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revision 1507, Mon Sep 4 18:41:34 2006 UTC revision 2137, Mon Mar 17 22:21:24 2008 UTC
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1    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
4            functionality; barely tested in
5            * tests/factorizing.R
6    
7            * src/Csparse.c (diag_tC): new functionality to enable faster
8            determinant(<dsCMatrix>, .) in
9            * R/dsCMatrix.R
10    
11    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
12    
13            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
14              src/CHMfactor.c, src/CHMfactor.h,
15              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
16              Log-determinant of the parent matrix from a CHMfactor object as
17              chm_factor_ldetL2; documentation and support
18    
19    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
22    
23    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
26            warning.
27    
28    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
31    
32            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
33              <diagonal> o <sparse_triangular>
34              setAs(., "nMatrix") added.
35    
36            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
37    
38            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
39                    new argument 'checkDense = FALSE'.
40    
41    
42    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
45            back-permutation of the matrix exponential.
46    
47            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
48    
49            * DESCRIPTION (Date,Version): ready to release 0.999375-5
50    
51            * tests/simple.R: testing diagN2U
52    
53    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Auxiliaries.R (diagN2U): interface to
56    
57            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
58    
59            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
60    
61    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * src/chm_common.c (chm_diagN2U): new utility.
64    
65            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
66            make use of chm_diagN2U() and hence now preserve triangularity and
67            unit-triangularity.
68    
69            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
70    
71    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
74    
75            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
76            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
77    
78            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
79    
80            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
81    
82            * src/chm_common.c (AS_CHM_FINISH): add note about problem
83            for triangular (diag = "U").
84    
85    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
88            * R/bind.R:  .Call(dense_to_Csparse, *)
89    
90    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Matrix.R (Matrix): no longer use coercions to specific classes
93                    (since we are discouraging them in user code).
94    
95            * tests/*.R: also replaces coercions to specific classes by
96            coercions to super classes.
97    
98            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
99    
100    
101    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
104    
105            * src/dense.c (dense_band): generalized from ddense_band
106    
107            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
108              now for "denseMatrix" (instead of just "ddense*"); much
109              simplified setMethod()s for these.
110    
111            * src/dense.c (dense_to_symmetric): generalized from ddense_*
112    
113    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
116            version of as(*, "symmetricMatric").
117    
118            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
119            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
120    
121    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Matrix.R (subset.ij): utility, as first step to faster
124               M [ <ij-matrix> ] indexing.
125    
126            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
127    
128            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
129            for more efficient symmpart() and skewpart() methods.
130    
131            * src/Mutils.c (equal_string_vectors): utility
132    
133            * src/dense.c (ddense_to_symmetric): new function used in
134    
135            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
136    
137            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
138            order to match the generic (and evade .local(..)).
139    
140            * R/dsCMatrix.R: dgC -> dsC: use C code!
141    
142            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
143            as per TODO
144    
145            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
146    
147            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
148    
149    
150    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
153    
154            * R/Auxiliaries.R (non0.i): take out of non0ind
155    
156            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
157            make tril(), triu(), band() work for "matrix" and all "dense*"
158    
159            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
160            * tests/simple.R: test the fix above
161    
162            * R/sparseMatrix.R ([): simplification: no coerce to <general>
163                    before we use as(., <Tsparse>)[...] anyway
164    
165            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
166    
167            * R/triangularMatrix.R (isTriangular): methods for all subclasses
168            instead of "triangularMatrix" -- just to disambiguate
169    
170    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
173            * tests/indexing.R: example that fails above
174    
175    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
178            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
179                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
180    
181            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
182            * src/Tsparse.h, init.c: ditto
183            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
184                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
185            * R/sparseMatrix.R (isTriangular): hence simplified
186    
187    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Ops.R (.Arith.Csparse): new utility factored out of former
190              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
191    
192    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
195    
196            * inst/test-tools.R (isOrthogonal): new function; also file restructured
197    
198    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
201            coercion to "nMatrix" and "pMatrix"
202    
203            * R/AllClass.R: "Schur" class;  "number" class union
204            * man/number-class.Rd:
205            * man/Schur-class.Rd:
206    
207            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
208            (.simpleSchur): Schur() method for diagonal matrices
209            (.triSchur):    Schur() method for triangular matrices
210            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
211    
212    
213    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
216    
217    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
220                    in order to ensure 'system = *' is not lost;
221                    formals()$system instead of cut&paste.
222            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
223    
224    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * DESCRIPTION (Date): make ready for release --> 0.999375-4
227    
228            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
229    
230    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
233                    and hence does as.vector(.).
234            * man/pMatrix-class.Rd: docs
235            * R/sparseMatrix.R: fix for printing "integer sparse"
236    
237            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
238    
239            * R/Matrix.R and others: use "exact" function argument list for
240                    both "["   : (x, i,j, ..., drop)
241                    and  "[<-" : (x, i,j, ..., value)
242    
243            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
244            * R/Tsparse.R (replTmat):    ditto
245            * R/diagMatrix.R (replDiag): ditto
246            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
247            * tests/indexing.R: testing the above
248    
249    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/sparseMatrix.R (cov2cor): method for sparse matrices
252    
253            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
254    
255            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
256    
257            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
258    
259    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Matrix.R: "generic" cov2cor() method
262    
263            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
264                    speed up Q %*% D %*% t(Q)
265            * tests/dpoMatrix.R: test nearPD()
266    
267    2007-12-05  Doug Bates and Martin Maechler
268    
269            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
270            stats::xtabs() allowing to create sparse matrices.
271    
272    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
275    
276    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
279    
280    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/LU.R: solve() method for "denseLU"
283    
284    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.999375-3 preparing for release
287    
288            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
289    
290            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
291    
292    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
295              thanks to Kasper Kristensen.
296            * tests/matprod.R: regression test for that.
297    
298    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
299    
300            * [r4778] R/AllGeneric.R: Check R version before defining generics for
301              primitives
302    
303    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/denseMatrix.R (rcond): method
306            * R/sparseQR.R (rcond): method, use x or t(x)
307    
308    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
311            matrices.
312            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
313    
314            * man/rcond.Rd: mention the more general definition, and add
315            example for non-square matrices.
316    
317            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
318    
319    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
322    
323    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
326            * tests/indexing.R: add new regression for the above cases.
327    
328    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * src/Mutils.h (__sun): clause for alloca.h on Solaris
331    
332    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * DESCRIPTION (Date, Version): 0.999375-2
335    
336    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/HBMM.R (readMM): make work for pattern matrices as well
339    
340    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
341    
342            * [r4730] src/Mutils.h: declare alloca
343            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
344              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
345              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
346              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
347              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
348              methods; switch writeMM to use CHOLMOD code; repair readMM
349    
350    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
353            Oehlschlaegel's ... result type still to be discussed!
354    
355    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * man/image-methods.Rd: new, combining all image() methods
358    
359    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
362            to work via dgC...
363    
364            * R/Matrix.R (Matrix): special treatment for "table" (S3)
365    
366    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * R/dgTMatrix.R (image): change defaults to
369                    aspect = "iso", colorkey = FALSE
370    
371    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
374            must copy its *expanded* x slot before LAPACK call.
375    
376            * tests/matprod.R: test the last days' changes.
377    
378    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
379    
380            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
381              as well as in sources
382            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
383              Lapack call
384    
385    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
388                    ("Matrix", "matrix") which is needed in some cases.
389            Ditto for solve().
390    
391            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
392            infinite recursion in dispatch for some cases.
393    
394    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
395    
396            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
397              so pointers match
398    
399    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * DESCRIPTION (Date): set ready for release -- 0.999375-1
402    
403    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
404    
405            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
406              src/chm_common.c, src/chm_common.h: Change API for
407              numeric_as_chm_dense and N_AS_CHM_DN
408    
409    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
412            * tests/matprod.R: regr.test for it
413    
414    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
417            * tests/group-methods.R: and regression-test it
418    
419    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
420    
421            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
422              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
423              triplet_to_sparse, documentation, use typedefs
424    
425    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * man/dpoMatrix-class.Rd: added 'corMatrix' example
428    
429            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
430            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
431            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
432    
433            * R/lsparseMatrix.R: bug fix in "all" method
434            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
435    
436            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
437            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
438                    + matrix |-> nMatrix coercion
439            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
440            * man/pMatrix-class.Rd: ditto
441    
442            * R/Matrix.R (Summary): method for non-dMatrix
443    
444            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
445            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
446                    test all Summary methods.
447    
448    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
451    
452    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
453    
454            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
455    
456            * R/pMatrix.R (t?crossprod): methods for pMatrix
457    
458    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
459    
460            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
461    
462    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
463    
464            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
465              trying to fix a subtle bug - which has been somewhere else.
466    
467    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
468    
469            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
470              solve the bug
471    
472    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * src/dgCMatrix.c (compressed_to_TMatrix):
475    
476    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * src/Csparse.c (Rsparse_validate): new, to have some validity
479            checking for RsparseMatrix
480            * src/dgCMatrix.c (xRMatrix_validate): ditto
481            * src/dtCMatrix.c (tRMatrix_validate): ditto
482    
483    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
484    
485            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
486              lgRMatrix
487            * [r4568] DESCRIPTION: Prepare for bug-fix release
488            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
489              for declaration of cholmod_symmetry
490    
491    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
494            release.
495    
496    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
497    
498            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
499              functions - no longer used
500            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
501              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
502              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
503              Alloca
504    
505    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
506    
507            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
508              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
509              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
510              src/t_gCMatrix_colSums.c: more R_CheckStack()s
511    
512    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
513    
514            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
515              the required amount of memory then call M_numeric_as_chm_dense.
516            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
517              (like Calloc but calling alloca)
518    
519    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
522            and extended with more sophisticated 'col.names' option.
523            * NAMESPACE: export  printSparseMatrix()
524            * man/printSpMatrix.Rd: document, incl. examples
525    
526    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
527    
528            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
529              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
530              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
531    
532    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * DESCRIPTION (Version): 0.99875-4
535    
536            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
537            some dimnames perservation.
538    
539            * R/dsTMatrix.R (t-method): keep dimnames
540            * R/dtTMatrix.R:  ditto
541    
542            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
543            and ncol(.) < 10
544    
545            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
546            from Mutils.h
547    
548            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
549            e.g. in as(<ngCMatrix>, "matrix")
550    
551    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
552    
553            * [r4529] .: Create a branch for the API changes from the 0.99875
554              series to the 0.999375 series
555            * [r4530] DESCRIPTION, inst/include/Matrix.h,
556              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
557              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
558              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
559              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
560              as_cholmod_x functions
561    
562    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
563    
564            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
565              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
566              to Comparisons
567    
568    >>>>>>> .merge-right.r4561
569    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * DESCRIPTION (Version): 0.99875-3 ready to be released.
572    
573            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
574    
575            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
576            that should also work in a future version of R.
577    
578    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
581    
582            * R/sparseVector.R: more *sparseVector coercions, notably for
583            non - double ones.
584    
585    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
588              notably the new ones building on the new .Call(.)s:
589    
590            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
591            all 4 of [dlin]gCMatrix_colSums().
592    
593    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
594    
595            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
596            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
597              result
598    
599    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/kronecker.R: fix typo (could lead to inf.recursion)
602            * test/simple.R: testing that
603    
604            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
605            method as well (which can have arguments, show() can't).
606    
607    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
608    
609            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
610              added dgCMatrix_colSums for [col,row][Sums,Means]
611    
612    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
613    
614            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
615              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
616              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
617            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
618              class
619            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
620              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
621              row names to store the levels - duh!  Added an example.
622    
623    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * src/Csparse.c (Csparse_validate): check for *repeated* entries
626            thanks to example from Christian Buchta; with a test here:
627            * tests/simple.R:
628    
629    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
632            of colSums(*, sparseResult = TRUE)
633    
634    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
637            'na.rm = FALSE' as "everywhere" else in R.
638    
639    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
640    
641            * [r4421] src/CSparse_install.sh: Modify for new organization of
642              CSparse package
643            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
644              SuiteSparse
645            * [r4426] src/Makefile: add ./UFconfig to the include path for
646              compilation
647            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
648            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
649              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
650    
651    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
654            * R/sparseMatrix.R (prSpMatrix): now gives a message about
655            suppressed column names.
656    
657    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
658    
659            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
660              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
661              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
662              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
663              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
664              Remove warnings after change to const char* CHAR
665    
666    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
667    
668            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
669              type of M_cholmod_ssmult
670    
671    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
672    
673            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
674              src/init.c: Yet another cholmod export - cholmod_ssmult
675    
676    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * NAMESPACE: exported drop0(), since
679            * man/drop0.Rd: I have seen several cases, I really wanted to use
680            it, so our users may want too.
681    
682    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * man/colSums.Rd: separately document colSums() etc, since these
685            have the extra argument 'sparseResult'.
686    
687    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
688    
689            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
690            * man/spMatrix.Rd: docu., including examples
691    
692            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
693            in order to make colMeans() etc fast *and* correct.
694            * R/sparseVector.R (replSPvec): "[<-" functionality for
695            sparseVectors; tested in
696            * tests/simple.R:
697    
698    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
701            (very) sparse Matrices; output similar to Matlab's print().
702    
703    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
704    
705            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
706            0-based, indices (Jose Quesada <quesada@gmail.com>).
707    
708    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
709    
710            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
711    
712    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * R/Auxiliaries.R (sparsapply): new utility, much faster than
715            tapply1() for large sparse matrices.
716    
717    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
718    
719            * R/Matrix.R (dim<-): reshape now via sparseVector.
720    
721            * R/sparseVector.R: methods and function for
722            * R/AllClass.R: new "sparseVector" class and daughters.
723            * NAMESPACE: export new classes
724    
725    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * DESCRIPTION (Version): 0.99875-1
728            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
729    
730    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
733            indexing
734            * tests/indexing.R: test set for that.
735    
736    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
739            entries.
740            * tests/indexing.R(out): add regression test for it
741    
742    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
745            name for "!" method definitions.
746    
747    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * R/Tsparse.R (intI): new utility, used for "[" :
750                    Cleanup up there, and fixes for duplicated indices - more TODO!
751    
752            * tests/indexing.R(out): more tests
753    
754    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
757            code that is now part of the R Lapack library.
758    
759            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
760            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
761    
762    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
765    
766    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
767    
768            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
769            up with extraneous names '0'...'<n-1>'
770    
771    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/dgTMatrix.R (mat2dgT): care about NAs
774    
775    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/kronecker.R: triangularity preserving methods
778    
779    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/kronecker.R: new file collecting kronecker() methods in one
782                    place.  Goal: become much faster!
783    
784    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
787            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
788            can be much faster.
789    
790            * tests/matprod.R: add regression tests for these (upper & lower).
791    
792    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
793    
794            * R/Matrix.R (diff): method for our Matrices.
795    
796            * R/sparseMatrix.R (isDiagonal): check dim()!
797    
798    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Matrix.R (dim<-): new method for "reshape()" built on a
801            proposal from Tamas Papp.
802    
803    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
806    
807            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
808            rather define and export  cBind() and rBind() only.
809            --> useRs *must* change code that used to have cbind()/rbind() !!
810    
811            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
812            * R/bind.Rout.save: ditto
813    
814    2007-02-16  Douglas Bates  <bates@r-project.org>
815    
816            * DESCRIPTION (Date, Version): 0.9975-11 with new date
817            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
818            const modifier on declaration of the array 'valid'
819    
820    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
821    
822            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
823    
824    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
827    
828            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
829            * tests/simple.R: test the above and some of these coercions:
830    
831            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
832                    be careful to avoid infinite recursion, using new coercions in
833            * R/ngCMatrix.R and nsC... and ntC...
834            * R/lsparseMatrix.R: ditto
835    
836            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
837    
838            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
839            * R/Rsparse.R: reactivate .Call()s
840    
841            * tests/Class+Meth.R: a bit more on actual classes
842    
843    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
844    
845            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
846    
847    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * DESCRIPTION (Version): 0.9975-10 to upload
850    
851            * tests/Class+Meth.R (tstMatrixClass): require coercions to
852            specific classes less unconditionally.
853    
854            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
855    
856            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
857    
858            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
859            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
860            R_to_CMatrix segfaults on one platform.
861            Eliminate most coercion method to *specific* classes, and replace
862            with virtual classes coercions.
863    
864    
865    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
866    
867            * src/init.c: export the CHM...._validate() placeholders, since
868            they *are* called.
869    
870            * tests/Class+Meth.R (classCanCoerce): and starting to test
871            all as(<from>, <to>)
872    
873    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
876            * tests/indexing.R: tested now
877            * tests/indexing.Rout.save: updated
878    
879            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
880            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
881            appropriate.
882    
883            * NAMESPACE: export a trivial
884            * R/Matrix.R: drop() Matrix-method
885    
886            * R/AllClass.R: moved all prototypes to virtual super classes.
887    
888            * R/Rsparse.R: many more coercions to have less exceptions in
889            * tests/Class+Meth.R:
890    
891            * R/Ops.R (Compare): tweak for case with NA
892            * tests/simpl.R: hence another 'FIXME' eliminated
893    
894    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
895    
896            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
897            objects.
898    
899            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
900              and more of "!", "&", "|", all, any; coercions
901    
902            * R/Rsparse.R: many coercions (which enable quite a few other
903            methods), thanks to enhancements in
904            * src/dgCMatrix.c (R_to_CMatrix): new, and
905            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
906            symmetric & triangular and ..RMatrix objects.
907    
908            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
909            renamed file from src/dsTMatrix.c;
910            now dealing with symmetric and triangular Tsparse coercions, both
911            to dense and general.
912    
913    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
914    
915            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
916    
917            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
918            where sensible when the <numeric> is of length > 1.
919    
920    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
921    
922            * R/Matrix.R ([<-): for M[] <- value: fix length
923    
924    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
927            * R/ndenseMatrix.R: new coercions n* -> l*
928    
929    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
932    
933            * R/Ops.R ("Logic"): and other "Ops", many updates
934    
935    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
936    
937            * src/Mutils.h (SET_DimNames): new utility
938    
939            * R/Auxiliaries.R (nnzero): improved and now exported via
940    
941            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
942    
943    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * R/diagMatrix.R (!): fix typo.
946    
947    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
948    
949            * R/Auxiliaries.R (as_Csparse): and quite a few others:
950                    allow to pass class definition --> speedup
951            * R/sparseMatrix.R: apply the above
952    
953            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
954    
955            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
956            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
957            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
958    
959            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
960    
961            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
962            and use it for "sparse*" as well, since it's faster than the
963            as_Csparse(.) way.
964    
965    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
966    
967            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
968    
969    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
972            as method for   M[ ij ] <- v
973            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
974    
975            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
976            FALSE answer
977    
978            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
979            * tests/indexing.R: test it, and some of the above
980    
981    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
982    
983            * R/Auxiliaries.R (is_duplicatedT): new utility
984    
985    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
986    
987            * src/init.c (R_init_Matrix): export cholmod_scale
988    
989    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
992            base::as.matrix to (x, ...)
993    
994    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
995    
996            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
997            file; start using "Logic", hence
998    
999            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1000            * NAMESPACE: import and export "Logic"
1001    
1002    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1003    
1004            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1005            only needed previously to R version 2.5.0.
1006    
1007    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1010    
1011            * R/Tsparse.R (replTmat): fix subassignment of triangular
1012            * R/Csparse.R (replCmat): ditto
1013            * tests/indexing.R: more tests, incl the above fix
1014    
1015    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1016    
1017            * R/Auxiliaries.R (drop0): extend for non CSparse
1018            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1019    
1020            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1021                    use uplo correctly (!); other places: use uplo_P() macro
1022    
1023            * R/Csparse.R (replCmat): call diagU2N() when needed
1024            * R/Tsparse.R (replTmat): ditto
1025    
1026            * src/dtCMatrix.c (tCMatrix_validate): new
1027            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1028            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1029    
1030            * R/diagMatrix.R (replDiag): to use in [<-
1031    
1032    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1033    
1034            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1035                    also more general diagU2N().
1036    
1037    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1038    
1039            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1040            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1041    
1042    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * tests/bind.R: a few more cases
1045            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1046    
1047            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1048            * R/ddenseMatrix.R (cbind2/rbind2)
1049            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1050            * tests/indexing.R
1051            * tests/indexing.Rout.save: updated
1052    
1053    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1054    
1055            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1056            * tests/indexing.R
1057    
1058    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1059    
1060            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1061            align with proper position of "0", i.e., right for integers.
1062            argument 'align' by default is "fancy".
1063    
1064    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1065    
1066            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1067            * R/Csparse.R: and fix "Compare" for more cases.
1068            * tests/Class+Meth.R: test some of these (m == m, m != m)
1069    
1070    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1071    
1072            * R/lsparseMatrix.R: all() and any() methods
1073            * R/ldenseMatrix.R:      ditto
1074            * NAMESPACE, R/Matrix.R: ditto
1075    
1076            * man/all-methods.Rd: document them minimally
1077    
1078            * tests/simple.R: add a few examples for these
1079    
1080    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1081    
1082            * R/Tsparse.R ([): fix long standing typo in symmetric case
1083            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1084    
1085    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1086    
1087            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1088            to LL before converting to a sparse matrix. (The LDL form can be
1089            converted to a sparse matrix but it is implicitly a unit
1090            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1091    
1092    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1093    
1094            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1095    
1096    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1097    
1098            * DESCRIPTION (Version): updated -> release 0.9975-7
1099            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1100    
1101    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1104    
1105    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1106    
1107            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1108            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1109            is exactly singular.
1110    
1111    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1112    
1113            * DESCRIPTION (Date): updated -> release 0.9975-6
1114    
1115    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1116    
1117            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1118            now returns symmetric.
1119    
1120            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1121    
1122            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1123            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1124    
1125            * R/Auxiliaries.R (.type.kind): added
1126    
1127    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1130            running src/CSparse_install.sh
1131    
1132            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1133    
1134    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1137            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1138    
1139            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1140    
1141            * tests/Class+Meth.R (tstMatrixClass): now assure
1142            the (important in method programming) property :
1143    
1144                    ###>>  Every "Matrix" is either
1145                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1146    
1147                    (where "*" stands for "Matrix")
1148    
1149            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1150    
1151            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1152            * tests/validObj.R: checks for "comparison"
1153    
1154            * R/sparseMatrix.R ([): improved indexing for sparse;
1155                    trying to keep <symmetric>[ n, n] symmmetric
1156    
1157            * tests/indexing.R: indexing for logical sparse now ok
1158    
1159    
1160    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1161    
1162            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1163    
1164            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1165    
1166    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1169    
1170            * tests/simple.R: validObject() checking the above.
1171    
1172            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1173            replacing both dgCMatrix_validate and lgCM*.
1174    
1175            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1176            fix dimnames setting in other places.
1177            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1178    
1179    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1182    
1183            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1184            symmetry test, via
1185            * R/Auxiliaries.R (.as.dgC.0.factors):
1186    
1187    2006-11-01  Douglas Bates  <bates@r-project.org>
1188    
1189            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1190            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1191            <CsparseMatrix>) added
1192    
1193    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1194    
1195            * tests/matprod.R: add a variation of Harri's example
1196    
1197            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1198            recursive infinitely.
1199    
1200            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1201    
1202            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1203    
1204    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1207            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1208            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1209            satisfy the above test.
1210    
1211    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1212    
1213            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1214    
1215            * R/dgCMatrix.R: solve(a, b="missing") based on
1216            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1217            RHS = NULL.
1218    
1219            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1220            add more (needed) [t]crossprod() methods.
1221    
1222            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1223    
1224            * R/Auxiliaries.R (as_CspClass): cleanup
1225            (drop0): internal utility for "Csparse_drop(*, 0)"
1226            (.bail.out.2): encourage active feedback
1227    
1228    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1229    
1230            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1231    
1232            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1233            non-valid or 'sorted' case).
1234    
1235            * R/dsparseMatrix.R: add "chol" method.
1236            * R/ddenseMatrix.R: ditto
1237    
1238            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1239            * NAMESPACE (Ops)
1240            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1241            coercion; deprecating direct lower level coercions.
1242    
1243            * R/*.R (seq): use seq_len() and seq_along() where possible.
1244    
1245    
1246    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1247    
1248            * DESCRIPTION (Version): 0.9975-5 ready for release
1249    
1250    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1251    
1252            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1253    
1254    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1255    
1256            * R/AllClass.R (corMatrix): add 'validity' check;
1257                    comment out unused "LDL" class definition
1258            * NAMESPACE: mention, but do not export "LDL" class
1259            * R/corMatrix.R: new (simple), needed for R-devel with
1260            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1261              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1262    
1263    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1264    
1265            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1266            use Rprintf and R's error handling.
1267    
1268    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1269    
1270            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1271            * tests/matprod.R: add tests for the bug fixed.
1272    
1273    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1274    
1275            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1276            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1277    
1278    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1279    
1280            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1281    
1282    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1283    
1284            * DESCRIPTION (Version): 0.9975-3
1285    
1286            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1287            (sparse) matrices.
1288            * man/bdiag.Rd: docu + examples
1289    
1290            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1291    
1292            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1293            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1294    
1295            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1296            that result is sparse or diagonal (and not dense).
1297    
1298            * man/Subassign-methods.Rd: fix examples
1299    
1300            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1301            should always return a sparse (and not sometimes a diagonal) matrix.
1302    
1303    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1304    
1305            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1306    
1307    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1308    
1309            * DESCRIPTION (Version): 0.9975-2
1310    
1311            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1312    
1313    2006-10-02  Douglas Bates  <bates@R-project.org>
1314    
1315            * tests/dg_Matrix.R: Simplify test taking into account new code.
1316    
1317    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1318    
1319            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1320    
1321            * R/lsTMatrix.R: new files w/ missing methods
1322            * R/nsTMatrix.R:  "  'for completeness'
1323    
1324            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1325    
1326            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1327    
1328    
1329    2006-09-28  Douglas Bates  <bates@R-project.org>
1330    
1331            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1332            included.
1333    
1334            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1335            Export C-callable functions used in Zt_create in lme4.
1336    
1337    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1338    
1339            * DESCRIPTION (Version): 0.9975-1
1340    
1341            * tests/simple.R: less checks fail; using NA, found that our
1342                    kronecker() is not base-compatible with NA's.
1343    
1344            * R/dMatrix.R: "Compare" method now implemented for all cases
1345    
1346            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1347    
1348            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1349    
1350            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1351            * src/dspMatrix.c (dspMatrix_validate): ditto
1352    
1353            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1354              including coercion to [nl]tTMatrix.
1355    
1356            * R/diagMatrix.R (show): print a header line as for other classes.
1357    
1358    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1359    
1360            * src/Makefile.win (SUBDIRS): fix typo
1361    
1362    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1363    
1364            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1365    
1366    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1367    
1368            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1369            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1370            accept a symmetric matrix).
1371            * tests/group-methods.R: Uncomment test of crossprod applied to
1372            lsCMatrix objects.
1373    
1374    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1375    
1376            * R/AllClass.R (symmetricMatrix): add validity method (available
1377            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1378    
1379            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1380    
1381            * tests/indexing.Rout.save:
1382            * tests/indexing.R: additions, mainly for 'lsparse'
1383    
1384            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1385            case.
1386    
1387            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1388    
1389    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1390    
1391            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1392                    as 'N' (1-letter - Ok?)
1393    
1394            * tests/group-methods.R: add test for logical + NAs
1395    
1396            * R/dMatrix.R ("Compare"): fix to work with NA's
1397    
1398            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1399    
1400            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1401                    which is implemented.
1402    
1403    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1404    
1405            * src/chm_common.c: coerce logical <-> double instead of
1406            typecasting;  needed for "l" matrix handling in cholmod.
1407    
1408            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1409    
1410            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1411            (Tsp2grNEL): other fixes needed
1412    
1413    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1414    
1415            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1416                    Matrices, since "lMatrix", also "lsparseM" can have NA
1417            * R/ndenseMatrix.R, etc: new source files
1418            * man/nsparseMatrix-classes.Rd, etc: new help files
1419            * tests/: adaptions
1420            * src/chm_common.c (chm_dense_to_SEXP): and others:
1421                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1422            * src/Csparse.c, etc: ditto
1423    
1424    2006-09-11  Douglas Bates  <bates@R-project.org>
1425    
1426            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1427            alloc_d**Matrix functions to the lme4 package.
1428    
1429    2006-09-09  Douglas Bates  <bates@R-project.org>
1430    
1431            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1432            fixed
1433    
1434    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1435    
1436            * R/lMatrix.R: new
1437    
1438            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1439    
1440            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1441            * man/tcrossprod.Rd: ditto
1442    
1443    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1444    
1445            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1446            for exported functions
1447            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1448            Remove partitioning algorithms for sparse matrix reordering.  The
1449            copyright on the Metis code was problematic and the methods were
1450            rarely used.
1451            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1452            operations are now done entirely in CHOLMOD code.
1453    
1454    2006-09-06  Douglas Bates  <bates@R-project.org>
1455    
1456            * src/Mutils.h: Remove functions that are no longer used.
1457    
1458  2006-09-04  Douglas Bates  <bates@R-project.org>  2006-09-04  Douglas Bates  <bates@R-project.org>
1459    
1460          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.          * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
# Line 24  Line 1481 
1481    
1482          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1483          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1484          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1485          * R/Csparse.R: dito          * R/Csparse.R: ditto
1486    
1487  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1488    
# Line 41  Line 1498 
1498    
1499          * 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
1500          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1501          (.is.diagonal): dito          (.is.diagonal): ditto
1502    
1503          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1504    

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