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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 2128, Thu Mar 13 23:08:34 2008 UTC
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1    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
4    
5            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
6              <diagonal> o <sparse_triangular>
7              setAs(., "nMatrix") added.
8    
9            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
10    
11            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
12                    new argument 'checkDense = FALSE'.
13    
14    
15    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
18            back-permutation of the matrix exponential.
19    
20            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
21    
22            * DESCRIPTION (Date,Version): ready to release 0.999375-5
23    
24            * tests/simple.R: testing diagN2U
25    
26    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (diagN2U): interface to
29    
30            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
31    
32            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
33    
34    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/chm_common.c (chm_diagN2U): new utility.
37    
38            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
39            make use of chm_diagN2U() and hence now preserve triangularity and
40            unit-triangularity.
41    
42            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
43    
44    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
47    
48            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
49            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
50    
51            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
52    
53            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
54    
55            * src/chm_common.c (AS_CHM_FINISH): add note about problem
56            for triangular (diag = "U").
57    
58    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
61            * R/bind.R:  .Call(dense_to_Csparse, *)
62    
63    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (Matrix): no longer use coercions to specific classes
66                    (since we are discouraging them in user code).
67    
68            * tests/*.R: also replaces coercions to specific classes by
69            coercions to super classes.
70    
71            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
72    
73    
74    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
77    
78            * src/dense.c (dense_band): generalized from ddense_band
79    
80            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
81              now for "denseMatrix" (instead of just "ddense*"); much
82              simplified setMethod()s for these.
83    
84            * src/dense.c (dense_to_symmetric): generalized from ddense_*
85    
86    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
89            version of as(*, "symmetricMatric").
90    
91            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
92            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
93    
94    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/Matrix.R (subset.ij): utility, as first step to faster
97               M [ <ij-matrix> ] indexing.
98    
99            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
100    
101            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
102            for more efficient symmpart() and skewpart() methods.
103    
104            * src/Mutils.c (equal_string_vectors): utility
105    
106            * src/dense.c (ddense_to_symmetric): new function used in
107    
108            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
109    
110            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
111            order to match the generic (and evade .local(..)).
112    
113            * R/dsCMatrix.R: dgC -> dsC: use C code!
114    
115            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
116            as per TODO
117    
118            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
119    
120            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
121    
122    
123    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
126    
127            * R/Auxiliaries.R (non0.i): take out of non0ind
128    
129            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
130            make tril(), triu(), band() work for "matrix" and all "dense*"
131    
132            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
133            * tests/simple.R: test the fix above
134    
135            * R/sparseMatrix.R ([): simplification: no coerce to <general>
136                    before we use as(., <Tsparse>)[...] anyway
137    
138            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
139    
140            * R/triangularMatrix.R (isTriangular): methods for all subclasses
141            instead of "triangularMatrix" -- just to disambiguate
142    
143    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
146            * tests/indexing.R: example that fails above
147    
148    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
151            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
152                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
153    
154            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
155            * src/Tsparse.h, init.c: ditto
156            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
157                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
158            * R/sparseMatrix.R (isTriangular): hence simplified
159    
160    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Ops.R (.Arith.Csparse): new utility factored out of former
163              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
164    
165    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
168    
169            * inst/test-tools.R (isOrthogonal): new function; also file restructured
170    
171    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
174            coercion to "nMatrix" and "pMatrix"
175    
176            * R/AllClass.R: "Schur" class;  "number" class union
177            * man/number-class.Rd:
178            * man/Schur-class.Rd:
179    
180            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
181            (.simpleSchur): Schur() method for diagonal matrices
182            (.triSchur):    Schur() method for triangular matrices
183            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
184    
185    
186    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
189    
190    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
193                    in order to ensure 'system = *' is not lost;
194                    formals()$system instead of cut&paste.
195            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
196    
197    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Date): make ready for release --> 0.999375-4
200    
201            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
202    
203    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
206                    and hence does as.vector(.).
207            * man/pMatrix-class.Rd: docs
208            * R/sparseMatrix.R: fix for printing "integer sparse"
209    
210            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
211    
212            * R/Matrix.R and others: use "exact" function argument list for
213                    both "["   : (x, i,j, ..., drop)
214                    and  "[<-" : (x, i,j, ..., value)
215    
216            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
217            * R/Tsparse.R (replTmat):    ditto
218            * R/diagMatrix.R (replDiag): ditto
219            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
220            * tests/indexing.R: testing the above
221    
222    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/sparseMatrix.R (cov2cor): method for sparse matrices
225    
226            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
227    
228            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
229    
230            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
231    
232    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/Matrix.R: "generic" cov2cor() method
235    
236            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
237                    speed up Q %*% D %*% t(Q)
238            * tests/dpoMatrix.R: test nearPD()
239    
240    2007-12-05  Doug Bates and Martin Maechler
241    
242            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
243            stats::xtabs() allowing to create sparse matrices.
244    
245    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
248    
249    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
252    
253    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/LU.R: solve() method for "denseLU"
256    
257    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.999375-3 preparing for release
260    
261            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
262    
263            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
264    
265    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
268              thanks to Kasper Kristensen.
269            * tests/matprod.R: regression test for that.
270    
271    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
272    
273            * [r4778] R/AllGeneric.R: Check R version before defining generics for
274              primitives
275    
276    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/denseMatrix.R (rcond): method
279            * R/sparseQR.R (rcond): method, use x or t(x)
280    
281    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
284            matrices.
285            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
286    
287            * man/rcond.Rd: mention the more general definition, and add
288            example for non-square matrices.
289    
290            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
291    
292    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
295    
296    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
299            * tests/indexing.R: add new regression for the above cases.
300    
301    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/Mutils.h (__sun): clause for alloca.h on Solaris
304    
305    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date, Version): 0.999375-2
308    
309    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/HBMM.R (readMM): make work for pattern matrices as well
312    
313    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
314    
315            * [r4730] src/Mutils.h: declare alloca
316            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
317              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
318              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
319              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
320              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
321              methods; switch writeMM to use CHOLMOD code; repair readMM
322    
323    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
326            Oehlschlaegel's ... result type still to be discussed!
327    
328    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * man/image-methods.Rd: new, combining all image() methods
331    
332    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
335            to work via dgC...
336    
337            * R/Matrix.R (Matrix): special treatment for "table" (S3)
338    
339    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/dgTMatrix.R (image): change defaults to
342                    aspect = "iso", colorkey = FALSE
343    
344    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
347            must copy its *expanded* x slot before LAPACK call.
348    
349            * tests/matprod.R: test the last days' changes.
350    
351    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
352    
353            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
354              as well as in sources
355            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
356              Lapack call
357    
358    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
361                    ("Matrix", "matrix") which is needed in some cases.
362            Ditto for solve().
363    
364            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
365            infinite recursion in dispatch for some cases.
366    
367    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
368    
369            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
370              so pointers match
371    
372    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * DESCRIPTION (Date): set ready for release -- 0.999375-1
375    
376    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
377    
378            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
379              src/chm_common.c, src/chm_common.h: Change API for
380              numeric_as_chm_dense and N_AS_CHM_DN
381    
382    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
385            * tests/matprod.R: regr.test for it
386    
387    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
390            * tests/group-methods.R: and regression-test it
391    
392    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
393    
394            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
395              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
396              triplet_to_sparse, documentation, use typedefs
397    
398    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * man/dpoMatrix-class.Rd: added 'corMatrix' example
401    
402            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
403            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
404            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
405    
406            * R/lsparseMatrix.R: bug fix in "all" method
407            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
408    
409            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
410            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
411                    + matrix |-> nMatrix coercion
412            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
413            * man/pMatrix-class.Rd: ditto
414    
415            * R/Matrix.R (Summary): method for non-dMatrix
416    
417            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
418            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
419                    test all Summary methods.
420    
421    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
424    
425    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
428    
429            * R/pMatrix.R (t?crossprod): methods for pMatrix
430    
431    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
432    
433            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
434    
435    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
436    
437            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
438              trying to fix a subtle bug - which has been somewhere else.
439    
440    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
441    
442            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
443              solve the bug
444    
445    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * src/dgCMatrix.c (compressed_to_TMatrix):
448    
449    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * src/Csparse.c (Rsparse_validate): new, to have some validity
452            checking for RsparseMatrix
453            * src/dgCMatrix.c (xRMatrix_validate): ditto
454            * src/dtCMatrix.c (tRMatrix_validate): ditto
455    
456    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
457    
458            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
459              lgRMatrix
460            * [r4568] DESCRIPTION: Prepare for bug-fix release
461            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
462              for declaration of cholmod_symmetry
463    
464    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
467            release.
468    
469    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
470    
471            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
472              functions - no longer used
473            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
474              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
475              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
476              Alloca
477    
478    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
479    
480            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
481              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
482              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
483              src/t_gCMatrix_colSums.c: more R_CheckStack()s
484    
485    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
486    
487            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
488              the required amount of memory then call M_numeric_as_chm_dense.
489            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
490              (like Calloc but calling alloca)
491    
492    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
495            and extended with more sophisticated 'col.names' option.
496            * NAMESPACE: export  printSparseMatrix()
497            * man/printSpMatrix.Rd: document, incl. examples
498    
499    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
500    
501            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
502              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
503              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
504    
505    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * DESCRIPTION (Version): 0.99875-4
508    
509            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
510            some dimnames perservation.
511    
512            * R/dsTMatrix.R (t-method): keep dimnames
513            * R/dtTMatrix.R:  ditto
514    
515            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
516            and ncol(.) < 10
517    
518            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
519            from Mutils.h
520    
521            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
522            e.g. in as(<ngCMatrix>, "matrix")
523    
524    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
525    
526            * [r4529] .: Create a branch for the API changes from the 0.99875
527              series to the 0.999375 series
528            * [r4530] DESCRIPTION, inst/include/Matrix.h,
529              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
530              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
531              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
532              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
533              as_cholmod_x functions
534    
535    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
536    
537            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
538              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
539              to Comparisons
540    
541    >>>>>>> .merge-right.r4561
542    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * DESCRIPTION (Version): 0.99875-3 ready to be released.
545    
546            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
547    
548            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
549            that should also work in a future version of R.
550    
551    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
554    
555            * R/sparseVector.R: more *sparseVector coercions, notably for
556            non - double ones.
557    
558    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
561              notably the new ones building on the new .Call(.)s:
562    
563            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
564            all 4 of [dlin]gCMatrix_colSums().
565    
566    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
567    
568            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
569            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
570              result
571    
572    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/kronecker.R: fix typo (could lead to inf.recursion)
575            * test/simple.R: testing that
576    
577            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
578            method as well (which can have arguments, show() can't).
579    
580    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
581    
582            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
583              added dgCMatrix_colSums for [col,row][Sums,Means]
584    
585    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
586    
587            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
588              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
589              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
590            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
591              class
592            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
593              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
594              row names to store the levels - duh!  Added an example.
595    
596    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * src/Csparse.c (Csparse_validate): check for *repeated* entries
599            thanks to example from Christian Buchta; with a test here:
600            * tests/simple.R:
601    
602    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
605            of colSums(*, sparseResult = TRUE)
606    
607    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
610            'na.rm = FALSE' as "everywhere" else in R.
611    
612    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
613    
614            * [r4421] src/CSparse_install.sh: Modify for new organization of
615              CSparse package
616            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
617              SuiteSparse
618            * [r4426] src/Makefile: add ./UFconfig to the include path for
619              compilation
620            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
621            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
622              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
623    
624    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
627            * R/sparseMatrix.R (prSpMatrix): now gives a message about
628            suppressed column names.
629    
630    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
631    
632            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
633              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
634              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
635              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
636              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
637              Remove warnings after change to const char* CHAR
638    
639    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
640    
641            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
642              type of M_cholmod_ssmult
643    
644    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
645    
646            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
647              src/init.c: Yet another cholmod export - cholmod_ssmult
648    
649    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * NAMESPACE: exported drop0(), since
652            * man/drop0.Rd: I have seen several cases, I really wanted to use
653            it, so our users may want too.
654    
655    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * man/colSums.Rd: separately document colSums() etc, since these
658            have the extra argument 'sparseResult'.
659    
660    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
663            * man/spMatrix.Rd: docu., including examples
664    
665            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
666            in order to make colMeans() etc fast *and* correct.
667            * R/sparseVector.R (replSPvec): "[<-" functionality for
668            sparseVectors; tested in
669            * tests/simple.R:
670    
671    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
674            (very) sparse Matrices; output similar to Matlab's print().
675    
676    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
677    
678            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
679            0-based, indices (Jose Quesada <quesada@gmail.com>).
680    
681    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
684    
685    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/Auxiliaries.R (sparsapply): new utility, much faster than
688            tapply1() for large sparse matrices.
689    
690    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Matrix.R (dim<-): reshape now via sparseVector.
693    
694            * R/sparseVector.R: methods and function for
695            * R/AllClass.R: new "sparseVector" class and daughters.
696            * NAMESPACE: export new classes
697    
698    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * DESCRIPTION (Version): 0.99875-1
701            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
702    
703    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
706            indexing
707            * tests/indexing.R: test set for that.
708    
709    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
712            entries.
713            * tests/indexing.R(out): add regression test for it
714    
715    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
718            name for "!" method definitions.
719    
720    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/Tsparse.R (intI): new utility, used for "[" :
723                    Cleanup up there, and fixes for duplicated indices - more TODO!
724    
725            * tests/indexing.R(out): more tests
726    
727    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
730            code that is now part of the R Lapack library.
731    
732            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
733            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
734    
735    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
738    
739    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
742            up with extraneous names '0'...'<n-1>'
743    
744    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/dgTMatrix.R (mat2dgT): care about NAs
747    
748    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/kronecker.R: triangularity preserving methods
751    
752    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/kronecker.R: new file collecting kronecker() methods in one
755                    place.  Goal: become much faster!
756    
757    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
760            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
761            can be much faster.
762    
763            * tests/matprod.R: add regression tests for these (upper & lower).
764    
765    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/Matrix.R (diff): method for our Matrices.
768    
769            * R/sparseMatrix.R (isDiagonal): check dim()!
770    
771    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/Matrix.R (dim<-): new method for "reshape()" built on a
774            proposal from Tamas Papp.
775    
776    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
779    
780            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
781            rather define and export  cBind() and rBind() only.
782            --> useRs *must* change code that used to have cbind()/rbind() !!
783    
784            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
785            * R/bind.Rout.save: ditto
786    
787    2007-02-16  Douglas Bates  <bates@r-project.org>
788    
789            * DESCRIPTION (Date, Version): 0.9975-11 with new date
790            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
791            const modifier on declaration of the array 'valid'
792    
793    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
794    
795            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
796    
797    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
800    
801            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
802            * tests/simple.R: test the above and some of these coercions:
803    
804            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
805                    be careful to avoid infinite recursion, using new coercions in
806            * R/ngCMatrix.R and nsC... and ntC...
807            * R/lsparseMatrix.R: ditto
808    
809            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
810    
811            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
812            * R/Rsparse.R: reactivate .Call()s
813    
814            * tests/Class+Meth.R: a bit more on actual classes
815    
816    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
817    
818            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
819    
820    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * DESCRIPTION (Version): 0.9975-10 to upload
823    
824            * tests/Class+Meth.R (tstMatrixClass): require coercions to
825            specific classes less unconditionally.
826    
827            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
828    
829            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
830    
831            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
832            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
833            R_to_CMatrix segfaults on one platform.
834            Eliminate most coercion method to *specific* classes, and replace
835            with virtual classes coercions.
836    
837    
838    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
839    
840            * src/init.c: export the CHM...._validate() placeholders, since
841            they *are* called.
842    
843            * tests/Class+Meth.R (classCanCoerce): and starting to test
844            all as(<from>, <to>)
845    
846    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
849            * tests/indexing.R: tested now
850            * tests/indexing.Rout.save: updated
851    
852            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
853            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
854            appropriate.
855    
856            * NAMESPACE: export a trivial
857            * R/Matrix.R: drop() Matrix-method
858    
859            * R/AllClass.R: moved all prototypes to virtual super classes.
860    
861            * R/Rsparse.R: many more coercions to have less exceptions in
862            * tests/Class+Meth.R:
863    
864            * R/Ops.R (Compare): tweak for case with NA
865            * tests/simpl.R: hence another 'FIXME' eliminated
866    
867    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
870            objects.
871    
872            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
873              and more of "!", "&", "|", all, any; coercions
874    
875            * R/Rsparse.R: many coercions (which enable quite a few other
876            methods), thanks to enhancements in
877            * src/dgCMatrix.c (R_to_CMatrix): new, and
878            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
879            symmetric & triangular and ..RMatrix objects.
880    
881            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
882            renamed file from src/dsTMatrix.c;
883            now dealing with symmetric and triangular Tsparse coercions, both
884            to dense and general.
885    
886    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
889    
890            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
891            where sensible when the <numeric> is of length > 1.
892    
893    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
894    
895            * R/Matrix.R ([<-): for M[] <- value: fix length
896    
897    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
900            * R/ndenseMatrix.R: new coercions n* -> l*
901    
902    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
903    
904            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
905    
906            * R/Ops.R ("Logic"): and other "Ops", many updates
907    
908    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
909    
910            * src/Mutils.h (SET_DimNames): new utility
911    
912            * R/Auxiliaries.R (nnzero): improved and now exported via
913    
914            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
915    
916    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
917    
918            * R/diagMatrix.R (!): fix typo.
919    
920    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * R/Auxiliaries.R (as_Csparse): and quite a few others:
923                    allow to pass class definition --> speedup
924            * R/sparseMatrix.R: apply the above
925    
926            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
927    
928            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
929            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
930            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
931    
932            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
933    
934            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
935            and use it for "sparse*" as well, since it's faster than the
936            as_Csparse(.) way.
937    
938    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
941    
942    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
945            as method for   M[ ij ] <- v
946            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
947    
948            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
949            FALSE answer
950    
951            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
952            * tests/indexing.R: test it, and some of the above
953    
954    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956            * R/Auxiliaries.R (is_duplicatedT): new utility
957    
958    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
959    
960            * src/init.c (R_init_Matrix): export cholmod_scale
961    
962    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
963    
964            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
965            base::as.matrix to (x, ...)
966    
967    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
968    
969            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
970            file; start using "Logic", hence
971    
972            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
973            * NAMESPACE: import and export "Logic"
974    
975    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
978            only needed previously to R version 2.5.0.
979    
980    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
983    
984            * R/Tsparse.R (replTmat): fix subassignment of triangular
985            * R/Csparse.R (replCmat): ditto
986            * tests/indexing.R: more tests, incl the above fix
987    
988    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * R/Auxiliaries.R (drop0): extend for non CSparse
991            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
992    
993            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
994                    use uplo correctly (!); other places: use uplo_P() macro
995    
996            * R/Csparse.R (replCmat): call diagU2N() when needed
997            * R/Tsparse.R (replTmat): ditto
998    
999            * src/dtCMatrix.c (tCMatrix_validate): new
1000            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1001            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1002    
1003            * R/diagMatrix.R (replDiag): to use in [<-
1004    
1005    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1008                    also more general diagU2N().
1009    
1010    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1011    
1012            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1013            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1014    
1015    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * tests/bind.R: a few more cases
1018            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1019    
1020            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1021            * R/ddenseMatrix.R (cbind2/rbind2)
1022            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1023            * tests/indexing.R
1024            * tests/indexing.Rout.save: updated
1025    
1026    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1029            * tests/indexing.R
1030    
1031    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1034            align with proper position of "0", i.e., right for integers.
1035            argument 'align' by default is "fancy".
1036    
1037    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1038    
1039            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1040            * R/Csparse.R: and fix "Compare" for more cases.
1041            * tests/Class+Meth.R: test some of these (m == m, m != m)
1042    
1043    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1044    
1045            * R/lsparseMatrix.R: all() and any() methods
1046            * R/ldenseMatrix.R:      ditto
1047            * NAMESPACE, R/Matrix.R: ditto
1048    
1049            * man/all-methods.Rd: document them minimally
1050    
1051            * tests/simple.R: add a few examples for these
1052    
1053    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1054    
1055            * R/Tsparse.R ([): fix long standing typo in symmetric case
1056            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1057    
1058    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1059    
1060            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1061            to LL before converting to a sparse matrix. (The LDL form can be
1062            converted to a sparse matrix but it is implicitly a unit
1063            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1064    
1065    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1066    
1067            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1068    
1069    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1070    
1071            * DESCRIPTION (Version): updated -> release 0.9975-7
1072            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1073    
1074    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1077    
1078    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1079    
1080            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1081            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1082            is exactly singular.
1083    
1084    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * DESCRIPTION (Date): updated -> release 0.9975-6
1087    
1088    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1091            now returns symmetric.
1092    
1093            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1094    
1095            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1096            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1097    
1098            * R/Auxiliaries.R (.type.kind): added
1099    
1100    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1103            running src/CSparse_install.sh
1104    
1105            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1106    
1107    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1108    
1109            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1110            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1111    
1112            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1113    
1114            * tests/Class+Meth.R (tstMatrixClass): now assure
1115            the (important in method programming) property :
1116    
1117                    ###>>  Every "Matrix" is either
1118                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1119    
1120                    (where "*" stands for "Matrix")
1121    
1122            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1123    
1124            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1125            * tests/validObj.R: checks for "comparison"
1126    
1127            * R/sparseMatrix.R ([): improved indexing for sparse;
1128                    trying to keep <symmetric>[ n, n] symmmetric
1129    
1130            * tests/indexing.R: indexing for logical sparse now ok
1131    
1132    
1133    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1134    
1135            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1136    
1137            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1138    
1139    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1140    
1141            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1142    
1143            * tests/simple.R: validObject() checking the above.
1144    
1145            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1146            replacing both dgCMatrix_validate and lgCM*.
1147    
1148            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1149            fix dimnames setting in other places.
1150            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1151    
1152    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1153    
1154            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1155    
1156            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1157            symmetry test, via
1158            * R/Auxiliaries.R (.as.dgC.0.factors):
1159    
1160    2006-11-01  Douglas Bates  <bates@r-project.org>
1161    
1162            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1163            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1164            <CsparseMatrix>) added
1165    
1166    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * tests/matprod.R: add a variation of Harri's example
1169    
1170            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1171            recursive infinitely.
1172    
1173            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1174    
1175            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1176    
1177    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1180            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1181            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1182            satisfy the above test.
1183    
1184    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1187    
1188            * R/dgCMatrix.R: solve(a, b="missing") based on
1189            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1190            RHS = NULL.
1191    
1192            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1193            add more (needed) [t]crossprod() methods.
1194    
1195            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1196    
1197            * R/Auxiliaries.R (as_CspClass): cleanup
1198            (drop0): internal utility for "Csparse_drop(*, 0)"
1199            (.bail.out.2): encourage active feedback
1200    
1201    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1202    
1203            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1204    
1205            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1206            non-valid or 'sorted' case).
1207    
1208            * R/dsparseMatrix.R: add "chol" method.
1209            * R/ddenseMatrix.R: ditto
1210    
1211            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1212            * NAMESPACE (Ops)
1213            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1214            coercion; deprecating direct lower level coercions.
1215    
1216            * R/*.R (seq): use seq_len() and seq_along() where possible.
1217    
1218    
1219    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1220    
1221            * DESCRIPTION (Version): 0.9975-5 ready for release
1222    
1223  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1224    
1225          * 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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