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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 2139, Mon Mar 17 23:25:31 2008 UTC
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1    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/UFsparse_download.sh: -->
4            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
5    
6    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
9            functionality; barely tested in
10            * tests/factorizing.R
11    
12            * src/Csparse.c (diag_tC): new functionality to enable faster
13            determinant(<dsCMatrix>, .) in
14            * R/dsCMatrix.R
15    
16    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
17    
18            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
19              src/CHMfactor.c, src/CHMfactor.h,
20              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
21              Log-determinant of the parent matrix from a CHMfactor object as
22              chm_factor_ldetL2; documentation and support
23    
24    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
27    
28    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
31            warning.
32    
33    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
36    
37            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
38              <diagonal> o <sparse_triangular>
39              setAs(., "nMatrix") added.
40    
41            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
42    
43            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
44                    new argument 'checkDense = FALSE'.
45    
46    
47    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
50            back-permutation of the matrix exponential.
51    
52            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
53    
54            * DESCRIPTION (Date,Version): ready to release 0.999375-5
55    
56            * tests/simple.R: testing diagN2U
57    
58    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Auxiliaries.R (diagN2U): interface to
61    
62            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
63    
64            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
65    
66    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * src/chm_common.c (chm_diagN2U): new utility.
69    
70            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
71            make use of chm_diagN2U() and hence now preserve triangularity and
72            unit-triangularity.
73    
74            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
75    
76    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
79    
80            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
81            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
82    
83            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
84    
85            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
86    
87            * src/chm_common.c (AS_CHM_FINISH): add note about problem
88            for triangular (diag = "U").
89    
90    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
93            * R/bind.R:  .Call(dense_to_Csparse, *)
94    
95    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R (Matrix): no longer use coercions to specific classes
98                    (since we are discouraging them in user code).
99    
100            * tests/*.R: also replaces coercions to specific classes by
101            coercions to super classes.
102    
103            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
104    
105    
106    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
109    
110            * src/dense.c (dense_band): generalized from ddense_band
111    
112            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
113              now for "denseMatrix" (instead of just "ddense*"); much
114              simplified setMethod()s for these.
115    
116            * src/dense.c (dense_to_symmetric): generalized from ddense_*
117    
118    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
121            version of as(*, "symmetricMatric").
122    
123            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
124            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
125    
126    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * R/Matrix.R (subset.ij): utility, as first step to faster
129               M [ <ij-matrix> ] indexing.
130    
131            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
132    
133            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
134            for more efficient symmpart() and skewpart() methods.
135    
136            * src/Mutils.c (equal_string_vectors): utility
137    
138            * src/dense.c (ddense_to_symmetric): new function used in
139    
140            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
141    
142            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
143            order to match the generic (and evade .local(..)).
144    
145            * R/dsCMatrix.R: dgC -> dsC: use C code!
146    
147            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
148            as per TODO
149    
150            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
151    
152            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
153    
154    
155    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
158    
159            * R/Auxiliaries.R (non0.i): take out of non0ind
160    
161            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
162            make tril(), triu(), band() work for "matrix" and all "dense*"
163    
164            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
165            * tests/simple.R: test the fix above
166    
167            * R/sparseMatrix.R ([): simplification: no coerce to <general>
168                    before we use as(., <Tsparse>)[...] anyway
169    
170            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
171    
172            * R/triangularMatrix.R (isTriangular): methods for all subclasses
173            instead of "triangularMatrix" -- just to disambiguate
174    
175    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
178            * tests/indexing.R: example that fails above
179    
180    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
183            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
184                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
185    
186            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
187            * src/Tsparse.h, init.c: ditto
188            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
189                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
190            * R/sparseMatrix.R (isTriangular): hence simplified
191    
192    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/Ops.R (.Arith.Csparse): new utility factored out of former
195              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
196    
197    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
200    
201            * inst/test-tools.R (isOrthogonal): new function; also file restructured
202    
203    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
206            coercion to "nMatrix" and "pMatrix"
207    
208            * R/AllClass.R: "Schur" class;  "number" class union
209            * man/number-class.Rd:
210            * man/Schur-class.Rd:
211    
212            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
213            (.simpleSchur): Schur() method for diagonal matrices
214            (.triSchur):    Schur() method for triangular matrices
215            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
216    
217    
218    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
221    
222    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
225                    in order to ensure 'system = *' is not lost;
226                    formals()$system instead of cut&paste.
227            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
228    
229    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
230    
231            * DESCRIPTION (Date): make ready for release --> 0.999375-4
232    
233            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
234    
235    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
238                    and hence does as.vector(.).
239            * man/pMatrix-class.Rd: docs
240            * R/sparseMatrix.R: fix for printing "integer sparse"
241    
242            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
243    
244            * R/Matrix.R and others: use "exact" function argument list for
245                    both "["   : (x, i,j, ..., drop)
246                    and  "[<-" : (x, i,j, ..., value)
247    
248            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
249            * R/Tsparse.R (replTmat):    ditto
250            * R/diagMatrix.R (replDiag): ditto
251            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
252            * tests/indexing.R: testing the above
253    
254    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/sparseMatrix.R (cov2cor): method for sparse matrices
257    
258            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
259    
260            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
261    
262            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
263    
264    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/Matrix.R: "generic" cov2cor() method
267    
268            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
269                    speed up Q %*% D %*% t(Q)
270            * tests/dpoMatrix.R: test nearPD()
271    
272    2007-12-05  Doug Bates and Martin Maechler
273    
274            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
275            stats::xtabs() allowing to create sparse matrices.
276    
277    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
280    
281    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
284    
285    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/LU.R: solve() method for "denseLU"
288    
289    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * DESCRIPTION (Version): 0.999375-3 preparing for release
292    
293            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
294    
295            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
296    
297    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
300              thanks to Kasper Kristensen.
301            * tests/matprod.R: regression test for that.
302    
303    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
304    
305            * [r4778] R/AllGeneric.R: Check R version before defining generics for
306              primitives
307    
308    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/denseMatrix.R (rcond): method
311            * R/sparseQR.R (rcond): method, use x or t(x)
312    
313    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
316            matrices.
317            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
318    
319            * man/rcond.Rd: mention the more general definition, and add
320            example for non-square matrices.
321    
322            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
323    
324    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
327    
328    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
331            * tests/indexing.R: add new regression for the above cases.
332    
333    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * src/Mutils.h (__sun): clause for alloca.h on Solaris
336    
337    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * DESCRIPTION (Date, Version): 0.999375-2
340    
341    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
342    
343            * R/HBMM.R (readMM): make work for pattern matrices as well
344    
345    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
346    
347            * [r4730] src/Mutils.h: declare alloca
348            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
349              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
350              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
351              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
352              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
353              methods; switch writeMM to use CHOLMOD code; repair readMM
354    
355    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
358            Oehlschlaegel's ... result type still to be discussed!
359    
360    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * man/image-methods.Rd: new, combining all image() methods
363    
364    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
367            to work via dgC...
368    
369            * R/Matrix.R (Matrix): special treatment for "table" (S3)
370    
371    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/dgTMatrix.R (image): change defaults to
374                    aspect = "iso", colorkey = FALSE
375    
376    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
379            must copy its *expanded* x slot before LAPACK call.
380    
381            * tests/matprod.R: test the last days' changes.
382    
383    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
384    
385            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
386              as well as in sources
387            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
388              Lapack call
389    
390    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
393                    ("Matrix", "matrix") which is needed in some cases.
394            Ditto for solve().
395    
396            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
397            infinite recursion in dispatch for some cases.
398    
399    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
400    
401            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
402              so pointers match
403    
404    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
405    
406            * DESCRIPTION (Date): set ready for release -- 0.999375-1
407    
408    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
409    
410            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
411              src/chm_common.c, src/chm_common.h: Change API for
412              numeric_as_chm_dense and N_AS_CHM_DN
413    
414    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
417            * tests/matprod.R: regr.test for it
418    
419    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
422            * tests/group-methods.R: and regression-test it
423    
424    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
425    
426            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
427              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
428              triplet_to_sparse, documentation, use typedefs
429    
430    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * man/dpoMatrix-class.Rd: added 'corMatrix' example
433    
434            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
435            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
436            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
437    
438            * R/lsparseMatrix.R: bug fix in "all" method
439            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
440    
441            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
442            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
443                    + matrix |-> nMatrix coercion
444            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
445            * man/pMatrix-class.Rd: ditto
446    
447            * R/Matrix.R (Summary): method for non-dMatrix
448    
449            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
450            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
451                    test all Summary methods.
452    
453    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
456    
457    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
458    
459            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
460    
461            * R/pMatrix.R (t?crossprod): methods for pMatrix
462    
463    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
464    
465            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
466    
467    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
468    
469            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
470              trying to fix a subtle bug - which has been somewhere else.
471    
472    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
473    
474            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
475              solve the bug
476    
477    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
478    
479            * src/dgCMatrix.c (compressed_to_TMatrix):
480    
481    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * src/Csparse.c (Rsparse_validate): new, to have some validity
484            checking for RsparseMatrix
485            * src/dgCMatrix.c (xRMatrix_validate): ditto
486            * src/dtCMatrix.c (tRMatrix_validate): ditto
487    
488    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
489    
490            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
491              lgRMatrix
492            * [r4568] DESCRIPTION: Prepare for bug-fix release
493            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
494              for declaration of cholmod_symmetry
495    
496    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
499            release.
500    
501    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
502    
503            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
504              functions - no longer used
505            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
506              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
507              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
508              Alloca
509    
510    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
511    
512            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
513              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
514              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
515              src/t_gCMatrix_colSums.c: more R_CheckStack()s
516    
517    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
518    
519            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
520              the required amount of memory then call M_numeric_as_chm_dense.
521            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
522              (like Calloc but calling alloca)
523    
524    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
527            and extended with more sophisticated 'col.names' option.
528            * NAMESPACE: export  printSparseMatrix()
529            * man/printSpMatrix.Rd: document, incl. examples
530    
531    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
532    
533            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
534              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
535              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
536    
537    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
538    
539            * DESCRIPTION (Version): 0.99875-4
540    
541            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
542            some dimnames perservation.
543    
544            * R/dsTMatrix.R (t-method): keep dimnames
545            * R/dtTMatrix.R:  ditto
546    
547            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
548            and ncol(.) < 10
549    
550            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
551            from Mutils.h
552    
553            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
554            e.g. in as(<ngCMatrix>, "matrix")
555    
556    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
557    
558            * [r4529] .: Create a branch for the API changes from the 0.99875
559              series to the 0.999375 series
560            * [r4530] DESCRIPTION, inst/include/Matrix.h,
561              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
562              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
563              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
564              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
565              as_cholmod_x functions
566    
567    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
568    
569            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
570              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
571              to Comparisons
572    
573    >>>>>>> .merge-right.r4561
574    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * DESCRIPTION (Version): 0.99875-3 ready to be released.
577    
578            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
579    
580            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
581            that should also work in a future version of R.
582    
583    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
586    
587            * R/sparseVector.R: more *sparseVector coercions, notably for
588            non - double ones.
589    
590    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
593              notably the new ones building on the new .Call(.)s:
594    
595            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
596            all 4 of [dlin]gCMatrix_colSums().
597    
598    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
599    
600            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
601            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
602              result
603    
604    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/kronecker.R: fix typo (could lead to inf.recursion)
607            * test/simple.R: testing that
608    
609            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
610            method as well (which can have arguments, show() can't).
611    
612    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
613    
614            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
615              added dgCMatrix_colSums for [col,row][Sums,Means]
616    
617    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
618    
619            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
620              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
621              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
622            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
623              class
624            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
625              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
626              row names to store the levels - duh!  Added an example.
627    
628    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * src/Csparse.c (Csparse_validate): check for *repeated* entries
631            thanks to example from Christian Buchta; with a test here:
632            * tests/simple.R:
633    
634    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
637            of colSums(*, sparseResult = TRUE)
638    
639    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
642            'na.rm = FALSE' as "everywhere" else in R.
643    
644    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
645    
646            * [r4421] src/CSparse_install.sh: Modify for new organization of
647              CSparse package
648            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
649              SuiteSparse
650            * [r4426] src/Makefile: add ./UFconfig to the include path for
651              compilation
652            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
653            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
654              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
655    
656    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
659            * R/sparseMatrix.R (prSpMatrix): now gives a message about
660            suppressed column names.
661    
662    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
663    
664            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
665              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
666              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
667              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
668              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
669              Remove warnings after change to const char* CHAR
670    
671    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
672    
673            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
674              type of M_cholmod_ssmult
675    
676    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
677    
678            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
679              src/init.c: Yet another cholmod export - cholmod_ssmult
680    
681    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * NAMESPACE: exported drop0(), since
684            * man/drop0.Rd: I have seen several cases, I really wanted to use
685            it, so our users may want too.
686    
687    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * man/colSums.Rd: separately document colSums() etc, since these
690            have the extra argument 'sparseResult'.
691    
692    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
695            * man/spMatrix.Rd: docu., including examples
696    
697            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
698            in order to make colMeans() etc fast *and* correct.
699            * R/sparseVector.R (replSPvec): "[<-" functionality for
700            sparseVectors; tested in
701            * tests/simple.R:
702    
703    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
706            (very) sparse Matrices; output similar to Matlab's print().
707    
708    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
709    
710            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
711            0-based, indices (Jose Quesada <quesada@gmail.com>).
712    
713    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
714    
715            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
716    
717    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/Auxiliaries.R (sparsapply): new utility, much faster than
720            tapply1() for large sparse matrices.
721    
722    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/Matrix.R (dim<-): reshape now via sparseVector.
725    
726            * R/sparseVector.R: methods and function for
727            * R/AllClass.R: new "sparseVector" class and daughters.
728            * NAMESPACE: export new classes
729    
730    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * DESCRIPTION (Version): 0.99875-1
733            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
734    
735    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
738            indexing
739            * tests/indexing.R: test set for that.
740    
741    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
744            entries.
745            * tests/indexing.R(out): add regression test for it
746    
747    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
750            name for "!" method definitions.
751    
752    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/Tsparse.R (intI): new utility, used for "[" :
755                    Cleanup up there, and fixes for duplicated indices - more TODO!
756    
757            * tests/indexing.R(out): more tests
758    
759    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
760    
761            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
762            code that is now part of the R Lapack library.
763    
764            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
765            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
766    
767    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
770    
771    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
774            up with extraneous names '0'...'<n-1>'
775    
776    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/dgTMatrix.R (mat2dgT): care about NAs
779    
780    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
781    
782            * R/kronecker.R: triangularity preserving methods
783    
784    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/kronecker.R: new file collecting kronecker() methods in one
787                    place.  Goal: become much faster!
788    
789    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
792            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
793            can be much faster.
794    
795            * tests/matprod.R: add regression tests for these (upper & lower).
796    
797    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/Matrix.R (diff): method for our Matrices.
800    
801            * R/sparseMatrix.R (isDiagonal): check dim()!
802    
803    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/Matrix.R (dim<-): new method for "reshape()" built on a
806            proposal from Tamas Papp.
807    
808    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
811    
812            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
813            rather define and export  cBind() and rBind() only.
814            --> useRs *must* change code that used to have cbind()/rbind() !!
815    
816            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
817            * R/bind.Rout.save: ditto
818    
819    2007-02-16  Douglas Bates  <bates@r-project.org>
820    
821            * DESCRIPTION (Date, Version): 0.9975-11 with new date
822            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
823            const modifier on declaration of the array 'valid'
824    
825    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
826    
827            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
828    
829    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
832    
833            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
834            * tests/simple.R: test the above and some of these coercions:
835    
836            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
837                    be careful to avoid infinite recursion, using new coercions in
838            * R/ngCMatrix.R and nsC... and ntC...
839            * R/lsparseMatrix.R: ditto
840    
841            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
842    
843            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
844            * R/Rsparse.R: reactivate .Call()s
845    
846            * tests/Class+Meth.R: a bit more on actual classes
847    
848    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
849    
850            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
851    
852    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * DESCRIPTION (Version): 0.9975-10 to upload
855    
856            * tests/Class+Meth.R (tstMatrixClass): require coercions to
857            specific classes less unconditionally.
858    
859            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
860    
861            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
862    
863            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
864            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
865            R_to_CMatrix segfaults on one platform.
866            Eliminate most coercion method to *specific* classes, and replace
867            with virtual classes coercions.
868    
869    
870    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
871    
872            * src/init.c: export the CHM...._validate() placeholders, since
873            they *are* called.
874    
875            * tests/Class+Meth.R (classCanCoerce): and starting to test
876            all as(<from>, <to>)
877    
878    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
881            * tests/indexing.R: tested now
882            * tests/indexing.Rout.save: updated
883    
884            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
885            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
886            appropriate.
887    
888            * NAMESPACE: export a trivial
889            * R/Matrix.R: drop() Matrix-method
890    
891            * R/AllClass.R: moved all prototypes to virtual super classes.
892    
893            * R/Rsparse.R: many more coercions to have less exceptions in
894            * tests/Class+Meth.R:
895    
896            * R/Ops.R (Compare): tweak for case with NA
897            * tests/simpl.R: hence another 'FIXME' eliminated
898    
899    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
902            objects.
903    
904            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
905              and more of "!", "&", "|", all, any; coercions
906    
907            * R/Rsparse.R: many coercions (which enable quite a few other
908            methods), thanks to enhancements in
909            * src/dgCMatrix.c (R_to_CMatrix): new, and
910            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
911            symmetric & triangular and ..RMatrix objects.
912    
913            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
914            renamed file from src/dsTMatrix.c;
915            now dealing with symmetric and triangular Tsparse coercions, both
916            to dense and general.
917    
918    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
921    
922            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
923            where sensible when the <numeric> is of length > 1.
924    
925    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/Matrix.R ([<-): for M[] <- value: fix length
928    
929    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
932            * R/ndenseMatrix.R: new coercions n* -> l*
933    
934    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
935    
936            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
937    
938            * R/Ops.R ("Logic"): and other "Ops", many updates
939    
940    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942            * src/Mutils.h (SET_DimNames): new utility
943    
944            * R/Auxiliaries.R (nnzero): improved and now exported via
945    
946            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
947    
948    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
949    
950            * R/diagMatrix.R (!): fix typo.
951    
952    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * R/Auxiliaries.R (as_Csparse): and quite a few others:
955                    allow to pass class definition --> speedup
956            * R/sparseMatrix.R: apply the above
957    
958            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
959    
960            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
961            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
962            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
963    
964            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
965    
966            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
967            and use it for "sparse*" as well, since it's faster than the
968            as_Csparse(.) way.
969    
970    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
971    
972            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
973    
974    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
975    
976            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
977            as method for   M[ ij ] <- v
978            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
979    
980            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
981            FALSE answer
982    
983            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
984            * tests/indexing.R: test it, and some of the above
985    
986    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
987    
988            * R/Auxiliaries.R (is_duplicatedT): new utility
989    
990    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
991    
992            * src/init.c (R_init_Matrix): export cholmod_scale
993    
994    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
997            base::as.matrix to (x, ...)
998    
999    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1002            file; start using "Logic", hence
1003    
1004            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1005            * NAMESPACE: import and export "Logic"
1006    
1007    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1010            only needed previously to R version 2.5.0.
1011    
1012    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1015    
1016            * R/Tsparse.R (replTmat): fix subassignment of triangular
1017            * R/Csparse.R (replCmat): ditto
1018            * tests/indexing.R: more tests, incl the above fix
1019    
1020    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * R/Auxiliaries.R (drop0): extend for non CSparse
1023            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1024    
1025            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1026                    use uplo correctly (!); other places: use uplo_P() macro
1027    
1028            * R/Csparse.R (replCmat): call diagU2N() when needed
1029            * R/Tsparse.R (replTmat): ditto
1030    
1031            * src/dtCMatrix.c (tCMatrix_validate): new
1032            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1033            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1034    
1035            * R/diagMatrix.R (replDiag): to use in [<-
1036    
1037    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1038    
1039            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1040                    also more general diagU2N().
1041    
1042    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1045            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1046    
1047    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * tests/bind.R: a few more cases
1050            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1051    
1052            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1053            * R/ddenseMatrix.R (cbind2/rbind2)
1054            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1055            * tests/indexing.R
1056            * tests/indexing.Rout.save: updated
1057    
1058    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1059    
1060            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1061            * tests/indexing.R
1062    
1063    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1064    
1065            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1066            align with proper position of "0", i.e., right for integers.
1067            argument 'align' by default is "fancy".
1068    
1069    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1070    
1071            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1072            * R/Csparse.R: and fix "Compare" for more cases.
1073            * tests/Class+Meth.R: test some of these (m == m, m != m)
1074    
1075    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1076    
1077            * R/lsparseMatrix.R: all() and any() methods
1078            * R/ldenseMatrix.R:      ditto
1079            * NAMESPACE, R/Matrix.R: ditto
1080    
1081            * man/all-methods.Rd: document them minimally
1082    
1083            * tests/simple.R: add a few examples for these
1084    
1085    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * R/Tsparse.R ([): fix long standing typo in symmetric case
1088            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1089    
1090    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1091    
1092            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1093            to LL before converting to a sparse matrix. (The LDL form can be
1094            converted to a sparse matrix but it is implicitly a unit
1095            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1096    
1097    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1098    
1099            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1100    
1101    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1102    
1103            * DESCRIPTION (Version): updated -> release 0.9975-7
1104            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1105    
1106    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1107    
1108            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1109    
1110    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1111    
1112            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1113            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1114            is exactly singular.
1115    
1116    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1117    
1118            * DESCRIPTION (Date): updated -> release 0.9975-6
1119    
1120    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1121    
1122            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1123            now returns symmetric.
1124    
1125            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1126    
1127            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1128            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1129    
1130            * R/Auxiliaries.R (.type.kind): added
1131    
1132    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1133    
1134            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1135            running src/CSparse_install.sh
1136    
1137            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1138    
1139    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1140    
1141            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1142            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1143    
1144            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1145    
1146            * tests/Class+Meth.R (tstMatrixClass): now assure
1147            the (important in method programming) property :
1148    
1149                    ###>>  Every "Matrix" is either
1150                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1151    
1152                    (where "*" stands for "Matrix")
1153    
1154            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1155    
1156            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1157            * tests/validObj.R: checks for "comparison"
1158    
1159            * R/sparseMatrix.R ([): improved indexing for sparse;
1160                    trying to keep <symmetric>[ n, n] symmmetric
1161    
1162            * tests/indexing.R: indexing for logical sparse now ok
1163    
1164    
1165    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1166    
1167            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1168    
1169            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1170    
1171    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1172    
1173            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1174    
1175            * tests/simple.R: validObject() checking the above.
1176    
1177            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1178            replacing both dgCMatrix_validate and lgCM*.
1179    
1180            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1181            fix dimnames setting in other places.
1182            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1183    
1184    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1187    
1188            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1189            symmetry test, via
1190            * R/Auxiliaries.R (.as.dgC.0.factors):
1191    
1192    2006-11-01  Douglas Bates  <bates@r-project.org>
1193    
1194            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1195            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1196            <CsparseMatrix>) added
1197    
1198    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1199    
1200            * tests/matprod.R: add a variation of Harri's example
1201    
1202            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1203            recursive infinitely.
1204    
1205            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1206    
1207            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1208    
1209    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1210    
1211            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1212            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1213            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1214            satisfy the above test.
1215    
1216    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1217    
1218            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1219    
1220            * R/dgCMatrix.R: solve(a, b="missing") based on
1221            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1222            RHS = NULL.
1223    
1224            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1225            add more (needed) [t]crossprod() methods.
1226    
1227            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1228    
1229            * R/Auxiliaries.R (as_CspClass): cleanup
1230            (drop0): internal utility for "Csparse_drop(*, 0)"
1231            (.bail.out.2): encourage active feedback
1232    
1233    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1234    
1235            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1236    
1237            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1238            non-valid or 'sorted' case).
1239    
1240            * R/dsparseMatrix.R: add "chol" method.
1241            * R/ddenseMatrix.R: ditto
1242    
1243            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1244            * NAMESPACE (Ops)
1245            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1246            coercion; deprecating direct lower level coercions.
1247    
1248            * R/*.R (seq): use seq_len() and seq_along() where possible.
1249    
1250    
1251    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * DESCRIPTION (Version): 0.9975-5 ready for release
1254    
1255  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1256    
1257          * 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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