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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 2165, Sat Mar 29 21:40:18 2008 UTC
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1    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375-9 --- need to release
4            for R-devel (and R 2.7.0 alpha soon).
5    
6            * R/AllClass.R: drop "double" from "atomicVector" class union
7    
8            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
9            * R/dgeMatrix.R: ditto
10    
11            * R/sparseMatrix.R (summary): count NAs
12    
13            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
14    
15    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
18            order to become compatible to new R 2.7.0 base::rcond().
19    
20    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
23    
24            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
25    
26            * inst/test-tools.R (isValid): new utility, used much in
27            * tests/simple.R:
28    
29            * man/BunchKaufman-methods.Rd: added too
30    
31    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/dsyMatrix.R: add BunchKaufman() methods.
34            * R/dspMatrix.R:
35    
36            * src/init.c: add dsyMatrix_trf
37    
38    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
39    
40            * DESCRIPTION (Version): release 0.999375-7
41            * src/CHMfactor.c (CHMfactor_update): fix
42    
43    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
46            internal_chm_factor().
47    
48            * R/AllGeneric.R: do *not* define a "chol" generic
49                    (but rather use the implicit one *without* making pivot
50                    part of the signature)
51            * R/*.R: drop the 'pivot' from chol's signature and make
52                    'pivot=FALSE' a default argument of method definitions.
53    
54            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
55            version of Matrix
56    
57    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
60    
61            * R/sparseMatrix.R (is.na): new simple method
62            * R/denseMatrix.R (is.na): ditto.
63    
64            * R/diagMatrix.R (.symDiagonal): newly exported utility.
65    
66            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
67    
68            * src/UFsparse_download.sh: -->
69            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
70    
71    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
74            functionality; barely tested in
75            * tests/factorizing.R
76    
77            * src/Csparse.c (diag_tC): new functionality to enable faster
78            determinant(<dsCMatrix>, .) in
79            * R/dsCMatrix.R
80    
81    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
82    
83            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
84              src/CHMfactor.c, src/CHMfactor.h,
85              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
86              Log-determinant of the parent matrix from a CHMfactor object as
87              chm_factor_ldetL2; documentation and support
88    
89    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
92    
93    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
96            warning.
97    
98    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
101    
102            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
103              <diagonal> o <sparse_triangular>
104              setAs(., "nMatrix") added.
105    
106            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
107    
108            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
109                    new argument 'checkDense = FALSE'.
110    
111    
112    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
115            back-permutation of the matrix exponential.
116    
117            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
118    
119            * DESCRIPTION (Date,Version): ready to release 0.999375-5
120    
121            * tests/simple.R: testing diagN2U
122    
123    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Auxiliaries.R (diagN2U): interface to
126    
127            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
128    
129            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
130    
131    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * src/chm_common.c (chm_diagN2U): new utility.
134    
135            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
136            make use of chm_diagN2U() and hence now preserve triangularity and
137            unit-triangularity.
138    
139            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
140    
141    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
144    
145            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
146            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
147    
148            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
149    
150            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
151    
152            * src/chm_common.c (AS_CHM_FINISH): add note about problem
153            for triangular (diag = "U").
154    
155    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
158            * R/bind.R:  .Call(dense_to_Csparse, *)
159    
160    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Matrix.R (Matrix): no longer use coercions to specific classes
163                    (since we are discouraging them in user code).
164    
165            * tests/*.R: also replaces coercions to specific classes by
166            coercions to super classes.
167    
168            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
169    
170    
171    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
174    
175            * src/dense.c (dense_band): generalized from ddense_band
176    
177            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
178              now for "denseMatrix" (instead of just "ddense*"); much
179              simplified setMethod()s for these.
180    
181            * src/dense.c (dense_to_symmetric): generalized from ddense_*
182    
183    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
186            version of as(*, "symmetricMatric").
187    
188            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
189            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
190    
191    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R (subset.ij): utility, as first step to faster
194               M [ <ij-matrix> ] indexing.
195    
196            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
197    
198            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
199            for more efficient symmpart() and skewpart() methods.
200    
201            * src/Mutils.c (equal_string_vectors): utility
202    
203            * src/dense.c (ddense_to_symmetric): new function used in
204    
205            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
206    
207            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
208            order to match the generic (and evade .local(..)).
209    
210            * R/dsCMatrix.R: dgC -> dsC: use C code!
211    
212            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
213            as per TODO
214    
215            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
216    
217            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
218    
219    
220    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
223    
224            * R/Auxiliaries.R (non0.i): take out of non0ind
225    
226            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
227            make tril(), triu(), band() work for "matrix" and all "dense*"
228    
229            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
230            * tests/simple.R: test the fix above
231    
232            * R/sparseMatrix.R ([): simplification: no coerce to <general>
233                    before we use as(., <Tsparse>)[...] anyway
234    
235            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
236    
237            * R/triangularMatrix.R (isTriangular): methods for all subclasses
238            instead of "triangularMatrix" -- just to disambiguate
239    
240    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
243            * tests/indexing.R: example that fails above
244    
245    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
248            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
249                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
250    
251            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
252            * src/Tsparse.h, init.c: ditto
253            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
254                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
255            * R/sparseMatrix.R (isTriangular): hence simplified
256    
257    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Ops.R (.Arith.Csparse): new utility factored out of former
260              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
261    
262    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
265    
266            * inst/test-tools.R (isOrthogonal): new function; also file restructured
267    
268    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
271            coercion to "nMatrix" and "pMatrix"
272    
273            * R/AllClass.R: "Schur" class;  "number" class union
274            * man/number-class.Rd:
275            * man/Schur-class.Rd:
276    
277            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
278            (.simpleSchur): Schur() method for diagonal matrices
279            (.triSchur):    Schur() method for triangular matrices
280            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
281    
282    
283    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
286    
287    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
290                    in order to ensure 'system = *' is not lost;
291                    formals()$system instead of cut&paste.
292            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
293    
294    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * DESCRIPTION (Date): make ready for release --> 0.999375-4
297    
298            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
299    
300    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
303                    and hence does as.vector(.).
304            * man/pMatrix-class.Rd: docs
305            * R/sparseMatrix.R: fix for printing "integer sparse"
306    
307            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
308    
309            * R/Matrix.R and others: use "exact" function argument list for
310                    both "["   : (x, i,j, ..., drop)
311                    and  "[<-" : (x, i,j, ..., value)
312    
313            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
314            * R/Tsparse.R (replTmat):    ditto
315            * R/diagMatrix.R (replDiag): ditto
316            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
317            * tests/indexing.R: testing the above
318    
319    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/sparseMatrix.R (cov2cor): method for sparse matrices
322    
323            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
324    
325            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
326    
327            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
328    
329    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Matrix.R: "generic" cov2cor() method
332    
333            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
334                    speed up Q %*% D %*% t(Q)
335            * tests/dpoMatrix.R: test nearPD()
336    
337    2007-12-05  Doug Bates and Martin Maechler
338    
339            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
340            stats::xtabs() allowing to create sparse matrices.
341    
342    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
345    
346    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
349    
350    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/LU.R: solve() method for "denseLU"
353    
354    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * DESCRIPTION (Version): 0.999375-3 preparing for release
357    
358            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
359    
360            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
361    
362    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
363    
364            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
365              thanks to Kasper Kristensen.
366            * tests/matprod.R: regression test for that.
367    
368    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
369    
370            * [r4778] R/AllGeneric.R: Check R version before defining generics for
371              primitives
372    
373    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/denseMatrix.R (rcond): method
376            * R/sparseQR.R (rcond): method, use x or t(x)
377    
378    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
381            matrices.
382            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
383    
384            * man/rcond.Rd: mention the more general definition, and add
385            example for non-square matrices.
386    
387            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
388    
389    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
392    
393    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
396            * tests/indexing.R: add new regression for the above cases.
397    
398    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * src/Mutils.h (__sun): clause for alloca.h on Solaris
401    
402    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * DESCRIPTION (Date, Version): 0.999375-2
405    
406    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/HBMM.R (readMM): make work for pattern matrices as well
409    
410    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
411    
412            * [r4730] src/Mutils.h: declare alloca
413            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
414              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
415              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
416              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
417              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
418              methods; switch writeMM to use CHOLMOD code; repair readMM
419    
420    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
423            Oehlschlaegel's ... result type still to be discussed!
424    
425    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * man/image-methods.Rd: new, combining all image() methods
428    
429    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
432            to work via dgC...
433    
434            * R/Matrix.R (Matrix): special treatment for "table" (S3)
435    
436    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/dgTMatrix.R (image): change defaults to
439                    aspect = "iso", colorkey = FALSE
440    
441    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
444            must copy its *expanded* x slot before LAPACK call.
445    
446            * tests/matprod.R: test the last days' changes.
447    
448    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
449    
450            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
451              as well as in sources
452            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
453              Lapack call
454    
455    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
458                    ("Matrix", "matrix") which is needed in some cases.
459            Ditto for solve().
460    
461            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
462            infinite recursion in dispatch for some cases.
463    
464    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
465    
466            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
467              so pointers match
468    
469    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
470    
471            * DESCRIPTION (Date): set ready for release -- 0.999375-1
472    
473    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
474    
475            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
476              src/chm_common.c, src/chm_common.h: Change API for
477              numeric_as_chm_dense and N_AS_CHM_DN
478    
479    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
482            * tests/matprod.R: regr.test for it
483    
484    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
487            * tests/group-methods.R: and regression-test it
488    
489    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
490    
491            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
492              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
493              triplet_to_sparse, documentation, use typedefs
494    
495    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * man/dpoMatrix-class.Rd: added 'corMatrix' example
498    
499            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
500            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
501            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
502    
503            * R/lsparseMatrix.R: bug fix in "all" method
504            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
505    
506            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
507            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
508                    + matrix |-> nMatrix coercion
509            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
510            * man/pMatrix-class.Rd: ditto
511    
512            * R/Matrix.R (Summary): method for non-dMatrix
513    
514            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
515            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
516                    test all Summary methods.
517    
518    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
521    
522    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
523    
524            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
525    
526            * R/pMatrix.R (t?crossprod): methods for pMatrix
527    
528    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
529    
530            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
531    
532    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
533    
534            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
535              trying to fix a subtle bug - which has been somewhere else.
536    
537    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
538    
539            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
540              solve the bug
541    
542    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * src/dgCMatrix.c (compressed_to_TMatrix):
545    
546    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
547    
548            * src/Csparse.c (Rsparse_validate): new, to have some validity
549            checking for RsparseMatrix
550            * src/dgCMatrix.c (xRMatrix_validate): ditto
551            * src/dtCMatrix.c (tRMatrix_validate): ditto
552    
553    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
554    
555            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
556              lgRMatrix
557            * [r4568] DESCRIPTION: Prepare for bug-fix release
558            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
559              for declaration of cholmod_symmetry
560    
561    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
564            release.
565    
566    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
567    
568            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
569              functions - no longer used
570            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
571              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
572              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
573              Alloca
574    
575    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
576    
577            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
578              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
579              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
580              src/t_gCMatrix_colSums.c: more R_CheckStack()s
581    
582    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
583    
584            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
585              the required amount of memory then call M_numeric_as_chm_dense.
586            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
587              (like Calloc but calling alloca)
588    
589    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
592            and extended with more sophisticated 'col.names' option.
593            * NAMESPACE: export  printSparseMatrix()
594            * man/printSpMatrix.Rd: document, incl. examples
595    
596    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
597    
598            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
599              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
600              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
601    
602    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * DESCRIPTION (Version): 0.99875-4
605    
606            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
607            some dimnames perservation.
608    
609            * R/dsTMatrix.R (t-method): keep dimnames
610            * R/dtTMatrix.R:  ditto
611    
612            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
613            and ncol(.) < 10
614    
615            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
616            from Mutils.h
617    
618            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
619            e.g. in as(<ngCMatrix>, "matrix")
620    
621    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
622    
623            * [r4529] .: Create a branch for the API changes from the 0.99875
624              series to the 0.999375 series
625            * [r4530] DESCRIPTION, inst/include/Matrix.h,
626              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
627              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
628              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
629              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
630              as_cholmod_x functions
631    
632    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
633    
634            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
635              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
636              to Comparisons
637    
638    >>>>>>> .merge-right.r4561
639    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
640    
641            * DESCRIPTION (Version): 0.99875-3 ready to be released.
642    
643            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
644    
645            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
646            that should also work in a future version of R.
647    
648    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
649    
650            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
651    
652            * R/sparseVector.R: more *sparseVector coercions, notably for
653            non - double ones.
654    
655    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
658              notably the new ones building on the new .Call(.)s:
659    
660            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
661            all 4 of [dlin]gCMatrix_colSums().
662    
663    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
664    
665            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
666            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
667              result
668    
669    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
670    
671            * R/kronecker.R: fix typo (could lead to inf.recursion)
672            * test/simple.R: testing that
673    
674            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
675            method as well (which can have arguments, show() can't).
676    
677    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
678    
679            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
680              added dgCMatrix_colSums for [col,row][Sums,Means]
681    
682    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
683    
684            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
685              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
686              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
687            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
688              class
689            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
690              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
691              row names to store the levels - duh!  Added an example.
692    
693    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * src/Csparse.c (Csparse_validate): check for *repeated* entries
696            thanks to example from Christian Buchta; with a test here:
697            * tests/simple.R:
698    
699    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
702            of colSums(*, sparseResult = TRUE)
703    
704    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
707            'na.rm = FALSE' as "everywhere" else in R.
708    
709    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
710    
711            * [r4421] src/CSparse_install.sh: Modify for new organization of
712              CSparse package
713            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
714              SuiteSparse
715            * [r4426] src/Makefile: add ./UFconfig to the include path for
716              compilation
717            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
718            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
719              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
720    
721    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
724            * R/sparseMatrix.R (prSpMatrix): now gives a message about
725            suppressed column names.
726    
727    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
728    
729            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
730              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
731              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
732              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
733              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
734              Remove warnings after change to const char* CHAR
735    
736    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
737    
738            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
739              type of M_cholmod_ssmult
740    
741    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
742    
743            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
744              src/init.c: Yet another cholmod export - cholmod_ssmult
745    
746    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
747    
748            * NAMESPACE: exported drop0(), since
749            * man/drop0.Rd: I have seen several cases, I really wanted to use
750            it, so our users may want too.
751    
752    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * man/colSums.Rd: separately document colSums() etc, since these
755            have the extra argument 'sparseResult'.
756    
757    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
760            * man/spMatrix.Rd: docu., including examples
761    
762            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
763            in order to make colMeans() etc fast *and* correct.
764            * R/sparseVector.R (replSPvec): "[<-" functionality for
765            sparseVectors; tested in
766            * tests/simple.R:
767    
768    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
771            (very) sparse Matrices; output similar to Matlab's print().
772    
773    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
774    
775            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
776            0-based, indices (Jose Quesada <quesada@gmail.com>).
777    
778    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
779    
780            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
781    
782    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
783    
784            * R/Auxiliaries.R (sparsapply): new utility, much faster than
785            tapply1() for large sparse matrices.
786    
787    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * R/Matrix.R (dim<-): reshape now via sparseVector.
790    
791            * R/sparseVector.R: methods and function for
792            * R/AllClass.R: new "sparseVector" class and daughters.
793            * NAMESPACE: export new classes
794    
795    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * DESCRIPTION (Version): 0.99875-1
798            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
799    
800    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
801    
802            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
803            indexing
804            * tests/indexing.R: test set for that.
805    
806    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
807    
808            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
809            entries.
810            * tests/indexing.R(out): add regression test for it
811    
812    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
815            name for "!" method definitions.
816    
817    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
818    
819            * R/Tsparse.R (intI): new utility, used for "[" :
820                    Cleanup up there, and fixes for duplicated indices - more TODO!
821    
822            * tests/indexing.R(out): more tests
823    
824    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
825    
826            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
827            code that is now part of the R Lapack library.
828    
829            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
830            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
831    
832    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
835    
836    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
837    
838            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
839            up with extraneous names '0'...'<n-1>'
840    
841    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
842    
843            * R/dgTMatrix.R (mat2dgT): care about NAs
844    
845    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
846    
847            * R/kronecker.R: triangularity preserving methods
848    
849    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
850    
851            * R/kronecker.R: new file collecting kronecker() methods in one
852                    place.  Goal: become much faster!
853    
854    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
857            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
858            can be much faster.
859    
860            * tests/matprod.R: add regression tests for these (upper & lower).
861    
862    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * R/Matrix.R (diff): method for our Matrices.
865    
866            * R/sparseMatrix.R (isDiagonal): check dim()!
867    
868    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
869    
870            * R/Matrix.R (dim<-): new method for "reshape()" built on a
871            proposal from Tamas Papp.
872    
873    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
876    
877            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
878            rather define and export  cBind() and rBind() only.
879            --> useRs *must* change code that used to have cbind()/rbind() !!
880    
881            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
882            * R/bind.Rout.save: ditto
883    
884    2007-02-16  Douglas Bates  <bates@r-project.org>
885    
886            * DESCRIPTION (Date, Version): 0.9975-11 with new date
887            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
888            const modifier on declaration of the array 'valid'
889    
890    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
891    
892            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
893    
894    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
897    
898            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
899            * tests/simple.R: test the above and some of these coercions:
900    
901            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
902                    be careful to avoid infinite recursion, using new coercions in
903            * R/ngCMatrix.R and nsC... and ntC...
904            * R/lsparseMatrix.R: ditto
905    
906            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
907    
908            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
909            * R/Rsparse.R: reactivate .Call()s
910    
911            * tests/Class+Meth.R: a bit more on actual classes
912    
913    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
914    
915            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
916    
917    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
918    
919            * DESCRIPTION (Version): 0.9975-10 to upload
920    
921            * tests/Class+Meth.R (tstMatrixClass): require coercions to
922            specific classes less unconditionally.
923    
924            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
925    
926            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
927    
928            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
929            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
930            R_to_CMatrix segfaults on one platform.
931            Eliminate most coercion method to *specific* classes, and replace
932            with virtual classes coercions.
933    
934    
935    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
936    
937            * src/init.c: export the CHM...._validate() placeholders, since
938            they *are* called.
939    
940            * tests/Class+Meth.R (classCanCoerce): and starting to test
941            all as(<from>, <to>)
942    
943    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
946            * tests/indexing.R: tested now
947            * tests/indexing.Rout.save: updated
948    
949            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
950            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
951            appropriate.
952    
953            * NAMESPACE: export a trivial
954            * R/Matrix.R: drop() Matrix-method
955    
956            * R/AllClass.R: moved all prototypes to virtual super classes.
957    
958            * R/Rsparse.R: many more coercions to have less exceptions in
959            * tests/Class+Meth.R:
960    
961            * R/Ops.R (Compare): tweak for case with NA
962            * tests/simpl.R: hence another 'FIXME' eliminated
963    
964    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
967            objects.
968    
969            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
970              and more of "!", "&", "|", all, any; coercions
971    
972            * R/Rsparse.R: many coercions (which enable quite a few other
973            methods), thanks to enhancements in
974            * src/dgCMatrix.c (R_to_CMatrix): new, and
975            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
976            symmetric & triangular and ..RMatrix objects.
977    
978            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
979            renamed file from src/dsTMatrix.c;
980            now dealing with symmetric and triangular Tsparse coercions, both
981            to dense and general.
982    
983    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
984    
985            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
986    
987            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
988            where sensible when the <numeric> is of length > 1.
989    
990    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
991    
992            * R/Matrix.R ([<-): for M[] <- value: fix length
993    
994    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
997            * R/ndenseMatrix.R: new coercions n* -> l*
998    
999    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1000    
1001            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1002    
1003            * R/Ops.R ("Logic"): and other "Ops", many updates
1004    
1005    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * src/Mutils.h (SET_DimNames): new utility
1008    
1009            * R/Auxiliaries.R (nnzero): improved and now exported via
1010    
1011            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1012    
1013    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1014    
1015            * R/diagMatrix.R (!): fix typo.
1016    
1017    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1018    
1019            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1020                    allow to pass class definition --> speedup
1021            * R/sparseMatrix.R: apply the above
1022    
1023            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1024    
1025            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1026            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1027            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1028    
1029            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1030    
1031            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1032            and use it for "sparse*" as well, since it's faster than the
1033            as_Csparse(.) way.
1034    
1035    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1038    
1039    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1040    
1041            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1042            as method for   M[ ij ] <- v
1043            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1044    
1045            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1046            FALSE answer
1047    
1048            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1049            * tests/indexing.R: test it, and some of the above
1050    
1051    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1052    
1053            * R/Auxiliaries.R (is_duplicatedT): new utility
1054    
1055    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1056    
1057            * src/init.c (R_init_Matrix): export cholmod_scale
1058    
1059    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1060    
1061            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1062            base::as.matrix to (x, ...)
1063    
1064    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1065    
1066            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1067            file; start using "Logic", hence
1068    
1069            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1070            * NAMESPACE: import and export "Logic"
1071    
1072    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1075            only needed previously to R version 2.5.0.
1076    
1077    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1078    
1079            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1080    
1081            * R/Tsparse.R (replTmat): fix subassignment of triangular
1082            * R/Csparse.R (replCmat): ditto
1083            * tests/indexing.R: more tests, incl the above fix
1084    
1085    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1086    
1087            * R/Auxiliaries.R (drop0): extend for non CSparse
1088            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1089    
1090            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1091                    use uplo correctly (!); other places: use uplo_P() macro
1092    
1093            * R/Csparse.R (replCmat): call diagU2N() when needed
1094            * R/Tsparse.R (replTmat): ditto
1095    
1096            * src/dtCMatrix.c (tCMatrix_validate): new
1097            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1098            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1099    
1100            * R/diagMatrix.R (replDiag): to use in [<-
1101    
1102    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1103    
1104            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1105                    also more general diagU2N().
1106    
1107    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1108    
1109            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1110            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1111    
1112    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1113    
1114            * tests/bind.R: a few more cases
1115            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1116    
1117            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1118            * R/ddenseMatrix.R (cbind2/rbind2)
1119            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1120            * tests/indexing.R
1121            * tests/indexing.Rout.save: updated
1122    
1123    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1126            * tests/indexing.R
1127    
1128    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1129    
1130            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1131            align with proper position of "0", i.e., right for integers.
1132            argument 'align' by default is "fancy".
1133    
1134    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1137            * R/Csparse.R: and fix "Compare" for more cases.
1138            * tests/Class+Meth.R: test some of these (m == m, m != m)
1139    
1140    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * R/lsparseMatrix.R: all() and any() methods
1143            * R/ldenseMatrix.R:      ditto
1144            * NAMESPACE, R/Matrix.R: ditto
1145    
1146            * man/all-methods.Rd: document them minimally
1147    
1148            * tests/simple.R: add a few examples for these
1149    
1150    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1151    
1152            * R/Tsparse.R ([): fix long standing typo in symmetric case
1153            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1154    
1155    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1156    
1157            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1158            to LL before converting to a sparse matrix. (The LDL form can be
1159            converted to a sparse matrix but it is implicitly a unit
1160            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1161    
1162    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1163    
1164            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1165    
1166    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1167    
1168            * DESCRIPTION (Version): updated -> release 0.9975-7
1169            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1170    
1171    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1172    
1173            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1174    
1175    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1176    
1177            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1178            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1179            is exactly singular.
1180    
1181    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1182    
1183            * DESCRIPTION (Date): updated -> release 0.9975-6
1184    
1185    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1188            now returns symmetric.
1189    
1190            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1191    
1192            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1193            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1194    
1195            * R/Auxiliaries.R (.type.kind): added
1196    
1197    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1200            running src/CSparse_install.sh
1201    
1202            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1203    
1204    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1207            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1208    
1209            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1210    
1211            * tests/Class+Meth.R (tstMatrixClass): now assure
1212            the (important in method programming) property :
1213    
1214                    ###>>  Every "Matrix" is either
1215                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1216    
1217                    (where "*" stands for "Matrix")
1218    
1219            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1220    
1221            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1222            * tests/validObj.R: checks for "comparison"
1223    
1224            * R/sparseMatrix.R ([): improved indexing for sparse;
1225                    trying to keep <symmetric>[ n, n] symmmetric
1226    
1227            * tests/indexing.R: indexing for logical sparse now ok
1228    
1229    
1230    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1231    
1232            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1233    
1234            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1235    
1236    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1237    
1238            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1239    
1240            * tests/simple.R: validObject() checking the above.
1241    
1242            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1243            replacing both dgCMatrix_validate and lgCM*.
1244    
1245            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1246            fix dimnames setting in other places.
1247            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1248    
1249    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1250    
1251            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1252    
1253            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1254            symmetry test, via
1255            * R/Auxiliaries.R (.as.dgC.0.factors):
1256    
1257    2006-11-01  Douglas Bates  <bates@r-project.org>
1258    
1259            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1260            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1261            <CsparseMatrix>) added
1262    
1263    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1264    
1265            * tests/matprod.R: add a variation of Harri's example
1266    
1267            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1268            recursive infinitely.
1269    
1270            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1271    
1272            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1273    
1274    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1275    
1276            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1277            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1278            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1279            satisfy the above test.
1280    
1281    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1282    
1283            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1284    
1285            * R/dgCMatrix.R: solve(a, b="missing") based on
1286            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1287            RHS = NULL.
1288    
1289            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1290            add more (needed) [t]crossprod() methods.
1291    
1292            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1293    
1294            * R/Auxiliaries.R (as_CspClass): cleanup
1295            (drop0): internal utility for "Csparse_drop(*, 0)"
1296            (.bail.out.2): encourage active feedback
1297    
1298    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1299    
1300            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1301    
1302            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1303            non-valid or 'sorted' case).
1304    
1305            * R/dsparseMatrix.R: add "chol" method.
1306            * R/ddenseMatrix.R: ditto
1307    
1308            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1309            * NAMESPACE (Ops)
1310            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1311            coercion; deprecating direct lower level coercions.
1312    
1313            * R/*.R (seq): use seq_len() and seq_along() where possible.
1314    
1315    
1316    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1317    
1318            * DESCRIPTION (Version): 0.9975-5 ready for release
1319    
1320    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1321    
1322            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1323    
1324    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1325    
1326            * R/AllClass.R (corMatrix): add 'validity' check;
1327                    comment out unused "LDL" class definition
1328            * NAMESPACE: mention, but do not export "LDL" class
1329            * R/corMatrix.R: new (simple), needed for R-devel with
1330            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1331              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1332    
1333    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1334    
1335            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1336            use Rprintf and R's error handling.
1337    
1338    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1339    
1340            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1341            * tests/matprod.R: add tests for the bug fixed.
1342    
1343    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1344    
1345            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1346            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1347    
1348    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1349    
1350            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1351    
1352    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1353    
1354            * DESCRIPTION (Version): 0.9975-3
1355    
1356            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1357            (sparse) matrices.
1358            * man/bdiag.Rd: docu + examples
1359    
1360            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1361    
1362            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1363            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1364    
1365            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1366            that result is sparse or diagonal (and not dense).
1367    
1368            * man/Subassign-methods.Rd: fix examples
1369    
1370            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1371            should always return a sparse (and not sometimes a diagonal) matrix.
1372    
1373    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1374    
1375            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1376    
1377    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1378    
1379            * DESCRIPTION (Version): 0.9975-2
1380    
1381            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1382    
1383    2006-10-02  Douglas Bates  <bates@R-project.org>
1384    
1385            * tests/dg_Matrix.R: Simplify test taking into account new code.
1386    
1387    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1388    
1389            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1390    
1391            * R/lsTMatrix.R: new files w/ missing methods
1392            * R/nsTMatrix.R:  "  'for completeness'
1393    
1394            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1395    
1396            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1397    
1398    
1399    2006-09-28  Douglas Bates  <bates@R-project.org>
1400    
1401            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1402            included.
1403    
1404            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1405            Export C-callable functions used in Zt_create in lme4.
1406    
1407    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1408    
1409            * DESCRIPTION (Version): 0.9975-1
1410    
1411            * tests/simple.R: less checks fail; using NA, found that our
1412                    kronecker() is not base-compatible with NA's.
1413    
1414            * R/dMatrix.R: "Compare" method now implemented for all cases
1415    
1416            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1417    
1418            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1419    
1420            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1421            * src/dspMatrix.c (dspMatrix_validate): ditto
1422    
1423            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1424              including coercion to [nl]tTMatrix.
1425    
1426            * R/diagMatrix.R (show): print a header line as for other classes.
1427    
1428    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * src/Makefile.win (SUBDIRS): fix typo
1431    
1432    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1433    
1434            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1435    
1436    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1437    
1438            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1439            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1440            accept a symmetric matrix).
1441            * tests/group-methods.R: Uncomment test of crossprod applied to
1442            lsCMatrix objects.
1443    
1444    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1445    
1446            * R/AllClass.R (symmetricMatrix): add validity method (available
1447            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1448    
1449            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1450    
1451            * tests/indexing.Rout.save:
1452            * tests/indexing.R: additions, mainly for 'lsparse'
1453    
1454            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1455            case.
1456    
1457            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1458    
1459    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1460    
1461            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1462                    as 'N' (1-letter - Ok?)
1463    
1464            * tests/group-methods.R: add test for logical + NAs
1465    
1466            * R/dMatrix.R ("Compare"): fix to work with NA's
1467    
1468            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1469    
1470            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1471                    which is implemented.
1472    
1473    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1474    
1475            * src/chm_common.c: coerce logical <-> double instead of
1476            typecasting;  needed for "l" matrix handling in cholmod.
1477    
1478            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1479    
1480            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1481            (Tsp2grNEL): other fixes needed
1482    
1483  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1484    
1485          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 1489 
1489          * tests/: adaptions          * tests/: adaptions
1490          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
1491                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1492          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
1493    
1494  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
1495    
# Line 26  Line 1508 
1508          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1509    
1510          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1511          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
1512    
1513  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1514    
# Line 69  Line 1551 
1551    
1552          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1553          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1554          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1555          * R/Csparse.R: dito          * R/Csparse.R: ditto
1556    
1557  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1558    
# Line 86  Line 1568 
1568    
1569          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1570          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1571          (.is.diagonal): dito          (.is.diagonal): ditto
1572    
1573          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1574    

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