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revision 1767, Mon Feb 5 16:53:17 2007 UTC revision 2154, Sat Mar 22 21:23:12 2008 UTC
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1    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
4            internal_chm_factor().
5    
6            * R/AllGeneric.R: do *not* define a "chol" generic
7                    (but rather use the implicit one *without* making pivot
8                    part of the signature)
9            * R/*.R: drop the 'pivot' from chol's signature and make
10                    'pivot=FALSE' a default argument of method definitions.
11    
12            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
13            version of Matrix
14    
15    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
18    
19            * R/sparseMatrix.R (is.na): new simple method
20            * R/denseMatrix.R (is.na): ditto.
21    
22            * R/diagMatrix.R (.symDiagonal): newly exported utility.
23    
24            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
25    
26            * src/UFsparse_download.sh: -->
27            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
28    
29    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
32            functionality; barely tested in
33            * tests/factorizing.R
34    
35            * src/Csparse.c (diag_tC): new functionality to enable faster
36            determinant(<dsCMatrix>, .) in
37            * R/dsCMatrix.R
38    
39    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
40    
41            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
42              src/CHMfactor.c, src/CHMfactor.h,
43              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
44              Log-determinant of the parent matrix from a CHMfactor object as
45              chm_factor_ldetL2; documentation and support
46    
47    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
50    
51    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
54            warning.
55    
56    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
59    
60            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
61              <diagonal> o <sparse_triangular>
62              setAs(., "nMatrix") added.
63    
64            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
65    
66            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
67                    new argument 'checkDense = FALSE'.
68    
69    
70    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
73            back-permutation of the matrix exponential.
74    
75            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
76    
77            * DESCRIPTION (Date,Version): ready to release 0.999375-5
78    
79            * tests/simple.R: testing diagN2U
80    
81    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * R/Auxiliaries.R (diagN2U): interface to
84    
85            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
86    
87            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
88    
89    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * src/chm_common.c (chm_diagN2U): new utility.
92    
93            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
94            make use of chm_diagN2U() and hence now preserve triangularity and
95            unit-triangularity.
96    
97            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
98    
99    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
102    
103            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
104            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
105    
106            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
107    
108            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
109    
110            * src/chm_common.c (AS_CHM_FINISH): add note about problem
111            for triangular (diag = "U").
112    
113    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
116            * R/bind.R:  .Call(dense_to_Csparse, *)
117    
118    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
119    
120            * R/Matrix.R (Matrix): no longer use coercions to specific classes
121                    (since we are discouraging them in user code).
122    
123            * tests/*.R: also replaces coercions to specific classes by
124            coercions to super classes.
125    
126            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
127    
128    
129    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
132    
133            * src/dense.c (dense_band): generalized from ddense_band
134    
135            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
136              now for "denseMatrix" (instead of just "ddense*"); much
137              simplified setMethod()s for these.
138    
139            * src/dense.c (dense_to_symmetric): generalized from ddense_*
140    
141    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
144            version of as(*, "symmetricMatric").
145    
146            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
147            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
148    
149    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Matrix.R (subset.ij): utility, as first step to faster
152               M [ <ij-matrix> ] indexing.
153    
154            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
155    
156            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
157            for more efficient symmpart() and skewpart() methods.
158    
159            * src/Mutils.c (equal_string_vectors): utility
160    
161            * src/dense.c (ddense_to_symmetric): new function used in
162    
163            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
164    
165            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
166            order to match the generic (and evade .local(..)).
167    
168            * R/dsCMatrix.R: dgC -> dsC: use C code!
169    
170            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
171            as per TODO
172    
173            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
174    
175            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
176    
177    
178    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
181    
182            * R/Auxiliaries.R (non0.i): take out of non0ind
183    
184            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
185            make tril(), triu(), band() work for "matrix" and all "dense*"
186    
187            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
188            * tests/simple.R: test the fix above
189    
190            * R/sparseMatrix.R ([): simplification: no coerce to <general>
191                    before we use as(., <Tsparse>)[...] anyway
192    
193            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
194    
195            * R/triangularMatrix.R (isTriangular): methods for all subclasses
196            instead of "triangularMatrix" -- just to disambiguate
197    
198    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
201            * tests/indexing.R: example that fails above
202    
203    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
206            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
207                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
208    
209            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
210            * src/Tsparse.h, init.c: ditto
211            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
212                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
213            * R/sparseMatrix.R (isTriangular): hence simplified
214    
215    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/Ops.R (.Arith.Csparse): new utility factored out of former
218              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
219    
220    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
221    
222            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
223    
224            * inst/test-tools.R (isOrthogonal): new function; also file restructured
225    
226    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
229            coercion to "nMatrix" and "pMatrix"
230    
231            * R/AllClass.R: "Schur" class;  "number" class union
232            * man/number-class.Rd:
233            * man/Schur-class.Rd:
234    
235            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
236            (.simpleSchur): Schur() method for diagonal matrices
237            (.triSchur):    Schur() method for triangular matrices
238            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
239    
240    
241    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
244    
245    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
248                    in order to ensure 'system = *' is not lost;
249                    formals()$system instead of cut&paste.
250            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
251    
252    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * DESCRIPTION (Date): make ready for release --> 0.999375-4
255    
256            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
257    
258    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
261                    and hence does as.vector(.).
262            * man/pMatrix-class.Rd: docs
263            * R/sparseMatrix.R: fix for printing "integer sparse"
264    
265            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
266    
267            * R/Matrix.R and others: use "exact" function argument list for
268                    both "["   : (x, i,j, ..., drop)
269                    and  "[<-" : (x, i,j, ..., value)
270    
271            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
272            * R/Tsparse.R (replTmat):    ditto
273            * R/diagMatrix.R (replDiag): ditto
274            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
275            * tests/indexing.R: testing the above
276    
277    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/sparseMatrix.R (cov2cor): method for sparse matrices
280    
281            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
282    
283            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
284    
285            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
286    
287    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/Matrix.R: "generic" cov2cor() method
290    
291            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
292                    speed up Q %*% D %*% t(Q)
293            * tests/dpoMatrix.R: test nearPD()
294    
295    2007-12-05  Doug Bates and Martin Maechler
296    
297            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
298            stats::xtabs() allowing to create sparse matrices.
299    
300    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
303    
304    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
307    
308    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/LU.R: solve() method for "denseLU"
311    
312    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * DESCRIPTION (Version): 0.999375-3 preparing for release
315    
316            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
317    
318            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
319    
320    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
323              thanks to Kasper Kristensen.
324            * tests/matprod.R: regression test for that.
325    
326    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
327    
328            * [r4778] R/AllGeneric.R: Check R version before defining generics for
329              primitives
330    
331    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/denseMatrix.R (rcond): method
334            * R/sparseQR.R (rcond): method, use x or t(x)
335    
336    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
339            matrices.
340            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
341    
342            * man/rcond.Rd: mention the more general definition, and add
343            example for non-square matrices.
344    
345            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
346    
347    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
350    
351    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
354            * tests/indexing.R: add new regression for the above cases.
355    
356    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/Mutils.h (__sun): clause for alloca.h on Solaris
359    
360    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * DESCRIPTION (Date, Version): 0.999375-2
363    
364    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/HBMM.R (readMM): make work for pattern matrices as well
367    
368    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
369    
370            * [r4730] src/Mutils.h: declare alloca
371            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
372              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
373              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
374              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
375              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
376              methods; switch writeMM to use CHOLMOD code; repair readMM
377    
378    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
381            Oehlschlaegel's ... result type still to be discussed!
382    
383    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * man/image-methods.Rd: new, combining all image() methods
386    
387    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
390            to work via dgC...
391    
392            * R/Matrix.R (Matrix): special treatment for "table" (S3)
393    
394    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/dgTMatrix.R (image): change defaults to
397                    aspect = "iso", colorkey = FALSE
398    
399    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
402            must copy its *expanded* x slot before LAPACK call.
403    
404            * tests/matprod.R: test the last days' changes.
405    
406    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
407    
408            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
409              as well as in sources
410            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
411              Lapack call
412    
413    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
414    
415            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
416                    ("Matrix", "matrix") which is needed in some cases.
417            Ditto for solve().
418    
419            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
420            infinite recursion in dispatch for some cases.
421    
422    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
423    
424            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
425              so pointers match
426    
427    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * DESCRIPTION (Date): set ready for release -- 0.999375-1
430    
431    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
432    
433            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
434              src/chm_common.c, src/chm_common.h: Change API for
435              numeric_as_chm_dense and N_AS_CHM_DN
436    
437    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
438    
439            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
440            * tests/matprod.R: regr.test for it
441    
442    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
445            * tests/group-methods.R: and regression-test it
446    
447    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
448    
449            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
450              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
451              triplet_to_sparse, documentation, use typedefs
452    
453    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * man/dpoMatrix-class.Rd: added 'corMatrix' example
456    
457            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
458            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
459            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
460    
461            * R/lsparseMatrix.R: bug fix in "all" method
462            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
463    
464            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
465            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
466                    + matrix |-> nMatrix coercion
467            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
468            * man/pMatrix-class.Rd: ditto
469    
470            * R/Matrix.R (Summary): method for non-dMatrix
471    
472            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
473            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
474                    test all Summary methods.
475    
476    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
479    
480    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
483    
484            * R/pMatrix.R (t?crossprod): methods for pMatrix
485    
486    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
487    
488            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
489    
490    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
491    
492            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
493              trying to fix a subtle bug - which has been somewhere else.
494    
495    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
496    
497            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
498              solve the bug
499    
500    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * src/dgCMatrix.c (compressed_to_TMatrix):
503    
504    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * src/Csparse.c (Rsparse_validate): new, to have some validity
507            checking for RsparseMatrix
508            * src/dgCMatrix.c (xRMatrix_validate): ditto
509            * src/dtCMatrix.c (tRMatrix_validate): ditto
510    
511    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
512    
513            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
514              lgRMatrix
515            * [r4568] DESCRIPTION: Prepare for bug-fix release
516            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
517              for declaration of cholmod_symmetry
518    
519    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
522            release.
523    
524    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
525    
526            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
527              functions - no longer used
528            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
529              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
530              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
531              Alloca
532    
533    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
534    
535            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
536              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
537              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
538              src/t_gCMatrix_colSums.c: more R_CheckStack()s
539    
540    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
541    
542            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
543              the required amount of memory then call M_numeric_as_chm_dense.
544            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
545              (like Calloc but calling alloca)
546    
547    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
548    
549            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
550            and extended with more sophisticated 'col.names' option.
551            * NAMESPACE: export  printSparseMatrix()
552            * man/printSpMatrix.Rd: document, incl. examples
553    
554    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
555    
556            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
557              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
558              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
559    
560    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
561    
562            * DESCRIPTION (Version): 0.99875-4
563    
564            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
565            some dimnames perservation.
566    
567            * R/dsTMatrix.R (t-method): keep dimnames
568            * R/dtTMatrix.R:  ditto
569    
570            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
571            and ncol(.) < 10
572    
573            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
574            from Mutils.h
575    
576            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
577            e.g. in as(<ngCMatrix>, "matrix")
578    
579    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
580    
581            * [r4529] .: Create a branch for the API changes from the 0.99875
582              series to the 0.999375 series
583            * [r4530] DESCRIPTION, inst/include/Matrix.h,
584              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
585              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
586              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
587              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
588              as_cholmod_x functions
589    
590    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
591    
592            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
593              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
594              to Comparisons
595    
596    >>>>>>> .merge-right.r4561
597    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * DESCRIPTION (Version): 0.99875-3 ready to be released.
600    
601            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
602    
603            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
604            that should also work in a future version of R.
605    
606    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
609    
610            * R/sparseVector.R: more *sparseVector coercions, notably for
611            non - double ones.
612    
613    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
614    
615            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
616              notably the new ones building on the new .Call(.)s:
617    
618            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
619            all 4 of [dlin]gCMatrix_colSums().
620    
621    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
622    
623            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
624            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
625              result
626    
627    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/kronecker.R: fix typo (could lead to inf.recursion)
630            * test/simple.R: testing that
631    
632            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
633            method as well (which can have arguments, show() can't).
634    
635    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
636    
637            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
638              added dgCMatrix_colSums for [col,row][Sums,Means]
639    
640    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
641    
642            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
643              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
644              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
645            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
646              class
647            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
648              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
649              row names to store the levels - duh!  Added an example.
650    
651    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * src/Csparse.c (Csparse_validate): check for *repeated* entries
654            thanks to example from Christian Buchta; with a test here:
655            * tests/simple.R:
656    
657    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
660            of colSums(*, sparseResult = TRUE)
661    
662    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
665            'na.rm = FALSE' as "everywhere" else in R.
666    
667    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
668    
669            * [r4421] src/CSparse_install.sh: Modify for new organization of
670              CSparse package
671            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
672              SuiteSparse
673            * [r4426] src/Makefile: add ./UFconfig to the include path for
674              compilation
675            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
676            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
677              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
678    
679    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
680    
681            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
682            * R/sparseMatrix.R (prSpMatrix): now gives a message about
683            suppressed column names.
684    
685    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
686    
687            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
688              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
689              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
690              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
691              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
692              Remove warnings after change to const char* CHAR
693    
694    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
695    
696            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
697              type of M_cholmod_ssmult
698    
699    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
700    
701            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
702              src/init.c: Yet another cholmod export - cholmod_ssmult
703    
704    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * NAMESPACE: exported drop0(), since
707            * man/drop0.Rd: I have seen several cases, I really wanted to use
708            it, so our users may want too.
709    
710    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
711    
712            * man/colSums.Rd: separately document colSums() etc, since these
713            have the extra argument 'sparseResult'.
714    
715    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
718            * man/spMatrix.Rd: docu., including examples
719    
720            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
721            in order to make colMeans() etc fast *and* correct.
722            * R/sparseVector.R (replSPvec): "[<-" functionality for
723            sparseVectors; tested in
724            * tests/simple.R:
725    
726    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
729            (very) sparse Matrices; output similar to Matlab's print().
730    
731    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
732    
733            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
734            0-based, indices (Jose Quesada <quesada@gmail.com>).
735    
736    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
737    
738            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
739    
740    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * R/Auxiliaries.R (sparsapply): new utility, much faster than
743            tapply1() for large sparse matrices.
744    
745    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/Matrix.R (dim<-): reshape now via sparseVector.
748    
749            * R/sparseVector.R: methods and function for
750            * R/AllClass.R: new "sparseVector" class and daughters.
751            * NAMESPACE: export new classes
752    
753    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * DESCRIPTION (Version): 0.99875-1
756            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
757    
758    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
761            indexing
762            * tests/indexing.R: test set for that.
763    
764    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
767            entries.
768            * tests/indexing.R(out): add regression test for it
769    
770    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
773            name for "!" method definitions.
774    
775    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * R/Tsparse.R (intI): new utility, used for "[" :
778                    Cleanup up there, and fixes for duplicated indices - more TODO!
779    
780            * tests/indexing.R(out): more tests
781    
782    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
783    
784            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
785            code that is now part of the R Lapack library.
786    
787            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
788            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
789    
790    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
793    
794    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
795    
796            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
797            up with extraneous names '0'...'<n-1>'
798    
799    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * R/dgTMatrix.R (mat2dgT): care about NAs
802    
803    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/kronecker.R: triangularity preserving methods
806    
807    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/kronecker.R: new file collecting kronecker() methods in one
810                    place.  Goal: become much faster!
811    
812    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
815            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
816            can be much faster.
817    
818            * tests/matprod.R: add regression tests for these (upper & lower).
819    
820    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/Matrix.R (diff): method for our Matrices.
823    
824            * R/sparseMatrix.R (isDiagonal): check dim()!
825    
826    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
827    
828            * R/Matrix.R (dim<-): new method for "reshape()" built on a
829            proposal from Tamas Papp.
830    
831    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
834    
835            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
836            rather define and export  cBind() and rBind() only.
837            --> useRs *must* change code that used to have cbind()/rbind() !!
838    
839            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
840            * R/bind.Rout.save: ditto
841    
842    2007-02-16  Douglas Bates  <bates@r-project.org>
843    
844            * DESCRIPTION (Date, Version): 0.9975-11 with new date
845            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
846            const modifier on declaration of the array 'valid'
847    
848    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
849    
850            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
851    
852  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
855    
856          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
857          * tests/simple.R: test the above and some of these coercions:          * tests/simple.R: test the above and some of these coercions:
858    

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