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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 2193, Mon May 5 06:56:21 2008 UTC
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1    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
4            * NAMESPACE (unname): finally exported
5    
6    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/Auxiliaries.R (cholMat): possibly keep packed
9    
10            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
11            for R < 2.7.0.
12    
13            * R/Tsparse.R ([): for triangularMatrix, check if result may be
14            triangular.
15            * tests/indexing.R: regression test
16    
17    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
20            * R/Ops.R: more methods, for lMatrix/nMatrix
21    
22    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/expm.R: new file for all expm() methods; notably new ones for
25            diagonal*, triangular*, symmetric* and also simple "matrix".
26    
27    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
30    
31            * inst/test-tools.R (assert.EQ.mat): better message when not equal
32    
33            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
34    
35            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
36            [dl]denseMatrix {identical slots; but more logical method dispatch}
37    
38    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
39    
40            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
41    
42            * R/diagMatrix.R (determinant): method
43    
44    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
47    
48            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
49    
50            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
51            its diagonal
52    
53    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
56    
57            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
58    
59            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
60    
61            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
62    
63    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
66    
67            * R/Ops.R (.do.Logic.lsparse): fix NA case
68    
69            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
70    
71            * R/Auxiliaries.R (nnzero): fix special cases, using
72            * R/Auxiliaries.R (indDiag): new utility
73            * R/Auxiliaries.R (indTri): new argument 'diag'
74    
75            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
76    
77    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
80    
81            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
82            ".tCMatrix" triangular matrix.
83    
84            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
85            'clx' can be class *or* class representation.
86            (nnzSparse): new.
87            (non0ind): new 'xtendSymm' argument; used in
88            * R/Ops.R:
89    
90            * R/pMatrix.R: more efficient determinant() method
91    
92    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
95            * [disactivated] NAMESPACE: export(det)
96    
97            * R/diagMatrix.R (mkDiag): new substitute for diag()
98    
99            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
100            (as0, as1): new utility.
101    
102            * R/Csparse.R (diag, band): need diagU2N()
103    
104            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
105    
106            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
107    
108            * R/Ops.R (Compare): fix <nsp> o <nsp> case
109    
110            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
111    
112    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/Auxiliaries.R (signPerm): new utility for
115            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
116    
117            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
118            since we have our own error handler (and can use tryCatch() from R).
119    
120    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
123    
124            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
125            when not positive definite.
126    
127            * R/Auxiliaries.R (asTri): new auxiliary
128            (non0.i): make *much* faster for Tsparse with many non-zero
129            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
130    
131            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
132            test-tools.R , see below
133    
134            * R/dMatrix.R: fix "Summary" method: + diagU2N()
135    
136            * NAMESPACE, R/Matrix.R: add mean() method
137    
138    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
141            cold-hot colors; try *changed* default useAbs = FALSE
142            * man/image-methods.Rd:  nice examples
143    
144    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * inst/test-tools.R (checkMatrix): new function for modularizing part
147            of tstMatrixClass() in tests/Class+Meth.R
148    
149            * R/dsCMatrix.R: coercion from "matrix"
150            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
151    
152            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
153            add test for as(matrix(,0,0), <class>)
154    
155    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
158            work as determinant(matrix(,0,0)).
159    
160            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
161            * man/sparseLU-class.Rd: ditto
162    
163            * R/dgCMatrix.R (determinant): method building on lu()
164            * R/sparseMatrix.R, Matrix.R, ...: ditto
165    
166            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
167    
168    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
171            pattern matrices.
172    
173    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * src/dense.c (dense_to_Csparse): all declarations *before*
176            R_CheckStack(); needed e.g. for ancient gcc 2.96.
177    
178    
179    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * DESCRIPTION (Version): 0.999375-9 --- need to release
182            for R-devel (and R 2.7.0 alpha soon).
183    
184            * R/AllClass.R: drop "double" from "atomicVector" class union
185    
186            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
187            * R/dgeMatrix.R: ditto
188    
189            * R/sparseMatrix.R (summary): count NAs
190    
191            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
192    
193    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
196            order to become compatible to new R 2.7.0 base::rcond().
197    
198    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
201    
202            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
203    
204            * inst/test-tools.R (isValid): new utility, used much in
205            * tests/simple.R:
206    
207            * man/BunchKaufman-methods.Rd: added too
208    
209    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/dsyMatrix.R: add BunchKaufman() methods.
212            * R/dspMatrix.R:
213    
214            * src/init.c: add dsyMatrix_trf
215    
216    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
217    
218            * DESCRIPTION (Version): release 0.999375-7
219            * src/CHMfactor.c (CHMfactor_update): fix
220    
221    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
224            internal_chm_factor().
225    
226            * R/AllGeneric.R: do *not* define a "chol" generic
227                    (but rather use the implicit one *without* making pivot
228                    part of the signature)
229            * R/*.R: drop the 'pivot' from chol's signature and make
230                    'pivot=FALSE' a default argument of method definitions.
231    
232            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
233            version of Matrix
234    
235    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
238    
239            * R/sparseMatrix.R (is.na): new simple method
240            * R/denseMatrix.R (is.na): ditto.
241    
242            * R/diagMatrix.R (.symDiagonal): newly exported utility.
243    
244            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
245    
246            * src/UFsparse_download.sh: -->
247            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
248    
249    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
252            functionality; barely tested in
253            * tests/factorizing.R
254    
255            * src/Csparse.c (diag_tC): new functionality to enable faster
256            determinant(<dsCMatrix>, .) in
257            * R/dsCMatrix.R
258    
259    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
260    
261            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
262              src/CHMfactor.c, src/CHMfactor.h,
263              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
264              Log-determinant of the parent matrix from a CHMfactor object as
265              chm_factor_ldetL2; documentation and support
266    
267    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
270    
271    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
274            warning.
275    
276    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
279    
280            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
281              <diagonal> o <sparse_triangular>
282              setAs(., "nMatrix") added.
283    
284            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
285    
286            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
287                    new argument 'checkDense = FALSE'.
288    
289    
290    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
293            back-permutation of the matrix exponential.
294    
295            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
296    
297            * DESCRIPTION (Date,Version): ready to release 0.999375-5
298    
299            * tests/simple.R: testing diagN2U
300    
301    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * R/Auxiliaries.R (diagN2U): interface to
304    
305            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
306    
307            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
308    
309    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * src/chm_common.c (chm_diagN2U): new utility.
312    
313            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
314            make use of chm_diagN2U() and hence now preserve triangularity and
315            unit-triangularity.
316    
317            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
318    
319    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
322    
323            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
324            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
325    
326            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
327    
328            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
329    
330            * src/chm_common.c (AS_CHM_FINISH): add note about problem
331            for triangular (diag = "U").
332    
333    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
336            * R/bind.R:  .Call(dense_to_Csparse, *)
337    
338    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * R/Matrix.R (Matrix): no longer use coercions to specific classes
341                    (since we are discouraging them in user code).
342    
343            * tests/*.R: also replaces coercions to specific classes by
344            coercions to super classes.
345    
346            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
347    
348    
349    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
352    
353            * src/dense.c (dense_band): generalized from ddense_band
354    
355            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
356              now for "denseMatrix" (instead of just "ddense*"); much
357              simplified setMethod()s for these.
358    
359            * src/dense.c (dense_to_symmetric): generalized from ddense_*
360    
361    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
364            version of as(*, "symmetricMatric").
365    
366            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
367            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
368    
369    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * R/Matrix.R (subset.ij): utility, as first step to faster
372               M [ <ij-matrix> ] indexing.
373    
374            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
375    
376            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
377            for more efficient symmpart() and skewpart() methods.
378    
379            * src/Mutils.c (equal_string_vectors): utility
380    
381            * src/dense.c (ddense_to_symmetric): new function used in
382    
383            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
384    
385            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
386            order to match the generic (and evade .local(..)).
387    
388            * R/dsCMatrix.R: dgC -> dsC: use C code!
389    
390            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
391            as per TODO
392    
393            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
394    
395            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
396    
397    
398    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
401    
402            * R/Auxiliaries.R (non0.i): take out of non0ind
403    
404            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
405            make tril(), triu(), band() work for "matrix" and all "dense*"
406    
407            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
408            * tests/simple.R: test the fix above
409    
410            * R/sparseMatrix.R ([): simplification: no coerce to <general>
411                    before we use as(., <Tsparse>)[...] anyway
412    
413            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
414    
415            * R/triangularMatrix.R (isTriangular): methods for all subclasses
416            instead of "triangularMatrix" -- just to disambiguate
417    
418    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
421            * tests/indexing.R: example that fails above
422    
423    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
426            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
427                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
428    
429            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
430            * src/Tsparse.h, init.c: ditto
431            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
432                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
433            * R/sparseMatrix.R (isTriangular): hence simplified
434    
435    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/Ops.R (.Arith.Csparse): new utility factored out of former
438              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
439    
440    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
443    
444            * inst/test-tools.R (isOrthogonal): new function; also file restructured
445    
446    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
449            coercion to "nMatrix" and "pMatrix"
450    
451            * R/AllClass.R: "Schur" class;  "number" class union
452            * man/number-class.Rd:
453            * man/Schur-class.Rd:
454    
455            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
456            (.simpleSchur): Schur() method for diagonal matrices
457            (.triSchur):    Schur() method for triangular matrices
458            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
459    
460    
461    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
464    
465    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
468                    in order to ensure 'system = *' is not lost;
469                    formals()$system instead of cut&paste.
470            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
471    
472    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * DESCRIPTION (Date): make ready for release --> 0.999375-4
475    
476            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
477    
478    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
479    
480            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
481                    and hence does as.vector(.).
482            * man/pMatrix-class.Rd: docs
483            * R/sparseMatrix.R: fix for printing "integer sparse"
484    
485            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
486    
487            * R/Matrix.R and others: use "exact" function argument list for
488                    both "["   : (x, i,j, ..., drop)
489                    and  "[<-" : (x, i,j, ..., value)
490    
491            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
492            * R/Tsparse.R (replTmat):    ditto
493            * R/diagMatrix.R (replDiag): ditto
494            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
495            * tests/indexing.R: testing the above
496    
497    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * R/sparseMatrix.R (cov2cor): method for sparse matrices
500    
501            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
502    
503            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
504    
505            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
506    
507    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * R/Matrix.R: "generic" cov2cor() method
510    
511            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
512                    speed up Q %*% D %*% t(Q)
513            * tests/dpoMatrix.R: test nearPD()
514    
515    2007-12-05  Doug Bates and Martin Maechler
516    
517            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
518            stats::xtabs() allowing to create sparse matrices.
519    
520    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
523    
524    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
527    
528    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/LU.R: solve() method for "denseLU"
531    
532    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * DESCRIPTION (Version): 0.999375-3 preparing for release
535    
536            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
537    
538            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
539    
540    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
543              thanks to Kasper Kristensen.
544            * tests/matprod.R: regression test for that.
545    
546    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
547    
548            * [r4778] R/AllGeneric.R: Check R version before defining generics for
549              primitives
550    
551    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/denseMatrix.R (rcond): method
554            * R/sparseQR.R (rcond): method, use x or t(x)
555    
556    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
559            matrices.
560            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
561    
562            * man/rcond.Rd: mention the more general definition, and add
563            example for non-square matrices.
564    
565            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
566    
567    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
570    
571    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
574            * tests/indexing.R: add new regression for the above cases.
575    
576    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * src/Mutils.h (__sun): clause for alloca.h on Solaris
579    
580    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * DESCRIPTION (Date, Version): 0.999375-2
583    
584    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
585    
586            * R/HBMM.R (readMM): make work for pattern matrices as well
587    
588    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
589    
590            * [r4730] src/Mutils.h: declare alloca
591            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
592              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
593              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
594              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
595              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
596              methods; switch writeMM to use CHOLMOD code; repair readMM
597    
598    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
601            Oehlschlaegel's ... result type still to be discussed!
602    
603    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * man/image-methods.Rd: new, combining all image() methods
606    
607    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
610            to work via dgC...
611    
612            * R/Matrix.R (Matrix): special treatment for "table" (S3)
613    
614    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/dgTMatrix.R (image): change defaults to
617                    aspect = "iso", colorkey = FALSE
618    
619    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
622            must copy its *expanded* x slot before LAPACK call.
623    
624            * tests/matprod.R: test the last days' changes.
625    
626    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
627    
628            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
629              as well as in sources
630            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
631              Lapack call
632    
633    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
636                    ("Matrix", "matrix") which is needed in some cases.
637            Ditto for solve().
638    
639            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
640            infinite recursion in dispatch for some cases.
641    
642    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
643    
644            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
645              so pointers match
646    
647    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * DESCRIPTION (Date): set ready for release -- 0.999375-1
650    
651    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
652    
653            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
654              src/chm_common.c, src/chm_common.h: Change API for
655              numeric_as_chm_dense and N_AS_CHM_DN
656    
657    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
660            * tests/matprod.R: regr.test for it
661    
662    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
665            * tests/group-methods.R: and regression-test it
666    
667    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
668    
669            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
670              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
671              triplet_to_sparse, documentation, use typedefs
672    
673    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
674    
675            * man/dpoMatrix-class.Rd: added 'corMatrix' example
676    
677            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
678            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
679            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
680    
681            * R/lsparseMatrix.R: bug fix in "all" method
682            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
683    
684            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
685            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
686                    + matrix |-> nMatrix coercion
687            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
688            * man/pMatrix-class.Rd: ditto
689    
690            * R/Matrix.R (Summary): method for non-dMatrix
691    
692            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
693            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
694                    test all Summary methods.
695    
696    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
699    
700    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
703    
704            * R/pMatrix.R (t?crossprod): methods for pMatrix
705    
706    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
707    
708            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
709    
710    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
711    
712            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
713              trying to fix a subtle bug - which has been somewhere else.
714    
715    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
716    
717            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
718              solve the bug
719    
720    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * src/dgCMatrix.c (compressed_to_TMatrix):
723    
724    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
725    
726            * src/Csparse.c (Rsparse_validate): new, to have some validity
727            checking for RsparseMatrix
728            * src/dgCMatrix.c (xRMatrix_validate): ditto
729            * src/dtCMatrix.c (tRMatrix_validate): ditto
730    
731    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
732    
733            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
734              lgRMatrix
735            * [r4568] DESCRIPTION: Prepare for bug-fix release
736            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
737              for declaration of cholmod_symmetry
738    
739    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
742            release.
743    
744    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
745    
746            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
747              functions - no longer used
748            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
749              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
750              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
751              Alloca
752    
753    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
754    
755            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
756              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
757              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
758              src/t_gCMatrix_colSums.c: more R_CheckStack()s
759    
760    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
761    
762            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
763              the required amount of memory then call M_numeric_as_chm_dense.
764            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
765              (like Calloc but calling alloca)
766    
767    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
770            and extended with more sophisticated 'col.names' option.
771            * NAMESPACE: export  printSparseMatrix()
772            * man/printSpMatrix.Rd: document, incl. examples
773    
774    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
775    
776            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
777              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
778              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
779    
780    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * DESCRIPTION (Version): 0.99875-4
783    
784            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
785            some dimnames perservation.
786    
787            * R/dsTMatrix.R (t-method): keep dimnames
788            * R/dtTMatrix.R:  ditto
789    
790            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
791            and ncol(.) < 10
792    
793            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
794            from Mutils.h
795    
796            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
797            e.g. in as(<ngCMatrix>, "matrix")
798    
799    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
800    
801            * [r4529] .: Create a branch for the API changes from the 0.99875
802              series to the 0.999375 series
803            * [r4530] DESCRIPTION, inst/include/Matrix.h,
804              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
805              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
806              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
807              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
808              as_cholmod_x functions
809    
810    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
811    
812            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
813              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
814              to Comparisons
815    
816    >>>>>>> .merge-right.r4561
817    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * DESCRIPTION (Version): 0.99875-3 ready to be released.
820    
821            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
822    
823            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
824            that should also work in a future version of R.
825    
826    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
829    
830            * R/sparseVector.R: more *sparseVector coercions, notably for
831            non - double ones.
832    
833    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
836              notably the new ones building on the new .Call(.)s:
837    
838            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
839            all 4 of [dlin]gCMatrix_colSums().
840    
841    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
842    
843            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
844            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
845              result
846    
847    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/kronecker.R: fix typo (could lead to inf.recursion)
850            * test/simple.R: testing that
851    
852            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
853            method as well (which can have arguments, show() can't).
854    
855    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
856    
857            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
858              added dgCMatrix_colSums for [col,row][Sums,Means]
859    
860    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
861    
862            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
863              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
864              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
865            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
866              class
867            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
868              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
869              row names to store the levels - duh!  Added an example.
870    
871    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * src/Csparse.c (Csparse_validate): check for *repeated* entries
874            thanks to example from Christian Buchta; with a test here:
875            * tests/simple.R:
876    
877    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
880            of colSums(*, sparseResult = TRUE)
881    
882    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
885            'na.rm = FALSE' as "everywhere" else in R.
886    
887    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
888    
889            * [r4421] src/CSparse_install.sh: Modify for new organization of
890              CSparse package
891            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
892              SuiteSparse
893            * [r4426] src/Makefile: add ./UFconfig to the include path for
894              compilation
895            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
896            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
897              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
898    
899    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
902            * R/sparseMatrix.R (prSpMatrix): now gives a message about
903            suppressed column names.
904    
905    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
906    
907            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
908              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
909              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
910              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
911              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
912              Remove warnings after change to const char* CHAR
913    
914    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
915    
916            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
917              type of M_cholmod_ssmult
918    
919    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
920    
921            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
922              src/init.c: Yet another cholmod export - cholmod_ssmult
923    
924    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * NAMESPACE: exported drop0(), since
927            * man/drop0.Rd: I have seen several cases, I really wanted to use
928            it, so our users may want too.
929    
930    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * man/colSums.Rd: separately document colSums() etc, since these
933            have the extra argument 'sparseResult'.
934    
935    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
936    
937            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
938            * man/spMatrix.Rd: docu., including examples
939    
940            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
941            in order to make colMeans() etc fast *and* correct.
942            * R/sparseVector.R (replSPvec): "[<-" functionality for
943            sparseVectors; tested in
944            * tests/simple.R:
945    
946    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
947    
948            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
949            (very) sparse Matrices; output similar to Matlab's print().
950    
951    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
952    
953            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
954            0-based, indices (Jose Quesada <quesada@gmail.com>).
955    
956    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
957    
958            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
959    
960    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * R/Auxiliaries.R (sparsapply): new utility, much faster than
963            tapply1() for large sparse matrices.
964    
965    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * R/Matrix.R (dim<-): reshape now via sparseVector.
968    
969            * R/sparseVector.R: methods and function for
970            * R/AllClass.R: new "sparseVector" class and daughters.
971            * NAMESPACE: export new classes
972    
973    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * DESCRIPTION (Version): 0.99875-1
976            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
977    
978    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
979    
980            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
981            indexing
982            * tests/indexing.R: test set for that.
983    
984    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
985    
986            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
987            entries.
988            * tests/indexing.R(out): add regression test for it
989    
990    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
993            name for "!" method definitions.
994    
995    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * R/Tsparse.R (intI): new utility, used for "[" :
998                    Cleanup up there, and fixes for duplicated indices - more TODO!
999    
1000            * tests/indexing.R(out): more tests
1001    
1002    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1003    
1004            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1005            code that is now part of the R Lapack library.
1006    
1007            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1008            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1009    
1010    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1013    
1014    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1017            up with extraneous names '0'...'<n-1>'
1018    
1019    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/dgTMatrix.R (mat2dgT): care about NAs
1022    
1023    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * R/kronecker.R: triangularity preserving methods
1026    
1027    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * R/kronecker.R: new file collecting kronecker() methods in one
1030                    place.  Goal: become much faster!
1031    
1032    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1035            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1036            can be much faster.
1037    
1038            * tests/matprod.R: add regression tests for these (upper & lower).
1039    
1040    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * R/Matrix.R (diff): method for our Matrices.
1043    
1044            * R/sparseMatrix.R (isDiagonal): check dim()!
1045    
1046    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1049            proposal from Tamas Papp.
1050    
1051    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1054    
1055            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1056            rather define and export  cBind() and rBind() only.
1057            --> useRs *must* change code that used to have cbind()/rbind() !!
1058    
1059            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1060            * R/bind.Rout.save: ditto
1061    
1062    2007-02-16  Douglas Bates  <bates@r-project.org>
1063    
1064            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1065            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1066            const modifier on declaration of the array 'valid'
1067    
1068    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1069    
1070            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1071    
1072    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1075    
1076            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1077            * tests/simple.R: test the above and some of these coercions:
1078    
1079            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1080                    be careful to avoid infinite recursion, using new coercions in
1081            * R/ngCMatrix.R and nsC... and ntC...
1082            * R/lsparseMatrix.R: ditto
1083    
1084            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1085    
1086            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1087            * R/Rsparse.R: reactivate .Call()s
1088    
1089            * tests/Class+Meth.R: a bit more on actual classes
1090    
1091    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1092    
1093            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1094    
1095    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * DESCRIPTION (Version): 0.9975-10 to upload
1098    
1099            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1100            specific classes less unconditionally.
1101    
1102            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1103    
1104            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1105    
1106            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1107            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1108            R_to_CMatrix segfaults on one platform.
1109            Eliminate most coercion method to *specific* classes, and replace
1110            with virtual classes coercions.
1111    
1112    
1113    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1114    
1115            * src/init.c: export the CHM...._validate() placeholders, since
1116            they *are* called.
1117    
1118            * tests/Class+Meth.R (classCanCoerce): and starting to test
1119            all as(<from>, <to>)
1120    
1121    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1122    
1123            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1124            * tests/indexing.R: tested now
1125            * tests/indexing.Rout.save: updated
1126    
1127            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1128            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1129            appropriate.
1130    
1131            * NAMESPACE: export a trivial
1132            * R/Matrix.R: drop() Matrix-method
1133    
1134            * R/AllClass.R: moved all prototypes to virtual super classes.
1135    
1136            * R/Rsparse.R: many more coercions to have less exceptions in
1137            * tests/Class+Meth.R:
1138    
1139            * R/Ops.R (Compare): tweak for case with NA
1140            * tests/simpl.R: hence another 'FIXME' eliminated
1141    
1142    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1143    
1144            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1145            objects.
1146    
1147            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1148              and more of "!", "&", "|", all, any; coercions
1149    
1150            * R/Rsparse.R: many coercions (which enable quite a few other
1151            methods), thanks to enhancements in
1152            * src/dgCMatrix.c (R_to_CMatrix): new, and
1153            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1154            symmetric & triangular and ..RMatrix objects.
1155    
1156            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1157            renamed file from src/dsTMatrix.c;
1158            now dealing with symmetric and triangular Tsparse coercions, both
1159            to dense and general.
1160    
1161    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1164    
1165            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1166            where sensible when the <numeric> is of length > 1.
1167    
1168    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1169    
1170            * R/Matrix.R ([<-): for M[] <- value: fix length
1171    
1172    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1175            * R/ndenseMatrix.R: new coercions n* -> l*
1176    
1177    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1180    
1181            * R/Ops.R ("Logic"): and other "Ops", many updates
1182    
1183    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * src/Mutils.h (SET_DimNames): new utility
1186    
1187            * R/Auxiliaries.R (nnzero): improved and now exported via
1188    
1189            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1190    
1191    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1192    
1193            * R/diagMatrix.R (!): fix typo.
1194    
1195    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1198                    allow to pass class definition --> speedup
1199            * R/sparseMatrix.R: apply the above
1200    
1201            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1202    
1203            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1204            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1205            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1206    
1207            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1208    
1209            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1210            and use it for "sparse*" as well, since it's faster than the
1211            as_Csparse(.) way.
1212    
1213    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1214    
1215            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1216    
1217    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1218    
1219            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1220            as method for   M[ ij ] <- v
1221            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1222    
1223            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1224            FALSE answer
1225    
1226            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1227            * tests/indexing.R: test it, and some of the above
1228    
1229    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1230    
1231            * R/Auxiliaries.R (is_duplicatedT): new utility
1232    
1233    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1234    
1235            * src/init.c (R_init_Matrix): export cholmod_scale
1236    
1237    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1240            base::as.matrix to (x, ...)
1241    
1242    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1245            file; start using "Logic", hence
1246    
1247            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1248            * NAMESPACE: import and export "Logic"
1249    
1250    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1251    
1252            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1253            only needed previously to R version 2.5.0.
1254    
1255    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1256    
1257            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1258    
1259            * R/Tsparse.R (replTmat): fix subassignment of triangular
1260            * R/Csparse.R (replCmat): ditto
1261            * tests/indexing.R: more tests, incl the above fix
1262    
1263    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1264    
1265            * R/Auxiliaries.R (drop0): extend for non CSparse
1266            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1267    
1268            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1269                    use uplo correctly (!); other places: use uplo_P() macro
1270    
1271            * R/Csparse.R (replCmat): call diagU2N() when needed
1272            * R/Tsparse.R (replTmat): ditto
1273    
1274            * src/dtCMatrix.c (tCMatrix_validate): new
1275            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1276            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1277    
1278            * R/diagMatrix.R (replDiag): to use in [<-
1279    
1280    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1283                    also more general diagU2N().
1284    
1285    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1286    
1287            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1288            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1289    
1290    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1291    
1292            * tests/bind.R: a few more cases
1293            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1294    
1295            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1296            * R/ddenseMatrix.R (cbind2/rbind2)
1297            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1298            * tests/indexing.R
1299            * tests/indexing.Rout.save: updated
1300    
1301    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1302    
1303            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1304            * tests/indexing.R
1305    
1306    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1307    
1308            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1309            align with proper position of "0", i.e., right for integers.
1310            argument 'align' by default is "fancy".
1311    
1312    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1313    
1314            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1315            * R/Csparse.R: and fix "Compare" for more cases.
1316            * tests/Class+Meth.R: test some of these (m == m, m != m)
1317    
1318    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * R/lsparseMatrix.R: all() and any() methods
1321            * R/ldenseMatrix.R:      ditto
1322            * NAMESPACE, R/Matrix.R: ditto
1323    
1324            * man/all-methods.Rd: document them minimally
1325    
1326            * tests/simple.R: add a few examples for these
1327    
1328    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1329    
1330            * R/Tsparse.R ([): fix long standing typo in symmetric case
1331            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1332    
1333    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1334    
1335            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1336            to LL before converting to a sparse matrix. (The LDL form can be
1337            converted to a sparse matrix but it is implicitly a unit
1338            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1339    
1340    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1341    
1342            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1343    
1344    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1345    
1346            * DESCRIPTION (Version): updated -> release 0.9975-7
1347            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1348    
1349  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1350    
1351          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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