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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 2166, Wed Apr 2 15:06:02 2008 UTC
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1    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dense.c (dense_to_Csparse): all declarations *before*
4            R_CheckStack(); needed e.g. for ancient gcc 2.96.
5    
6    
7    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * DESCRIPTION (Version): 0.999375-9 --- need to release
10            for R-devel (and R 2.7.0 alpha soon).
11    
12            * R/AllClass.R: drop "double" from "atomicVector" class union
13    
14            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
15            * R/dgeMatrix.R: ditto
16    
17            * R/sparseMatrix.R (summary): count NAs
18    
19            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
20    
21    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
24            order to become compatible to new R 2.7.0 base::rcond().
25    
26    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
29    
30            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
31    
32            * inst/test-tools.R (isValid): new utility, used much in
33            * tests/simple.R:
34    
35            * man/BunchKaufman-methods.Rd: added too
36    
37    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/dsyMatrix.R: add BunchKaufman() methods.
40            * R/dspMatrix.R:
41    
42            * src/init.c: add dsyMatrix_trf
43    
44    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
45    
46            * DESCRIPTION (Version): release 0.999375-7
47            * src/CHMfactor.c (CHMfactor_update): fix
48    
49    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
52            internal_chm_factor().
53    
54            * R/AllGeneric.R: do *not* define a "chol" generic
55                    (but rather use the implicit one *without* making pivot
56                    part of the signature)
57            * R/*.R: drop the 'pivot' from chol's signature and make
58                    'pivot=FALSE' a default argument of method definitions.
59    
60            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
61            version of Matrix
62    
63    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
66    
67            * R/sparseMatrix.R (is.na): new simple method
68            * R/denseMatrix.R (is.na): ditto.
69    
70            * R/diagMatrix.R (.symDiagonal): newly exported utility.
71    
72            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
73    
74            * src/UFsparse_download.sh: -->
75            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
76    
77    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
80            functionality; barely tested in
81            * tests/factorizing.R
82    
83            * src/Csparse.c (diag_tC): new functionality to enable faster
84            determinant(<dsCMatrix>, .) in
85            * R/dsCMatrix.R
86    
87    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
88    
89            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
90              src/CHMfactor.c, src/CHMfactor.h,
91              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
92              Log-determinant of the parent matrix from a CHMfactor object as
93              chm_factor_ldetL2; documentation and support
94    
95    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
98    
99    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
102            warning.
103    
104    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
107    
108            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
109              <diagonal> o <sparse_triangular>
110              setAs(., "nMatrix") added.
111    
112            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
113    
114            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
115                    new argument 'checkDense = FALSE'.
116    
117    
118    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
121            back-permutation of the matrix exponential.
122    
123            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
124    
125            * DESCRIPTION (Date,Version): ready to release 0.999375-5
126    
127            * tests/simple.R: testing diagN2U
128    
129    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/Auxiliaries.R (diagN2U): interface to
132    
133            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
134    
135            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
136    
137    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * src/chm_common.c (chm_diagN2U): new utility.
140    
141            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
142            make use of chm_diagN2U() and hence now preserve triangularity and
143            unit-triangularity.
144    
145            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
146    
147    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
150    
151            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
152            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
153    
154            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
155    
156            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
157    
158            * src/chm_common.c (AS_CHM_FINISH): add note about problem
159            for triangular (diag = "U").
160    
161    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
164            * R/bind.R:  .Call(dense_to_Csparse, *)
165    
166    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/Matrix.R (Matrix): no longer use coercions to specific classes
169                    (since we are discouraging them in user code).
170    
171            * tests/*.R: also replaces coercions to specific classes by
172            coercions to super classes.
173    
174            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
175    
176    
177    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
180    
181            * src/dense.c (dense_band): generalized from ddense_band
182    
183            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
184              now for "denseMatrix" (instead of just "ddense*"); much
185              simplified setMethod()s for these.
186    
187            * src/dense.c (dense_to_symmetric): generalized from ddense_*
188    
189    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
192            version of as(*, "symmetricMatric").
193    
194            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
195            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
196    
197    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/Matrix.R (subset.ij): utility, as first step to faster
200               M [ <ij-matrix> ] indexing.
201    
202            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
203    
204            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
205            for more efficient symmpart() and skewpart() methods.
206    
207            * src/Mutils.c (equal_string_vectors): utility
208    
209            * src/dense.c (ddense_to_symmetric): new function used in
210    
211            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
212    
213            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
214            order to match the generic (and evade .local(..)).
215    
216            * R/dsCMatrix.R: dgC -> dsC: use C code!
217    
218            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
219            as per TODO
220    
221            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
222    
223            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
224    
225    
226    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
229    
230            * R/Auxiliaries.R (non0.i): take out of non0ind
231    
232            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
233            make tril(), triu(), band() work for "matrix" and all "dense*"
234    
235            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
236            * tests/simple.R: test the fix above
237    
238            * R/sparseMatrix.R ([): simplification: no coerce to <general>
239                    before we use as(., <Tsparse>)[...] anyway
240    
241            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
242    
243            * R/triangularMatrix.R (isTriangular): methods for all subclasses
244            instead of "triangularMatrix" -- just to disambiguate
245    
246    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
249            * tests/indexing.R: example that fails above
250    
251    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
254            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
255                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
256    
257            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
258            * src/Tsparse.h, init.c: ditto
259            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
260                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
261            * R/sparseMatrix.R (isTriangular): hence simplified
262    
263    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Ops.R (.Arith.Csparse): new utility factored out of former
266              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
267    
268    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
271    
272            * inst/test-tools.R (isOrthogonal): new function; also file restructured
273    
274    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
277            coercion to "nMatrix" and "pMatrix"
278    
279            * R/AllClass.R: "Schur" class;  "number" class union
280            * man/number-class.Rd:
281            * man/Schur-class.Rd:
282    
283            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
284            (.simpleSchur): Schur() method for diagonal matrices
285            (.triSchur):    Schur() method for triangular matrices
286            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
287    
288    
289    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
292    
293    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
296                    in order to ensure 'system = *' is not lost;
297                    formals()$system instead of cut&paste.
298            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
299    
300    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * DESCRIPTION (Date): make ready for release --> 0.999375-4
303    
304            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
305    
306    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
309                    and hence does as.vector(.).
310            * man/pMatrix-class.Rd: docs
311            * R/sparseMatrix.R: fix for printing "integer sparse"
312    
313            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
314    
315            * R/Matrix.R and others: use "exact" function argument list for
316                    both "["   : (x, i,j, ..., drop)
317                    and  "[<-" : (x, i,j, ..., value)
318    
319            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
320            * R/Tsparse.R (replTmat):    ditto
321            * R/diagMatrix.R (replDiag): ditto
322            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
323            * tests/indexing.R: testing the above
324    
325    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/sparseMatrix.R (cov2cor): method for sparse matrices
328    
329            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
330    
331            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
332    
333            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
334    
335    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/Matrix.R: "generic" cov2cor() method
338    
339            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
340                    speed up Q %*% D %*% t(Q)
341            * tests/dpoMatrix.R: test nearPD()
342    
343    2007-12-05  Doug Bates and Martin Maechler
344    
345            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
346            stats::xtabs() allowing to create sparse matrices.
347    
348    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
351    
352    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
355    
356    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * R/LU.R: solve() method for "denseLU"
359    
360    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * DESCRIPTION (Version): 0.999375-3 preparing for release
363    
364            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
365    
366            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
367    
368    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
371              thanks to Kasper Kristensen.
372            * tests/matprod.R: regression test for that.
373    
374    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
375    
376            * [r4778] R/AllGeneric.R: Check R version before defining generics for
377              primitives
378    
379    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/denseMatrix.R (rcond): method
382            * R/sparseQR.R (rcond): method, use x or t(x)
383    
384    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
387            matrices.
388            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
389    
390            * man/rcond.Rd: mention the more general definition, and add
391            example for non-square matrices.
392    
393            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
394    
395    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
398    
399    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
402            * tests/indexing.R: add new regression for the above cases.
403    
404    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * src/Mutils.h (__sun): clause for alloca.h on Solaris
407    
408    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * DESCRIPTION (Date, Version): 0.999375-2
411    
412    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * R/HBMM.R (readMM): make work for pattern matrices as well
415    
416    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
417    
418            * [r4730] src/Mutils.h: declare alloca
419            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
420              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
421              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
422              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
423              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
424              methods; switch writeMM to use CHOLMOD code; repair readMM
425    
426    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
429            Oehlschlaegel's ... result type still to be discussed!
430    
431    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
432    
433            * man/image-methods.Rd: new, combining all image() methods
434    
435    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
438            to work via dgC...
439    
440            * R/Matrix.R (Matrix): special treatment for "table" (S3)
441    
442    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dgTMatrix.R (image): change defaults to
445                    aspect = "iso", colorkey = FALSE
446    
447    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
450            must copy its *expanded* x slot before LAPACK call.
451    
452            * tests/matprod.R: test the last days' changes.
453    
454    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
455    
456            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
457              as well as in sources
458            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
459              Lapack call
460    
461    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
464                    ("Matrix", "matrix") which is needed in some cases.
465            Ditto for solve().
466    
467            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
468            infinite recursion in dispatch for some cases.
469    
470    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
471    
472            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
473              so pointers match
474    
475    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * DESCRIPTION (Date): set ready for release -- 0.999375-1
478    
479    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
480    
481            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
482              src/chm_common.c, src/chm_common.h: Change API for
483              numeric_as_chm_dense and N_AS_CHM_DN
484    
485    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
488            * tests/matprod.R: regr.test for it
489    
490    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
493            * tests/group-methods.R: and regression-test it
494    
495    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
496    
497            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
498              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
499              triplet_to_sparse, documentation, use typedefs
500    
501    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
502    
503            * man/dpoMatrix-class.Rd: added 'corMatrix' example
504    
505            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
506            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
507            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
508    
509            * R/lsparseMatrix.R: bug fix in "all" method
510            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
511    
512            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
513            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
514                    + matrix |-> nMatrix coercion
515            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
516            * man/pMatrix-class.Rd: ditto
517    
518            * R/Matrix.R (Summary): method for non-dMatrix
519    
520            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
521            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
522                    test all Summary methods.
523    
524    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
527    
528    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
531    
532            * R/pMatrix.R (t?crossprod): methods for pMatrix
533    
534    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
535    
536            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
537    
538    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
539    
540            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
541              trying to fix a subtle bug - which has been somewhere else.
542    
543    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
544    
545            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
546              solve the bug
547    
548    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * src/dgCMatrix.c (compressed_to_TMatrix):
551    
552    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
553    
554            * src/Csparse.c (Rsparse_validate): new, to have some validity
555            checking for RsparseMatrix
556            * src/dgCMatrix.c (xRMatrix_validate): ditto
557            * src/dtCMatrix.c (tRMatrix_validate): ditto
558    
559    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
560    
561            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
562              lgRMatrix
563            * [r4568] DESCRIPTION: Prepare for bug-fix release
564            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
565              for declaration of cholmod_symmetry
566    
567    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
570            release.
571    
572    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
573    
574            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
575              functions - no longer used
576            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
577              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
578              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
579              Alloca
580    
581    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
582    
583            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
584              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
585              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
586              src/t_gCMatrix_colSums.c: more R_CheckStack()s
587    
588    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
589    
590            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
591              the required amount of memory then call M_numeric_as_chm_dense.
592            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
593              (like Calloc but calling alloca)
594    
595    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
596    
597            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
598            and extended with more sophisticated 'col.names' option.
599            * NAMESPACE: export  printSparseMatrix()
600            * man/printSpMatrix.Rd: document, incl. examples
601    
602    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
603    
604            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
605              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
606              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
607    
608    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * DESCRIPTION (Version): 0.99875-4
611    
612            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
613            some dimnames perservation.
614    
615            * R/dsTMatrix.R (t-method): keep dimnames
616            * R/dtTMatrix.R:  ditto
617    
618            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
619            and ncol(.) < 10
620    
621            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
622            from Mutils.h
623    
624            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
625            e.g. in as(<ngCMatrix>, "matrix")
626    
627    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
628    
629            * [r4529] .: Create a branch for the API changes from the 0.99875
630              series to the 0.999375 series
631            * [r4530] DESCRIPTION, inst/include/Matrix.h,
632              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
633              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
634              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
635              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
636              as_cholmod_x functions
637    
638    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
639    
640            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
641              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
642              to Comparisons
643    
644    >>>>>>> .merge-right.r4561
645    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * DESCRIPTION (Version): 0.99875-3 ready to be released.
648    
649            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
650    
651            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
652            that should also work in a future version of R.
653    
654    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
655    
656            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
657    
658            * R/sparseVector.R: more *sparseVector coercions, notably for
659            non - double ones.
660    
661    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
664              notably the new ones building on the new .Call(.)s:
665    
666            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
667            all 4 of [dlin]gCMatrix_colSums().
668    
669    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
670    
671            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
672            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
673              result
674    
675    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
676    
677            * R/kronecker.R: fix typo (could lead to inf.recursion)
678            * test/simple.R: testing that
679    
680            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
681            method as well (which can have arguments, show() can't).
682    
683    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
684    
685            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
686              added dgCMatrix_colSums for [col,row][Sums,Means]
687    
688    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
689    
690            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
691              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
692              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
693            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
694              class
695            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
696              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
697              row names to store the levels - duh!  Added an example.
698    
699    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * src/Csparse.c (Csparse_validate): check for *repeated* entries
702            thanks to example from Christian Buchta; with a test here:
703            * tests/simple.R:
704    
705    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
708            of colSums(*, sparseResult = TRUE)
709    
710    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
713            'na.rm = FALSE' as "everywhere" else in R.
714    
715    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
716    
717            * [r4421] src/CSparse_install.sh: Modify for new organization of
718              CSparse package
719            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
720              SuiteSparse
721            * [r4426] src/Makefile: add ./UFconfig to the include path for
722              compilation
723            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
724            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
725              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
726    
727    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
730            * R/sparseMatrix.R (prSpMatrix): now gives a message about
731            suppressed column names.
732    
733    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
734    
735            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
736              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
737              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
738              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
739              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
740              Remove warnings after change to const char* CHAR
741    
742    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
743    
744            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
745              type of M_cholmod_ssmult
746    
747    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
748    
749            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
750              src/init.c: Yet another cholmod export - cholmod_ssmult
751    
752    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * NAMESPACE: exported drop0(), since
755            * man/drop0.Rd: I have seen several cases, I really wanted to use
756            it, so our users may want too.
757    
758    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * man/colSums.Rd: separately document colSums() etc, since these
761            have the extra argument 'sparseResult'.
762    
763    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
766            * man/spMatrix.Rd: docu., including examples
767    
768            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
769            in order to make colMeans() etc fast *and* correct.
770            * R/sparseVector.R (replSPvec): "[<-" functionality for
771            sparseVectors; tested in
772            * tests/simple.R:
773    
774    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
777            (very) sparse Matrices; output similar to Matlab's print().
778    
779    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
782            0-based, indices (Jose Quesada <quesada@gmail.com>).
783    
784    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
785    
786            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
787    
788    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * R/Auxiliaries.R (sparsapply): new utility, much faster than
791            tapply1() for large sparse matrices.
792    
793    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
794    
795            * R/Matrix.R (dim<-): reshape now via sparseVector.
796    
797            * R/sparseVector.R: methods and function for
798            * R/AllClass.R: new "sparseVector" class and daughters.
799            * NAMESPACE: export new classes
800    
801    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * DESCRIPTION (Version): 0.99875-1
804            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
805    
806    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
809            indexing
810            * tests/indexing.R: test set for that.
811    
812    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
815            entries.
816            * tests/indexing.R(out): add regression test for it
817    
818    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
821            name for "!" method definitions.
822    
823    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * R/Tsparse.R (intI): new utility, used for "[" :
826                    Cleanup up there, and fixes for duplicated indices - more TODO!
827    
828            * tests/indexing.R(out): more tests
829    
830    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
831    
832            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
833            code that is now part of the R Lapack library.
834    
835            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
836            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
837    
838    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
841    
842    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
843    
844            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
845            up with extraneous names '0'...'<n-1>'
846    
847    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/dgTMatrix.R (mat2dgT): care about NAs
850    
851    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/kronecker.R: triangularity preserving methods
854    
855    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
856    
857            * R/kronecker.R: new file collecting kronecker() methods in one
858                    place.  Goal: become much faster!
859    
860    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
863            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
864            can be much faster.
865    
866            * tests/matprod.R: add regression tests for these (upper & lower).
867    
868    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * R/Matrix.R (diff): method for our Matrices.
871    
872            * R/sparseMatrix.R (isDiagonal): check dim()!
873    
874    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/Matrix.R (dim<-): new method for "reshape()" built on a
877            proposal from Tamas Papp.
878    
879    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
880    
881            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
882    
883            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
884            rather define and export  cBind() and rBind() only.
885            --> useRs *must* change code that used to have cbind()/rbind() !!
886    
887            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
888            * R/bind.Rout.save: ditto
889    
890    2007-02-16  Douglas Bates  <bates@r-project.org>
891    
892            * DESCRIPTION (Date, Version): 0.9975-11 with new date
893            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
894            const modifier on declaration of the array 'valid'
895    
896    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
897    
898            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
899    
900    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
901    
902            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
903    
904            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
905            * tests/simple.R: test the above and some of these coercions:
906    
907            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
908                    be careful to avoid infinite recursion, using new coercions in
909            * R/ngCMatrix.R and nsC... and ntC...
910            * R/lsparseMatrix.R: ditto
911    
912            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
913    
914            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
915            * R/Rsparse.R: reactivate .Call()s
916    
917            * tests/Class+Meth.R: a bit more on actual classes
918    
919    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
920    
921            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
922    
923    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * DESCRIPTION (Version): 0.9975-10 to upload
926    
927            * tests/Class+Meth.R (tstMatrixClass): require coercions to
928            specific classes less unconditionally.
929    
930            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
931    
932            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
933    
934            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
935            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
936            R_to_CMatrix segfaults on one platform.
937            Eliminate most coercion method to *specific* classes, and replace
938            with virtual classes coercions.
939    
940    
941    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
942    
943            * src/init.c: export the CHM...._validate() placeholders, since
944            they *are* called.
945    
946            * tests/Class+Meth.R (classCanCoerce): and starting to test
947            all as(<from>, <to>)
948    
949    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
952            * tests/indexing.R: tested now
953            * tests/indexing.Rout.save: updated
954    
955            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
956            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
957            appropriate.
958    
959            * NAMESPACE: export a trivial
960            * R/Matrix.R: drop() Matrix-method
961    
962            * R/AllClass.R: moved all prototypes to virtual super classes.
963    
964            * R/Rsparse.R: many more coercions to have less exceptions in
965            * tests/Class+Meth.R:
966    
967            * R/Ops.R (Compare): tweak for case with NA
968            * tests/simpl.R: hence another 'FIXME' eliminated
969    
970    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
971    
972            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
973            objects.
974    
975            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
976              and more of "!", "&", "|", all, any; coercions
977    
978            * R/Rsparse.R: many coercions (which enable quite a few other
979            methods), thanks to enhancements in
980            * src/dgCMatrix.c (R_to_CMatrix): new, and
981            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
982            symmetric & triangular and ..RMatrix objects.
983    
984            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
985            renamed file from src/dsTMatrix.c;
986            now dealing with symmetric and triangular Tsparse coercions, both
987            to dense and general.
988    
989    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
992    
993            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
994            where sensible when the <numeric> is of length > 1.
995    
996    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
997    
998            * R/Matrix.R ([<-): for M[] <- value: fix length
999    
1000    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1001    
1002            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1003            * R/ndenseMatrix.R: new coercions n* -> l*
1004    
1005    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1008    
1009            * R/Ops.R ("Logic"): and other "Ops", many updates
1010    
1011    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1012    
1013            * src/Mutils.h (SET_DimNames): new utility
1014    
1015            * R/Auxiliaries.R (nnzero): improved and now exported via
1016    
1017            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1018    
1019    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * R/diagMatrix.R (!): fix typo.
1022    
1023    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1026                    allow to pass class definition --> speedup
1027            * R/sparseMatrix.R: apply the above
1028    
1029            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1030    
1031            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1032            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1033            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1034    
1035            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1036    
1037            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1038            and use it for "sparse*" as well, since it's faster than the
1039            as_Csparse(.) way.
1040    
1041    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1042    
1043            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1044    
1045    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1046    
1047            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1048            as method for   M[ ij ] <- v
1049            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1050    
1051            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1052            FALSE answer
1053    
1054            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1055            * tests/indexing.R: test it, and some of the above
1056    
1057    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1058    
1059            * R/Auxiliaries.R (is_duplicatedT): new utility
1060    
1061    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1062    
1063            * src/init.c (R_init_Matrix): export cholmod_scale
1064    
1065    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1068            base::as.matrix to (x, ...)
1069    
1070    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1071    
1072            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1073            file; start using "Logic", hence
1074    
1075            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1076            * NAMESPACE: import and export "Logic"
1077    
1078    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1079    
1080            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1081            only needed previously to R version 2.5.0.
1082    
1083    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1084    
1085            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1086    
1087            * R/Tsparse.R (replTmat): fix subassignment of triangular
1088            * R/Csparse.R (replCmat): ditto
1089            * tests/indexing.R: more tests, incl the above fix
1090    
1091    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1092    
1093            * R/Auxiliaries.R (drop0): extend for non CSparse
1094            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1095    
1096            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1097                    use uplo correctly (!); other places: use uplo_P() macro
1098    
1099            * R/Csparse.R (replCmat): call diagU2N() when needed
1100            * R/Tsparse.R (replTmat): ditto
1101    
1102            * src/dtCMatrix.c (tCMatrix_validate): new
1103            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1104            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1105    
1106            * R/diagMatrix.R (replDiag): to use in [<-
1107    
1108    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1109    
1110            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1111                    also more general diagU2N().
1112    
1113    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1114    
1115            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1116            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1117    
1118    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1119    
1120            * tests/bind.R: a few more cases
1121            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1122    
1123            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1124            * R/ddenseMatrix.R (cbind2/rbind2)
1125            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1126            * tests/indexing.R
1127            * tests/indexing.Rout.save: updated
1128    
1129    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1132            * tests/indexing.R
1133    
1134    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1137            align with proper position of "0", i.e., right for integers.
1138            argument 'align' by default is "fancy".
1139    
1140    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1143            * R/Csparse.R: and fix "Compare" for more cases.
1144            * tests/Class+Meth.R: test some of these (m == m, m != m)
1145    
1146    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1147    
1148            * R/lsparseMatrix.R: all() and any() methods
1149            * R/ldenseMatrix.R:      ditto
1150            * NAMESPACE, R/Matrix.R: ditto
1151    
1152            * man/all-methods.Rd: document them minimally
1153    
1154            * tests/simple.R: add a few examples for these
1155    
1156    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1157    
1158            * R/Tsparse.R ([): fix long standing typo in symmetric case
1159            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1160    
1161    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1162    
1163            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1164            to LL before converting to a sparse matrix. (The LDL form can be
1165            converted to a sparse matrix but it is implicitly a unit
1166            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1167    
1168    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1169    
1170            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1171    
1172    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1173    
1174            * DESCRIPTION (Version): updated -> release 0.9975-7
1175            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1176    
1177    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1180    
1181    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1182    
1183            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1184            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1185            is exactly singular.
1186    
1187    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1188    
1189            * DESCRIPTION (Date): updated -> release 0.9975-6
1190    
1191    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1192    
1193            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1194            now returns symmetric.
1195    
1196            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1197    
1198            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1199            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1200    
1201            * R/Auxiliaries.R (.type.kind): added
1202    
1203    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1204    
1205            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1206            running src/CSparse_install.sh
1207    
1208            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1209    
1210    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1211    
1212            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1213            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1214    
1215            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1216    
1217            * tests/Class+Meth.R (tstMatrixClass): now assure
1218            the (important in method programming) property :
1219    
1220                    ###>>  Every "Matrix" is either
1221                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1222    
1223                    (where "*" stands for "Matrix")
1224    
1225            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1226    
1227            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1228            * tests/validObj.R: checks for "comparison"
1229    
1230            * R/sparseMatrix.R ([): improved indexing for sparse;
1231                    trying to keep <symmetric>[ n, n] symmmetric
1232    
1233            * tests/indexing.R: indexing for logical sparse now ok
1234    
1235    
1236    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1237    
1238            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1239    
1240            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1241    
1242    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1245    
1246            * tests/simple.R: validObject() checking the above.
1247    
1248            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1249            replacing both dgCMatrix_validate and lgCM*.
1250    
1251            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1252            fix dimnames setting in other places.
1253            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1254    
1255    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1256    
1257            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1258    
1259            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1260            symmetry test, via
1261            * R/Auxiliaries.R (.as.dgC.0.factors):
1262    
1263    2006-11-01  Douglas Bates  <bates@r-project.org>
1264    
1265            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1266            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1267            <CsparseMatrix>) added
1268    
1269    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1270    
1271            * tests/matprod.R: add a variation of Harri's example
1272    
1273            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1274            recursive infinitely.
1275    
1276            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1277    
1278            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1279    
1280    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1283            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1284            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1285            satisfy the above test.
1286    
1287    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1288    
1289            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1290    
1291            * R/dgCMatrix.R: solve(a, b="missing") based on
1292            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1293            RHS = NULL.
1294    
1295            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1296            add more (needed) [t]crossprod() methods.
1297    
1298            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1299    
1300            * R/Auxiliaries.R (as_CspClass): cleanup
1301            (drop0): internal utility for "Csparse_drop(*, 0)"
1302            (.bail.out.2): encourage active feedback
1303    
1304    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1305    
1306            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1307    
1308            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1309            non-valid or 'sorted' case).
1310    
1311            * R/dsparseMatrix.R: add "chol" method.
1312            * R/ddenseMatrix.R: ditto
1313    
1314            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1315            * NAMESPACE (Ops)
1316            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1317            coercion; deprecating direct lower level coercions.
1318    
1319            * R/*.R (seq): use seq_len() and seq_along() where possible.
1320    
1321    
1322    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1323    
1324            * DESCRIPTION (Version): 0.9975-5 ready for release
1325    
1326  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1327    
1328          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.

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