1209    
1210            * R/sparseMatrix.R ([): improved indexing for sparse;
1211                    trying to keep <symmetric>[ n, n] symmmetric
1212    
1213            * tests/indexing.R: indexing for logical sparse now ok
1214    
1215    
1216    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1217    
1218            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1219    
1220            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1221    
1222    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1223    
1224            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1225    
1226            * tests/simple.R: validObject() checking the above.
1227    
1228            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1229            replacing both dgCMatrix_validate and lgCM*.
1230    
1231            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1232            fix dimnames setting in other places.
1233            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1234    
1235    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1236    
1237            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1238    
1239            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1240            symmetry test, via
1241            * R/Auxiliaries.R (.as.dgC.0.factors):
1242    
1243    2006-11-01  Douglas Bates  <bates@r-project.org>
1244    
1245            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1246            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1247            <CsparseMatrix>) added
1248    
1249    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1250    
1251            * tests/matprod.R: add a variation of Harri's example
1252    
1253            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1254            recursive infinitely.
1255    
1256            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1257    
1258            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1259    
1260    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1261    
1262            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1263            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1264            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1265            satisfy the above test.
1266    
1267  2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1268    
1269            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1270    
1271          * R/dgCMatrix.R: solve(a, b="missing") based on          * R/dgCMatrix.R: solve(a, b="missing") based on
1272          * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with          * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1273          RHS = NULL.          RHS = NULL.

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