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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 2190, Mon Apr 28 16:24:15 2008 UTC
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1    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (cholMat): possibly keep packed
4    
5            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
6            for R < 2.7.0.
7    
8            * R/Tsparse.R ([): for triangularMatrix, check if result may be
9            triangular.
10            * tests/indexing.R: regression test
11    
12    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
15            * R/Ops.R: more methods, for lMatrix/nMatrix
16    
17    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * R/expm.R: new file for all expm() methods; notably new ones for
20            diagonal*, triangular*, symmetric* and also simple "matrix".
21    
22    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
25    
26            * inst/test-tools.R (assert.EQ.mat): better message when not equal
27    
28            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
29    
30            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
31            [dl]denseMatrix {identical slots; but more logical method dispatch}
32    
33    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
36    
37            * R/diagMatrix.R (determinant): method
38    
39    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
42    
43            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
44    
45            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
46            its diagonal
47    
48    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
51    
52            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
53    
54            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
55    
56            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
57    
58    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
61    
62            * R/Ops.R (.do.Logic.lsparse): fix NA case
63    
64            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
65    
66            * R/Auxiliaries.R (nnzero): fix special cases, using
67            * R/Auxiliaries.R (indDiag): new utility
68            * R/Auxiliaries.R (indTri): new argument 'diag'
69    
70            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
71    
72    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
75    
76            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
77            ".tCMatrix" triangular matrix.
78    
79            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
80            'clx' can be class *or* class representation.
81            (nnzSparse): new.
82            (non0ind): new 'xtendSymm' argument; used in
83            * R/Ops.R:
84    
85            * R/pMatrix.R: more efficient determinant() method
86    
87    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
90            * [disactivated] NAMESPACE: export(det)
91    
92            * R/diagMatrix.R (mkDiag): new substitute for diag()
93    
94            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
95            (as0, as1): new utility.
96    
97            * R/Csparse.R (diag, band): need diagU2N()
98    
99            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
100    
101            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
102    
103            * R/Ops.R (Compare): fix <nsp> o <nsp> case
104    
105            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
106    
107    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/Auxiliaries.R (signPerm): new utility for
110            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
111    
112            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
113            since we have our own error handler (and can use tryCatch() from R).
114    
115    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
118    
119            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
120            when not positive definite.
121    
122            * R/Auxiliaries.R (asTri): new auxiliary
123            (non0.i): make *much* faster for Tsparse with many non-zero
124            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
125    
126            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
127            test-tools.R , see below
128    
129            * R/dMatrix.R: fix "Summary" method: + diagU2N()
130    
131            * NAMESPACE, R/Matrix.R: add mean() method
132    
133    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
136            cold-hot colors; try *changed* default useAbs = FALSE
137            * man/image-methods.Rd:  nice examples
138    
139    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * inst/test-tools.R (checkMatrix): new function for modularizing part
142            of tstMatrixClass() in tests/Class+Meth.R
143    
144            * R/dsCMatrix.R: coercion from "matrix"
145            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
146    
147            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
148            add test for as(matrix(,0,0), <class>)
149    
150    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
153            work as determinant(matrix(,0,0)).
154    
155            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
156            * man/sparseLU-class.Rd: ditto
157    
158            * R/dgCMatrix.R (determinant): method building on lu()
159            * R/sparseMatrix.R, Matrix.R, ...: ditto
160    
161            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
162    
163    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
166            pattern matrices.
167    
168    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * src/dense.c (dense_to_Csparse): all declarations *before*
171            R_CheckStack(); needed e.g. for ancient gcc 2.96.
172    
173    
174    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * DESCRIPTION (Version): 0.999375-9 --- need to release
177            for R-devel (and R 2.7.0 alpha soon).
178    
179            * R/AllClass.R: drop "double" from "atomicVector" class union
180    
181            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
182            * R/dgeMatrix.R: ditto
183    
184            * R/sparseMatrix.R (summary): count NAs
185    
186            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
187    
188    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
191            order to become compatible to new R 2.7.0 base::rcond().
192    
193    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
196    
197            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
198    
199            * inst/test-tools.R (isValid): new utility, used much in
200            * tests/simple.R:
201    
202            * man/BunchKaufman-methods.Rd: added too
203    
204    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
205    
206            * R/dsyMatrix.R: add BunchKaufman() methods.
207            * R/dspMatrix.R:
208    
209            * src/init.c: add dsyMatrix_trf
210    
211    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
212    
213            * DESCRIPTION (Version): release 0.999375-7
214            * src/CHMfactor.c (CHMfactor_update): fix
215    
216    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
219            internal_chm_factor().
220    
221            * R/AllGeneric.R: do *not* define a "chol" generic
222                    (but rather use the implicit one *without* making pivot
223                    part of the signature)
224            * R/*.R: drop the 'pivot' from chol's signature and make
225                    'pivot=FALSE' a default argument of method definitions.
226    
227            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
228            version of Matrix
229    
230    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
233    
234            * R/sparseMatrix.R (is.na): new simple method
235            * R/denseMatrix.R (is.na): ditto.
236    
237            * R/diagMatrix.R (.symDiagonal): newly exported utility.
238    
239            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
240    
241            * src/UFsparse_download.sh: -->
242            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
243    
244    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
247            functionality; barely tested in
248            * tests/factorizing.R
249    
250            * src/Csparse.c (diag_tC): new functionality to enable faster
251            determinant(<dsCMatrix>, .) in
252            * R/dsCMatrix.R
253    
254    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
255    
256            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
257              src/CHMfactor.c, src/CHMfactor.h,
258              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
259              Log-determinant of the parent matrix from a CHMfactor object as
260              chm_factor_ldetL2; documentation and support
261    
262    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
265    
266    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
269            warning.
270    
271    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
274    
275            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
276              <diagonal> o <sparse_triangular>
277              setAs(., "nMatrix") added.
278    
279            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
280    
281            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
282                    new argument 'checkDense = FALSE'.
283    
284    
285    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
288            back-permutation of the matrix exponential.
289    
290            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
291    
292            * DESCRIPTION (Date,Version): ready to release 0.999375-5
293    
294            * tests/simple.R: testing diagN2U
295    
296    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/Auxiliaries.R (diagN2U): interface to
299    
300            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
301    
302            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
303    
304    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * src/chm_common.c (chm_diagN2U): new utility.
307    
308            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
309            make use of chm_diagN2U() and hence now preserve triangularity and
310            unit-triangularity.
311    
312            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
313    
314    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
317    
318            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
319            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
320    
321            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
322    
323            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
324    
325            * src/chm_common.c (AS_CHM_FINISH): add note about problem
326            for triangular (diag = "U").
327    
328    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
331            * R/bind.R:  .Call(dense_to_Csparse, *)
332    
333    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Matrix.R (Matrix): no longer use coercions to specific classes
336                    (since we are discouraging them in user code).
337    
338            * tests/*.R: also replaces coercions to specific classes by
339            coercions to super classes.
340    
341            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
342    
343    
344    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
347    
348            * src/dense.c (dense_band): generalized from ddense_band
349    
350            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
351              now for "denseMatrix" (instead of just "ddense*"); much
352              simplified setMethod()s for these.
353    
354            * src/dense.c (dense_to_symmetric): generalized from ddense_*
355    
356    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
359            version of as(*, "symmetricMatric").
360    
361            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
362            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
363    
364    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Matrix.R (subset.ij): utility, as first step to faster
367               M [ <ij-matrix> ] indexing.
368    
369            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
370    
371            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
372            for more efficient symmpart() and skewpart() methods.
373    
374            * src/Mutils.c (equal_string_vectors): utility
375    
376            * src/dense.c (ddense_to_symmetric): new function used in
377    
378            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
379    
380            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
381            order to match the generic (and evade .local(..)).
382    
383            * R/dsCMatrix.R: dgC -> dsC: use C code!
384    
385            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
386            as per TODO
387    
388            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
389    
390            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
391    
392    
393    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
396    
397            * R/Auxiliaries.R (non0.i): take out of non0ind
398    
399            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
400            make tril(), triu(), band() work for "matrix" and all "dense*"
401    
402            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
403            * tests/simple.R: test the fix above
404    
405            * R/sparseMatrix.R ([): simplification: no coerce to <general>
406                    before we use as(., <Tsparse>)[...] anyway
407    
408            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
409    
410            * R/triangularMatrix.R (isTriangular): methods for all subclasses
411            instead of "triangularMatrix" -- just to disambiguate
412    
413    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
416            * tests/indexing.R: example that fails above
417    
418    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
421            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
422                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
423    
424            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
425            * src/Tsparse.h, init.c: ditto
426            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
427                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
428            * R/sparseMatrix.R (isTriangular): hence simplified
429    
430    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/Ops.R (.Arith.Csparse): new utility factored out of former
433              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
434    
435    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
438    
439            * inst/test-tools.R (isOrthogonal): new function; also file restructured
440    
441    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
444            coercion to "nMatrix" and "pMatrix"
445    
446            * R/AllClass.R: "Schur" class;  "number" class union
447            * man/number-class.Rd:
448            * man/Schur-class.Rd:
449    
450            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
451            (.simpleSchur): Schur() method for diagonal matrices
452            (.triSchur):    Schur() method for triangular matrices
453            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
454    
455    
456    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
459    
460    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
463                    in order to ensure 'system = *' is not lost;
464                    formals()$system instead of cut&paste.
465            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
466    
467    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * DESCRIPTION (Date): make ready for release --> 0.999375-4
470    
471            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
472    
473    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
474    
475            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
476                    and hence does as.vector(.).
477            * man/pMatrix-class.Rd: docs
478            * R/sparseMatrix.R: fix for printing "integer sparse"
479    
480            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
481    
482            * R/Matrix.R and others: use "exact" function argument list for
483                    both "["   : (x, i,j, ..., drop)
484                    and  "[<-" : (x, i,j, ..., value)
485    
486            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
487            * R/Tsparse.R (replTmat):    ditto
488            * R/diagMatrix.R (replDiag): ditto
489            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
490            * tests/indexing.R: testing the above
491    
492    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/sparseMatrix.R (cov2cor): method for sparse matrices
495    
496            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
497    
498            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
499    
500            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
501    
502    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/Matrix.R: "generic" cov2cor() method
505    
506            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
507                    speed up Q %*% D %*% t(Q)
508            * tests/dpoMatrix.R: test nearPD()
509    
510    2007-12-05  Doug Bates and Martin Maechler
511    
512            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
513            stats::xtabs() allowing to create sparse matrices.
514    
515    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
518    
519    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
522    
523    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/LU.R: solve() method for "denseLU"
526    
527    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * DESCRIPTION (Version): 0.999375-3 preparing for release
530    
531            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
532    
533            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
534    
535    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
538              thanks to Kasper Kristensen.
539            * tests/matprod.R: regression test for that.
540    
541    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
542    
543            * [r4778] R/AllGeneric.R: Check R version before defining generics for
544              primitives
545    
546    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * R/denseMatrix.R (rcond): method
549            * R/sparseQR.R (rcond): method, use x or t(x)
550    
551    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
554            matrices.
555            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
556    
557            * man/rcond.Rd: mention the more general definition, and add
558            example for non-square matrices.
559    
560            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
561    
562    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
565    
566    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
569            * tests/indexing.R: add new regression for the above cases.
570    
571    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * src/Mutils.h (__sun): clause for alloca.h on Solaris
574    
575    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
576    
577            * DESCRIPTION (Date, Version): 0.999375-2
578    
579    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
580    
581            * R/HBMM.R (readMM): make work for pattern matrices as well
582    
583    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
584    
585            * [r4730] src/Mutils.h: declare alloca
586            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
587              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
588              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
589              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
590              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
591              methods; switch writeMM to use CHOLMOD code; repair readMM
592    
593    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
596            Oehlschlaegel's ... result type still to be discussed!
597    
598    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * man/image-methods.Rd: new, combining all image() methods
601    
602    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
605            to work via dgC...
606    
607            * R/Matrix.R (Matrix): special treatment for "table" (S3)
608    
609    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/dgTMatrix.R (image): change defaults to
612                    aspect = "iso", colorkey = FALSE
613    
614    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
617            must copy its *expanded* x slot before LAPACK call.
618    
619            * tests/matprod.R: test the last days' changes.
620    
621    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
622    
623            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
624              as well as in sources
625            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
626              Lapack call
627    
628    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
631                    ("Matrix", "matrix") which is needed in some cases.
632            Ditto for solve().
633    
634            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
635            infinite recursion in dispatch for some cases.
636    
637    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
638    
639            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
640              so pointers match
641    
642    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * DESCRIPTION (Date): set ready for release -- 0.999375-1
645    
646    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
647    
648            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
649              src/chm_common.c, src/chm_common.h: Change API for
650              numeric_as_chm_dense and N_AS_CHM_DN
651    
652    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
653    
654            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
655            * tests/matprod.R: regr.test for it
656    
657    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
660            * tests/group-methods.R: and regression-test it
661    
662    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
663    
664            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
665              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
666              triplet_to_sparse, documentation, use typedefs
667    
668    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * man/dpoMatrix-class.Rd: added 'corMatrix' example
671    
672            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
673            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
674            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
675    
676            * R/lsparseMatrix.R: bug fix in "all" method
677            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
678    
679            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
680            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
681                    + matrix |-> nMatrix coercion
682            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
683            * man/pMatrix-class.Rd: ditto
684    
685            * R/Matrix.R (Summary): method for non-dMatrix
686    
687            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
688            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
689                    test all Summary methods.
690    
691    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
694    
695    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
698    
699            * R/pMatrix.R (t?crossprod): methods for pMatrix
700    
701    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
702    
703            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
704    
705    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
706    
707            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
708              trying to fix a subtle bug - which has been somewhere else.
709    
710    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
711    
712            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
713              solve the bug
714    
715    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * src/dgCMatrix.c (compressed_to_TMatrix):
718    
719    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * src/Csparse.c (Rsparse_validate): new, to have some validity
722            checking for RsparseMatrix
723            * src/dgCMatrix.c (xRMatrix_validate): ditto
724            * src/dtCMatrix.c (tRMatrix_validate): ditto
725    
726    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
727    
728            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
729              lgRMatrix
730            * [r4568] DESCRIPTION: Prepare for bug-fix release
731            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
732              for declaration of cholmod_symmetry
733    
734    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
737            release.
738    
739    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
740    
741            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
742              functions - no longer used
743            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
744              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
745              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
746              Alloca
747    
748    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
749    
750            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
751              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
752              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
753              src/t_gCMatrix_colSums.c: more R_CheckStack()s
754    
755    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
756    
757            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
758              the required amount of memory then call M_numeric_as_chm_dense.
759            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
760              (like Calloc but calling alloca)
761    
762    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
765            and extended with more sophisticated 'col.names' option.
766            * NAMESPACE: export  printSparseMatrix()
767            * man/printSpMatrix.Rd: document, incl. examples
768    
769    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
770    
771            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
772              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
773              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
774    
775    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * DESCRIPTION (Version): 0.99875-4
778    
779            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
780            some dimnames perservation.
781    
782            * R/dsTMatrix.R (t-method): keep dimnames
783            * R/dtTMatrix.R:  ditto
784    
785            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
786            and ncol(.) < 10
787    
788            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
789            from Mutils.h
790    
791            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
792            e.g. in as(<ngCMatrix>, "matrix")
793    
794    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
795    
796            * [r4529] .: Create a branch for the API changes from the 0.99875
797              series to the 0.999375 series
798            * [r4530] DESCRIPTION, inst/include/Matrix.h,
799              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
800              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
801              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
802              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
803              as_cholmod_x functions
804    
805    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
806    
807            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
808              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
809              to Comparisons
810    
811    >>>>>>> .merge-right.r4561
812    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * DESCRIPTION (Version): 0.99875-3 ready to be released.
815    
816            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
817    
818            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
819            that should also work in a future version of R.
820    
821    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
824    
825            * R/sparseVector.R: more *sparseVector coercions, notably for
826            non - double ones.
827    
828    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
831              notably the new ones building on the new .Call(.)s:
832    
833            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
834            all 4 of [dlin]gCMatrix_colSums().
835    
836    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
837    
838            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
839            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
840              result
841    
842    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/kronecker.R: fix typo (could lead to inf.recursion)
845            * test/simple.R: testing that
846    
847            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
848            method as well (which can have arguments, show() can't).
849    
850    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
851    
852            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
853              added dgCMatrix_colSums for [col,row][Sums,Means]
854    
855    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
856    
857            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
858              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
859              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
860            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
861              class
862            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
863              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
864              row names to store the levels - duh!  Added an example.
865    
866    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * src/Csparse.c (Csparse_validate): check for *repeated* entries
869            thanks to example from Christian Buchta; with a test here:
870            * tests/simple.R:
871    
872    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
875            of colSums(*, sparseResult = TRUE)
876    
877    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
880            'na.rm = FALSE' as "everywhere" else in R.
881    
882    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
883    
884            * [r4421] src/CSparse_install.sh: Modify for new organization of
885              CSparse package
886            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
887              SuiteSparse
888            * [r4426] src/Makefile: add ./UFconfig to the include path for
889              compilation
890            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
891            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
892              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
893    
894    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
897            * R/sparseMatrix.R (prSpMatrix): now gives a message about
898            suppressed column names.
899    
900    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
901    
902            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
903              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
904              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
905              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
906              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
907              Remove warnings after change to const char* CHAR
908    
909    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
910    
911            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
912              type of M_cholmod_ssmult
913    
914    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
915    
916            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
917              src/init.c: Yet another cholmod export - cholmod_ssmult
918    
919    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * NAMESPACE: exported drop0(), since
922            * man/drop0.Rd: I have seen several cases, I really wanted to use
923            it, so our users may want too.
924    
925    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * man/colSums.Rd: separately document colSums() etc, since these
928            have the extra argument 'sparseResult'.
929    
930    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
931    
932            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
933            * man/spMatrix.Rd: docu., including examples
934    
935            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
936            in order to make colMeans() etc fast *and* correct.
937            * R/sparseVector.R (replSPvec): "[<-" functionality for
938            sparseVectors; tested in
939            * tests/simple.R:
940    
941    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
944            (very) sparse Matrices; output similar to Matlab's print().
945    
946    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
947    
948            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
949            0-based, indices (Jose Quesada <quesada@gmail.com>).
950    
951    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
952    
953            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
954    
955    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
956    
957            * R/Auxiliaries.R (sparsapply): new utility, much faster than
958            tapply1() for large sparse matrices.
959    
960    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
961    
962            * R/Matrix.R (dim<-): reshape now via sparseVector.
963    
964            * R/sparseVector.R: methods and function for
965            * R/AllClass.R: new "sparseVector" class and daughters.
966            * NAMESPACE: export new classes
967    
968    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
969    
970            * DESCRIPTION (Version): 0.99875-1
971            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
972    
973    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
974    
975            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
976            indexing
977            * tests/indexing.R: test set for that.
978    
979    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
980    
981            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
982            entries.
983            * tests/indexing.R(out): add regression test for it
984    
985    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
986    
987            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
988            name for "!" method definitions.
989    
990    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/Tsparse.R (intI): new utility, used for "[" :
993                    Cleanup up there, and fixes for duplicated indices - more TODO!
994    
995            * tests/indexing.R(out): more tests
996    
997    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
998    
999            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1000            code that is now part of the R Lapack library.
1001    
1002            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1003            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1004    
1005    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1008    
1009    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1010    
1011            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1012            up with extraneous names '0'...'<n-1>'
1013    
1014    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/dgTMatrix.R (mat2dgT): care about NAs
1017    
1018    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * R/kronecker.R: triangularity preserving methods
1021    
1022    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * R/kronecker.R: new file collecting kronecker() methods in one
1025                    place.  Goal: become much faster!
1026    
1027    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1030            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1031            can be much faster.
1032    
1033            * tests/matprod.R: add regression tests for these (upper & lower).
1034    
1035    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/Matrix.R (diff): method for our Matrices.
1038    
1039            * R/sparseMatrix.R (isDiagonal): check dim()!
1040    
1041    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1042    
1043            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1044            proposal from Tamas Papp.
1045    
1046    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1049    
1050            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1051            rather define and export  cBind() and rBind() only.
1052            --> useRs *must* change code that used to have cbind()/rbind() !!
1053    
1054            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1055            * R/bind.Rout.save: ditto
1056    
1057    2007-02-16  Douglas Bates  <bates@r-project.org>
1058    
1059            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1060            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1061            const modifier on declaration of the array 'valid'
1062    
1063    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1064    
1065            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1066    
1067    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1068    
1069            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1070    
1071            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1072            * tests/simple.R: test the above and some of these coercions:
1073    
1074            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1075                    be careful to avoid infinite recursion, using new coercions in
1076            * R/ngCMatrix.R and nsC... and ntC...
1077            * R/lsparseMatrix.R: ditto
1078    
1079            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1080    
1081            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1082            * R/Rsparse.R: reactivate .Call()s
1083    
1084            * tests/Class+Meth.R: a bit more on actual classes
1085    
1086    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1087    
1088            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1089    
1090    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1091    
1092            * DESCRIPTION (Version): 0.9975-10 to upload
1093    
1094            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1095            specific classes less unconditionally.
1096    
1097            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1098    
1099            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1100    
1101            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1102            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1103            R_to_CMatrix segfaults on one platform.
1104            Eliminate most coercion method to *specific* classes, and replace
1105            with virtual classes coercions.
1106    
1107    
1108    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1109    
1110            * src/init.c: export the CHM...._validate() placeholders, since
1111            they *are* called.
1112    
1113            * tests/Class+Meth.R (classCanCoerce): and starting to test
1114            all as(<from>, <to>)
1115    
1116    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1119            * tests/indexing.R: tested now
1120            * tests/indexing.Rout.save: updated
1121    
1122            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1123            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1124            appropriate.
1125    
1126            * NAMESPACE: export a trivial
1127            * R/Matrix.R: drop() Matrix-method
1128    
1129            * R/AllClass.R: moved all prototypes to virtual super classes.
1130    
1131            * R/Rsparse.R: many more coercions to have less exceptions in
1132            * tests/Class+Meth.R:
1133    
1134            * R/Ops.R (Compare): tweak for case with NA
1135            * tests/simpl.R: hence another 'FIXME' eliminated
1136    
1137    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1138    
1139            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1140            objects.
1141    
1142            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1143              and more of "!", "&", "|", all, any; coercions
1144    
1145            * R/Rsparse.R: many coercions (which enable quite a few other
1146            methods), thanks to enhancements in
1147            * src/dgCMatrix.c (R_to_CMatrix): new, and
1148            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1149            symmetric & triangular and ..RMatrix objects.
1150    
1151            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1152            renamed file from src/dsTMatrix.c;
1153            now dealing with symmetric and triangular Tsparse coercions, both
1154            to dense and general.
1155    
1156    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1157    
1158            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1159    
1160            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1161            where sensible when the <numeric> is of length > 1.
1162    
1163    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1164    
1165            * R/Matrix.R ([<-): for M[] <- value: fix length
1166    
1167    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1168    
1169            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1170            * R/ndenseMatrix.R: new coercions n* -> l*
1171    
1172    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1175    
1176            * R/Ops.R ("Logic"): and other "Ops", many updates
1177    
1178    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * src/Mutils.h (SET_DimNames): new utility
1181    
1182            * R/Auxiliaries.R (nnzero): improved and now exported via
1183    
1184            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1185    
1186    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1187    
1188            * R/diagMatrix.R (!): fix typo.
1189    
1190    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1193                    allow to pass class definition --> speedup
1194            * R/sparseMatrix.R: apply the above
1195    
1196            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1197    
1198            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1199            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1200            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1201    
1202            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1203    
1204            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1205            and use it for "sparse*" as well, since it's faster than the
1206            as_Csparse(.) way.
1207    
1208    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1209    
1210            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1211    
1212    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1213    
1214            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1215            as method for   M[ ij ] <- v
1216            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1217    
1218            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1219            FALSE answer
1220    
1221            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1222            * tests/indexing.R: test it, and some of the above
1223    
1224    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1225    
1226            * R/Auxiliaries.R (is_duplicatedT): new utility
1227    
1228  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1229    
1230          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
1231    
1232    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1235            base::as.matrix to (x, ...)
1236    
1237  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R

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