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revision 1646, Sun Oct 22 22:42:40 2006 UTC revision 2225, Sat Jul 19 09:44:48 2008 UTC
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1    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
4            stumbled upon by Michael H.
5    
6            * tests/validObj.R: testing the bug-fix
7    
8            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
9            versions.
10    
11            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
12            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
13    
14            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
15              AS_CHM_SP() which includes diagU2N.
16    
17            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
18            adapt to 3 arguments.
19    
20    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
21    
22            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
23              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
24              new solve method
25            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
26              Csparse_diagU2N functionality into Matrix_as_cs
27    
28    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
31              vignette
32            * [r2214] R/AllGeneric.R: cosmetic
33            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
34    
35    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
36    
37            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
38              argument with default TRUE
39            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
40              Csparse_diagU2N
41            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
42              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
43              parent array; new solve method for signature(a = "dtCMatrix", b =
44              "sparseMatrix")
45    
46    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/diagMatrix.R (.bdiag): also keep triangular
49            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
50              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
51              bdiag() improvements of last week
52    
53    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
54    
55            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
56              messages
57    
58    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
61            symmetric- or nsparse-Matrix, also fixing the bug introduced with
62            the new version (.999375-10).
63    
64            * tests/Simple.R: regression test for the bugs.
65    
66    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/sparseVector.R (spV2M): fix for "isparseVector".
69            Further, fix <diag> -> <sparseVector> coercion
70            (repSpV): add rep(<sparseVector>, .) method
71    
72            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
73            use as.vector(.).
74    
75            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
76    
77            * R/AllClass.R: new (hidden) class union "scarceMatrix"
78            * R/AllClass.R: sparseVector: add prototype
79    
80            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
81            Kasper Kristensen
82    
83    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * tests/other-pkgs.R: add more interesting Matrix -> graph
86    
87    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
90            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
91    
92    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * DESCRIPTION: release 0.999375-10 to CRAN
95    
96            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
97            .bdiag().
98            * man/bdiag.Rd: update, including test.
99    
100    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/Simple.R: add minimal bdiag() checks
103    
104            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
105              factor out the Tsparse - internal computation into new .bdiag()
106    
107    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * R/nsparseMatrix.R: specific fast all() and any() methods.
110    
111            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
112            when trying to produce too large result.
113    
114            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
115            very large matrices.
116    
117            * R/sparseMatrix.R (printSpMatrix2): new function, used by
118            show(<sparseMatrix>).
119    
120            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
121    
122    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * src/Mutils.c (m_encodeInd, m_encodeInd2):
125            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
126    
127            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
128            big matrices): -> 2nd argument 'di' instead of 'nr' !
129    
130    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * R/dtCMatrix.R: faster dgC* -> dtC* method
133            * tests/Simple.R: (hence removed "FIXME")
134    
135            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
136            which can be be turned off for possible speed gains.
137    
138    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
141    
142            * R/not.R: fix !<ldiMatrix>
143            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
144    
145            * R/diagMatrix.R (Ops): fix one-off thinko in
146            <diagonal> o <numeric> methods
147    
148            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
149    
150    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
153            * tests/Simple.R: testing the above
154    
155    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
158    
159    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
162            * NAMESPACE (unname): finally exported
163    
164    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Auxiliaries.R (cholMat): possibly keep packed
167    
168            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
169            for R < 2.7.0.
170    
171            * R/Tsparse.R ([): for triangularMatrix, check if result may be
172            triangular.
173            * tests/indexing.R: regression test
174    
175    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
178            * R/Ops.R: more methods, for lMatrix/nMatrix
179    
180    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/expm.R: new file for all expm() methods; notably new ones for
183            diagonal*, triangular*, symmetric* and also simple "matrix".
184    
185    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
188    
189            * inst/test-tools.R (assert.EQ.mat): better message when not equal
190    
191            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
192    
193            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
194            [dl]denseMatrix {identical slots; but more logical method dispatch}
195    
196    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
199    
200            * R/diagMatrix.R (determinant): method
201    
202    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
205    
206            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
207    
208            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
209            its diagonal
210    
211    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
214    
215            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
216    
217            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
218    
219            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
220    
221    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
224    
225            * R/Ops.R (.do.Logic.lsparse): fix NA case
226    
227            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
228    
229            * R/Auxiliaries.R (nnzero): fix special cases, using
230            * R/Auxiliaries.R (indDiag): new utility
231            * R/Auxiliaries.R (indTri): new argument 'diag'
232    
233            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
234    
235    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
238    
239            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
240            ".tCMatrix" triangular matrix.
241    
242            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
243            'clx' can be class *or* class representation.
244            (nnzSparse): new.
245            (non0ind): new 'xtendSymm' argument; used in
246            * R/Ops.R:
247    
248            * R/pMatrix.R: more efficient determinant() method
249    
250    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
251    
252            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
253            * [disactivated] NAMESPACE: export(det)
254    
255            * R/diagMatrix.R (mkDiag): new substitute for diag()
256    
257            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
258            (as0, as1): new utility.
259    
260            * R/Csparse.R (diag, band): need diagU2N()
261    
262            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
263    
264            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
265    
266            * R/Ops.R (Compare): fix <nsp> o <nsp> case
267    
268            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
269    
270    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/Auxiliaries.R (signPerm): new utility for
273            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
274    
275            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
276            since we have our own error handler (and can use tryCatch() from R).
277    
278    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
281    
282            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
283            when not positive definite.
284    
285            * R/Auxiliaries.R (asTri): new auxiliary
286            (non0.i): make *much* faster for Tsparse with many non-zero
287            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
288    
289            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
290            test-tools.R , see below
291    
292            * R/dMatrix.R: fix "Summary" method: + diagU2N()
293    
294            * NAMESPACE, R/Matrix.R: add mean() method
295    
296    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
299            cold-hot colors; try *changed* default useAbs = FALSE
300            * man/image-methods.Rd:  nice examples
301    
302    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * inst/test-tools.R (checkMatrix): new function for modularizing part
305            of tstMatrixClass() in tests/Class+Meth.R
306    
307            * R/dsCMatrix.R: coercion from "matrix"
308            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
309    
310            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
311            add test for as(matrix(,0,0), <class>)
312    
313    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
316            work as determinant(matrix(,0,0)).
317    
318            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
319            * man/sparseLU-class.Rd: ditto
320    
321            * R/dgCMatrix.R (determinant): method building on lu()
322            * R/sparseMatrix.R, Matrix.R, ...: ditto
323    
324            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
325    
326    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
329            pattern matrices.
330    
331    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * src/dense.c (dense_to_Csparse): all declarations *before*
334            R_CheckStack(); needed e.g. for ancient gcc 2.96.
335    
336    
337    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * DESCRIPTION (Version): 0.999375-9 --- need to release
340            for R-devel (and R 2.7.0 alpha soon).
341    
342            * R/AllClass.R: drop "double" from "atomicVector" class union
343    
344            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
345            * R/dgeMatrix.R: ditto
346    
347            * R/sparseMatrix.R (summary): count NAs
348    
349            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
350    
351    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
354            order to become compatible to new R 2.7.0 base::rcond().
355    
356    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
359    
360            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
361    
362            * inst/test-tools.R (isValid): new utility, used much in
363            * tests/simple.R:
364    
365            * man/BunchKaufman-methods.Rd: added too
366    
367    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/dsyMatrix.R: add BunchKaufman() methods.
370            * R/dspMatrix.R:
371    
372            * src/init.c: add dsyMatrix_trf
373    
374    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
375    
376            * DESCRIPTION (Version): release 0.999375-7
377            * src/CHMfactor.c (CHMfactor_update): fix
378    
379    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
382            internal_chm_factor().
383    
384            * R/AllGeneric.R: do *not* define a "chol" generic
385                    (but rather use the implicit one *without* making pivot
386                    part of the signature)
387            * R/*.R: drop the 'pivot' from chol's signature and make
388                    'pivot=FALSE' a default argument of method definitions.
389    
390            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
391            version of Matrix
392    
393    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
396    
397            * R/sparseMatrix.R (is.na): new simple method
398            * R/denseMatrix.R (is.na): ditto.
399    
400            * R/diagMatrix.R (.symDiagonal): newly exported utility.
401    
402            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
403    
404            * src/UFsparse_download.sh: -->
405            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
406    
407    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
408    
409            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
410            functionality; barely tested in
411            * tests/factorizing.R
412    
413            * src/Csparse.c (diag_tC): new functionality to enable faster
414            determinant(<dsCMatrix>, .) in
415            * R/dsCMatrix.R
416    
417    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
418    
419            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
420              src/CHMfactor.c, src/CHMfactor.h,
421              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
422              Log-determinant of the parent matrix from a CHMfactor object as
423              chm_factor_ldetL2; documentation and support
424    
425    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
428    
429    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
432            warning.
433    
434    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
435    
436            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
437    
438            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
439              <diagonal> o <sparse_triangular>
440              setAs(., "nMatrix") added.
441    
442            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
443    
444            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
445                    new argument 'checkDense = FALSE'.
446    
447    
448    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
451            back-permutation of the matrix exponential.
452    
453            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
454    
455            * DESCRIPTION (Date,Version): ready to release 0.999375-5
456    
457            * tests/simple.R: testing diagN2U
458    
459    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/Auxiliaries.R (diagN2U): interface to
462    
463            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
464    
465            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
466    
467    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
468    
469            * src/chm_common.c (chm_diagN2U): new utility.
470    
471            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
472            make use of chm_diagN2U() and hence now preserve triangularity and
473            unit-triangularity.
474    
475            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
476    
477    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
478    
479            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
480    
481            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
482            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
483    
484            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
485    
486            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
487    
488            * src/chm_common.c (AS_CHM_FINISH): add note about problem
489            for triangular (diag = "U").
490    
491    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
492    
493            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
494            * R/bind.R:  .Call(dense_to_Csparse, *)
495    
496    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
497    
498            * R/Matrix.R (Matrix): no longer use coercions to specific classes
499                    (since we are discouraging them in user code).
500    
501            * tests/*.R: also replaces coercions to specific classes by
502            coercions to super classes.
503    
504            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
505    
506    
507    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
508    
509            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
510    
511            * src/dense.c (dense_band): generalized from ddense_band
512    
513            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
514              now for "denseMatrix" (instead of just "ddense*"); much
515              simplified setMethod()s for these.
516    
517            * src/dense.c (dense_to_symmetric): generalized from ddense_*
518    
519    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
522            version of as(*, "symmetricMatric").
523    
524            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
525            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
526    
527    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * R/Matrix.R (subset.ij): utility, as first step to faster
530               M [ <ij-matrix> ] indexing.
531    
532            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
533    
534            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
535            for more efficient symmpart() and skewpart() methods.
536    
537            * src/Mutils.c (equal_string_vectors): utility
538    
539            * src/dense.c (ddense_to_symmetric): new function used in
540    
541            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
542    
543            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
544            order to match the generic (and evade .local(..)).
545    
546            * R/dsCMatrix.R: dgC -> dsC: use C code!
547    
548            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
549            as per TODO
550    
551            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
552    
553            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
554    
555    
556    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
559    
560            * R/Auxiliaries.R (non0.i): take out of non0ind
561    
562            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
563            make tril(), triu(), band() work for "matrix" and all "dense*"
564    
565            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
566            * tests/simple.R: test the fix above
567    
568            * R/sparseMatrix.R ([): simplification: no coerce to <general>
569                    before we use as(., <Tsparse>)[...] anyway
570    
571            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
572    
573            * R/triangularMatrix.R (isTriangular): methods for all subclasses
574            instead of "triangularMatrix" -- just to disambiguate
575    
576    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
579            * tests/indexing.R: example that fails above
580    
581    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
584            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
585                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
586    
587            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
588            * src/Tsparse.h, init.c: ditto
589            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
590                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
591            * R/sparseMatrix.R (isTriangular): hence simplified
592    
593    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/Ops.R (.Arith.Csparse): new utility factored out of former
596              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
597    
598    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
599    
600            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
601    
602            * inst/test-tools.R (isOrthogonal): new function; also file restructured
603    
604    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
607            coercion to "nMatrix" and "pMatrix"
608    
609            * R/AllClass.R: "Schur" class;  "number" class union
610            * man/number-class.Rd:
611            * man/Schur-class.Rd:
612    
613            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
614            (.simpleSchur): Schur() method for diagonal matrices
615            (.triSchur):    Schur() method for triangular matrices
616            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
617    
618    
619    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
620    
621            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
622    
623    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
626                    in order to ensure 'system = *' is not lost;
627                    formals()$system instead of cut&paste.
628            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
629    
630    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * DESCRIPTION (Date): make ready for release --> 0.999375-4
633    
634            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
635    
636    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
639                    and hence does as.vector(.).
640            * man/pMatrix-class.Rd: docs
641            * R/sparseMatrix.R: fix for printing "integer sparse"
642    
643            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
644    
645            * R/Matrix.R and others: use "exact" function argument list for
646                    both "["   : (x, i,j, ..., drop)
647                    and  "[<-" : (x, i,j, ..., value)
648    
649            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
650            * R/Tsparse.R (replTmat):    ditto
651            * R/diagMatrix.R (replDiag): ditto
652            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
653            * tests/indexing.R: testing the above
654    
655    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/sparseMatrix.R (cov2cor): method for sparse matrices
658    
659            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
660    
661            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
662    
663            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
664    
665    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * R/Matrix.R: "generic" cov2cor() method
668    
669            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
670                    speed up Q %*% D %*% t(Q)
671            * tests/dpoMatrix.R: test nearPD()
672    
673    2007-12-05  Doug Bates and Martin Maechler
674    
675            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
676            stats::xtabs() allowing to create sparse matrices.
677    
678    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
681    
682    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
685    
686    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
687    
688            * R/LU.R: solve() method for "denseLU"
689    
690    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * DESCRIPTION (Version): 0.999375-3 preparing for release
693    
694            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
695    
696            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
697    
698    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
701              thanks to Kasper Kristensen.
702            * tests/matprod.R: regression test for that.
703    
704    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
705    
706            * [r4778] R/AllGeneric.R: Check R version before defining generics for
707              primitives
708    
709    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/denseMatrix.R (rcond): method
712            * R/sparseQR.R (rcond): method, use x or t(x)
713    
714    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
717            matrices.
718            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
719    
720            * man/rcond.Rd: mention the more general definition, and add
721            example for non-square matrices.
722    
723            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
724    
725    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
728    
729    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
732            * tests/indexing.R: add new regression for the above cases.
733    
734    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
735    
736            * src/Mutils.h (__sun): clause for alloca.h on Solaris
737    
738    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * DESCRIPTION (Date, Version): 0.999375-2
741    
742    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/HBMM.R (readMM): make work for pattern matrices as well
745    
746    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
747    
748            * [r4730] src/Mutils.h: declare alloca
749            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
750              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
751              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
752              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
753              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
754              methods; switch writeMM to use CHOLMOD code; repair readMM
755    
756    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
759            Oehlschlaegel's ... result type still to be discussed!
760    
761    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * man/image-methods.Rd: new, combining all image() methods
764    
765    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
768            to work via dgC...
769    
770            * R/Matrix.R (Matrix): special treatment for "table" (S3)
771    
772    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/dgTMatrix.R (image): change defaults to
775                    aspect = "iso", colorkey = FALSE
776    
777    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
780            must copy its *expanded* x slot before LAPACK call.
781    
782            * tests/matprod.R: test the last days' changes.
783    
784    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
785    
786            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
787              as well as in sources
788            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
789              Lapack call
790    
791    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
794                    ("Matrix", "matrix") which is needed in some cases.
795            Ditto for solve().
796    
797            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
798            infinite recursion in dispatch for some cases.
799    
800    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
801    
802            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
803              so pointers match
804    
805    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * DESCRIPTION (Date): set ready for release -- 0.999375-1
808    
809    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
810    
811            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
812              src/chm_common.c, src/chm_common.h: Change API for
813              numeric_as_chm_dense and N_AS_CHM_DN
814    
815    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
816    
817            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
818            * tests/matprod.R: regr.test for it
819    
820    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
823            * tests/group-methods.R: and regression-test it
824    
825    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
826    
827            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
828              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
829              triplet_to_sparse, documentation, use typedefs
830    
831    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * man/dpoMatrix-class.Rd: added 'corMatrix' example
834    
835            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
836            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
837            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
838    
839            * R/lsparseMatrix.R: bug fix in "all" method
840            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
841    
842            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
843            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
844                    + matrix |-> nMatrix coercion
845            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
846            * man/pMatrix-class.Rd: ditto
847    
848            * R/Matrix.R (Summary): method for non-dMatrix
849    
850            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
851            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
852                    test all Summary methods.
853    
854    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
857    
858    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
861    
862            * R/pMatrix.R (t?crossprod): methods for pMatrix
863    
864    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
865    
866            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
867    
868    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
869    
870            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
871              trying to fix a subtle bug - which has been somewhere else.
872    
873    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
874    
875            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
876              solve the bug
877    
878    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * src/dgCMatrix.c (compressed_to_TMatrix):
881    
882    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
883    
884            * src/Csparse.c (Rsparse_validate): new, to have some validity
885            checking for RsparseMatrix
886            * src/dgCMatrix.c (xRMatrix_validate): ditto
887            * src/dtCMatrix.c (tRMatrix_validate): ditto
888    
889    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
890    
891            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
892              lgRMatrix
893            * [r4568] DESCRIPTION: Prepare for bug-fix release
894            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
895              for declaration of cholmod_symmetry
896    
897    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
898    
899            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
900            release.
901    
902    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
903    
904            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
905              functions - no longer used
906            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
907              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
908              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
909              Alloca
910    
911    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
912    
913            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
914              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
915              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
916              src/t_gCMatrix_colSums.c: more R_CheckStack()s
917    
918    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
919    
920            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
921              the required amount of memory then call M_numeric_as_chm_dense.
922            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
923              (like Calloc but calling alloca)
924    
925    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
928            and extended with more sophisticated 'col.names' option.
929            * NAMESPACE: export  printSparseMatrix()
930            * man/printSpMatrix.Rd: document, incl. examples
931    
932    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
933    
934            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
935              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
936              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
937    
938    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * DESCRIPTION (Version): 0.99875-4
941    
942            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
943            some dimnames perservation.
944    
945            * R/dsTMatrix.R (t-method): keep dimnames
946            * R/dtTMatrix.R:  ditto
947    
948            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
949            and ncol(.) < 10
950    
951            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
952            from Mutils.h
953    
954            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
955            e.g. in as(<ngCMatrix>, "matrix")
956    
957    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
958    
959            * [r4529] .: Create a branch for the API changes from the 0.99875
960              series to the 0.999375 series
961            * [r4530] DESCRIPTION, inst/include/Matrix.h,
962              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
963              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
964              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
965              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
966              as_cholmod_x functions
967    
968    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
969    
970            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
971              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
972              to Comparisons
973    
974    >>>>>>> .merge-right.r4561
975    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
976    
977            * DESCRIPTION (Version): 0.99875-3 ready to be released.
978    
979            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
980    
981            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
982            that should also work in a future version of R.
983    
984    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
985    
986            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
987    
988            * R/sparseVector.R: more *sparseVector coercions, notably for
989            non - double ones.
990    
991    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
994              notably the new ones building on the new .Call(.)s:
995    
996            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
997            all 4 of [dlin]gCMatrix_colSums().
998    
999    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1000    
1001            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1002            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1003              result
1004    
1005    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/kronecker.R: fix typo (could lead to inf.recursion)
1008            * test/simple.R: testing that
1009    
1010            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1011            method as well (which can have arguments, show() can't).
1012    
1013    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1014    
1015            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1016              added dgCMatrix_colSums for [col,row][Sums,Means]
1017    
1018    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1019    
1020            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1021              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1022              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1023            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1024              class
1025            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1026              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1027              row names to store the levels - duh!  Added an example.
1028    
1029    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1030    
1031            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1032            thanks to example from Christian Buchta; with a test here:
1033            * tests/simple.R:
1034    
1035    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1038            of colSums(*, sparseResult = TRUE)
1039    
1040    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1043            'na.rm = FALSE' as "everywhere" else in R.
1044    
1045    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1046    
1047            * [r4421] src/CSparse_install.sh: Modify for new organization of
1048              CSparse package
1049            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1050              SuiteSparse
1051            * [r4426] src/Makefile: add ./UFconfig to the include path for
1052              compilation
1053            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1054            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1055              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1056    
1057    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1058    
1059            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1060            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1061            suppressed column names.
1062    
1063    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1064    
1065            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1066              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1067              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1068              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1069              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1070              Remove warnings after change to const char* CHAR
1071    
1072    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1073    
1074            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1075              type of M_cholmod_ssmult
1076    
1077    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1078    
1079            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1080              src/init.c: Yet another cholmod export - cholmod_ssmult
1081    
1082    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1083    
1084            * NAMESPACE: exported drop0(), since
1085            * man/drop0.Rd: I have seen several cases, I really wanted to use
1086            it, so our users may want too.
1087    
1088    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1089    
1090            * man/colSums.Rd: separately document colSums() etc, since these
1091            have the extra argument 'sparseResult'.
1092    
1093    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1096            * man/spMatrix.Rd: docu., including examples
1097    
1098            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1099            in order to make colMeans() etc fast *and* correct.
1100            * R/sparseVector.R (replSPvec): "[<-" functionality for
1101            sparseVectors; tested in
1102            * tests/simple.R:
1103    
1104    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1105    
1106            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1107            (very) sparse Matrices; output similar to Matlab's print().
1108    
1109    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1110    
1111            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1112            0-based, indices (Jose Quesada <quesada@gmail.com>).
1113    
1114    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1115    
1116            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1117    
1118    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1119    
1120            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1121            tapply1() for large sparse matrices.
1122    
1123    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1124    
1125            * R/Matrix.R (dim<-): reshape now via sparseVector.
1126    
1127            * R/sparseVector.R: methods and function for
1128            * R/AllClass.R: new "sparseVector" class and daughters.
1129            * NAMESPACE: export new classes
1130    
1131    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1132    
1133            * DESCRIPTION (Version): 0.99875-1
1134            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1135    
1136    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1137    
1138            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1139            indexing
1140            * tests/indexing.R: test set for that.
1141    
1142    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1143    
1144            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1145            entries.
1146            * tests/indexing.R(out): add regression test for it
1147    
1148    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1149    
1150            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1151            name for "!" method definitions.
1152    
1153    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * R/Tsparse.R (intI): new utility, used for "[" :
1156                    Cleanup up there, and fixes for duplicated indices - more TODO!
1157    
1158            * tests/indexing.R(out): more tests
1159    
1160    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1161    
1162            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1163            code that is now part of the R Lapack library.
1164    
1165            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1166            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1167    
1168    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1169    
1170            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1171    
1172    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1173    
1174            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1175            up with extraneous names '0'...'<n-1>'
1176    
1177    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1178    
1179            * R/dgTMatrix.R (mat2dgT): care about NAs
1180    
1181    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1182    
1183            * R/kronecker.R: triangularity preserving methods
1184    
1185    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/kronecker.R: new file collecting kronecker() methods in one
1188                    place.  Goal: become much faster!
1189    
1190    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1193            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1194            can be much faster.
1195    
1196            * tests/matprod.R: add regression tests for these (upper & lower).
1197    
1198    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1199    
1200            * R/Matrix.R (diff): method for our Matrices.
1201    
1202            * R/sparseMatrix.R (isDiagonal): check dim()!
1203    
1204    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1205    
1206            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1207            proposal from Tamas Papp.
1208    
1209    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1210    
1211            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1212    
1213            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1214            rather define and export  cBind() and rBind() only.
1215            --> useRs *must* change code that used to have cbind()/rbind() !!
1216    
1217            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1218            * R/bind.Rout.save: ditto
1219    
1220    2007-02-16  Douglas Bates  <bates@r-project.org>
1221    
1222            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1223            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1224            const modifier on declaration of the array 'valid'
1225    
1226    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1227    
1228            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1229    
1230    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1231    
1232            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1233    
1234            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1235            * tests/simple.R: test the above and some of these coercions:
1236    
1237            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1238                    be careful to avoid infinite recursion, using new coercions in
1239            * R/ngCMatrix.R and nsC... and ntC...
1240            * R/lsparseMatrix.R: ditto
1241    
1242            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1243    
1244            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1245            * R/Rsparse.R: reactivate .Call()s
1246    
1247            * tests/Class+Meth.R: a bit more on actual classes
1248    
1249    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1250    
1251            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1252    
1253    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * DESCRIPTION (Version): 0.9975-10 to upload
1256    
1257            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1258            specific classes less unconditionally.
1259    
1260            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1261    
1262            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1263    
1264            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1265            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1266            R_to_CMatrix segfaults on one platform.
1267            Eliminate most coercion method to *specific* classes, and replace
1268            with virtual classes coercions.
1269    
1270    
1271    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1272    
1273            * src/init.c: export the CHM...._validate() placeholders, since
1274            they *are* called.
1275    
1276            * tests/Class+Meth.R (classCanCoerce): and starting to test
1277            all as(<from>, <to>)
1278    
1279    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1280    
1281            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1282            * tests/indexing.R: tested now
1283            * tests/indexing.Rout.save: updated
1284    
1285            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1286            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1287            appropriate.
1288    
1289            * NAMESPACE: export a trivial
1290            * R/Matrix.R: drop() Matrix-method
1291    
1292            * R/AllClass.R: moved all prototypes to virtual super classes.
1293    
1294            * R/Rsparse.R: many more coercions to have less exceptions in
1295            * tests/Class+Meth.R:
1296    
1297            * R/Ops.R (Compare): tweak for case with NA
1298            * tests/simpl.R: hence another 'FIXME' eliminated
1299    
1300    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1303            objects.
1304    
1305            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1306              and more of "!", "&", "|", all, any; coercions
1307    
1308            * R/Rsparse.R: many coercions (which enable quite a few other
1309            methods), thanks to enhancements in
1310            * src/dgCMatrix.c (R_to_CMatrix): new, and
1311            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1312            symmetric & triangular and ..RMatrix objects.
1313    
1314            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1315            renamed file from src/dsTMatrix.c;
1316            now dealing with symmetric and triangular Tsparse coercions, both
1317            to dense and general.
1318    
1319    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1320    
1321            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1322    
1323            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1324            where sensible when the <numeric> is of length > 1.
1325    
1326    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1327    
1328            * R/Matrix.R ([<-): for M[] <- value: fix length
1329    
1330    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1331    
1332            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1333            * R/ndenseMatrix.R: new coercions n* -> l*
1334    
1335    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1336    
1337            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1338    
1339            * R/Ops.R ("Logic"): and other "Ops", many updates
1340    
1341    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1342    
1343            * src/Mutils.h (SET_DimNames): new utility
1344    
1345            * R/Auxiliaries.R (nnzero): improved and now exported via
1346    
1347            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1348    
1349    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1350    
1351            * R/diagMatrix.R (!): fix typo.
1352    
1353    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1356                    allow to pass class definition --> speedup
1357            * R/sparseMatrix.R: apply the above
1358    
1359            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1360    
1361            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1362            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1363            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1364    
1365            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1366    
1367            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1368            and use it for "sparse*" as well, since it's faster than the
1369            as_Csparse(.) way.
1370    
1371    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1372    
1373            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1374    
1375    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1376    
1377            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1378            as method for   M[ ij ] <- v
1379            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1380    
1381            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1382            FALSE answer
1383    
1384            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1385            * tests/indexing.R: test it, and some of the above
1386    
1387    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1388    
1389            * R/Auxiliaries.R (is_duplicatedT): new utility
1390    
1391    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1392    
1393            * src/init.c (R_init_Matrix): export cholmod_scale
1394    
1395    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1396    
1397            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1398            base::as.matrix to (x, ...)
1399    
1400    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1401    
1402            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1403            file; start using "Logic", hence
1404    
1405            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1406            * NAMESPACE: import and export "Logic"
1407    
1408    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1409    
1410            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1411            only needed previously to R version 2.5.0.
1412    
1413    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1414    
1415            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1416    
1417            * R/Tsparse.R (replTmat): fix subassignment of triangular
1418            * R/Csparse.R (replCmat): ditto
1419            * tests/indexing.R: more tests, incl the above fix
1420    
1421    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1422    
1423            * R/Auxiliaries.R (drop0): extend for non CSparse
1424            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1425    
1426            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1427                    use uplo correctly (!); other places: use uplo_P() macro
1428    
1429            * R/Csparse.R (replCmat): call diagU2N() when needed
1430            * R/Tsparse.R (replTmat): ditto
1431    
1432            * src/dtCMatrix.c (tCMatrix_validate): new
1433            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1434            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1435    
1436            * R/diagMatrix.R (replDiag): to use in [<-
1437    
1438    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1439    
1440            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1441                    also more general diagU2N().
1442    
1443    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1444    
1445            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1446            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1447    
1448    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1449    
1450            * tests/bind.R: a few more cases
1451            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1452    
1453            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1454            * R/ddenseMatrix.R (cbind2/rbind2)
1455            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1456            * tests/indexing.R
1457            * tests/indexing.Rout.save: updated
1458    
1459    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1460    
1461            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1462            * tests/indexing.R
1463    
1464    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1465    
1466            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1467            align with proper position of "0", i.e., right for integers.
1468            argument 'align' by default is "fancy".
1469    
1470    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1471    
1472            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1473            * R/Csparse.R: and fix "Compare" for more cases.
1474            * tests/Class+Meth.R: test some of these (m == m, m != m)
1475    
1476    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1477    
1478            * R/lsparseMatrix.R: all() and any() methods
1479            * R/ldenseMatrix.R:      ditto
1480            * NAMESPACE, R/Matrix.R: ditto
1481    
1482            * man/all-methods.Rd: document them minimally
1483    
1484            * tests/simple.R: add a few examples for these
1485    
1486    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1487    
1488            * R/Tsparse.R ([): fix long standing typo in symmetric case
1489            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1490    
1491    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1492    
1493            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1494            to LL before converting to a sparse matrix. (The LDL form can be
1495            converted to a sparse matrix but it is implicitly a unit
1496            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1497    
1498    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1499    
1500            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1501    
1502    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1503    
1504            * DESCRIPTION (Version): updated -> release 0.9975-7
1505            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1506    
1507    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1508    
1509            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1510    
1511    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1512    
1513            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1514            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1515            is exactly singular.
1516    
1517    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1518    
1519            * DESCRIPTION (Date): updated -> release 0.9975-6
1520    
1521    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1522    
1523            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1524            now returns symmetric.
1525    
1526            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1527    
1528            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1529            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1530    
1531            * R/Auxiliaries.R (.type.kind): added
1532    
1533    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1534    
1535            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1536            running src/CSparse_install.sh
1537    
1538            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1539    
1540    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1541    
1542            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1543            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1544    
1545            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1546    
1547            * tests/Class+Meth.R (tstMatrixClass): now assure
1548            the (important in method programming) property :
1549    
1550                    ###>>  Every "Matrix" is either
1551                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1552    
1553                    (where "*" stands for "Matrix")
1554    
1555            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1556    
1557            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1558            * tests/validObj.R: checks for "comparison"
1559    
1560            * R/sparseMatrix.R ([): improved indexing for sparse;
1561                    trying to keep <symmetric>[ n, n] symmmetric
1562    
1563            * tests/indexing.R: indexing for logical sparse now ok
1564    
1565    
1566    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1567    
1568            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1569    
1570            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1571    
1572    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1573    
1574            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1575    
1576            * tests/simple.R: validObject() checking the above.
1577    
1578            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1579            replacing both dgCMatrix_validate and lgCM*.
1580    
1581            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1582            fix dimnames setting in other places.
1583            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1584    
1585    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1586    
1587            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1588    
1589            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1590            symmetry test, via
1591            * R/Auxiliaries.R (.as.dgC.0.factors):
1592    
1593    2006-11-01  Douglas Bates  <bates@r-project.org>
1594    
1595            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1596            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1597            <CsparseMatrix>) added
1598    
1599    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1600    
1601            * tests/matprod.R: add a variation of Harri's example
1602    
1603            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1604            recursive infinitely.
1605    
1606            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1607    
1608            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1609    
1610    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1611    
1612            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1613            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1614            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1615            satisfy the above test.
1616    
1617    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1618    
1619            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1620    
1621            * R/dgCMatrix.R: solve(a, b="missing") based on
1622            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1623            RHS = NULL.
1624    
1625            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1626            add more (needed) [t]crossprod() methods.
1627    
1628            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1629    
1630            * R/Auxiliaries.R (as_CspClass): cleanup
1631            (drop0): internal utility for "Csparse_drop(*, 0)"
1632            (.bail.out.2): encourage active feedback
1633    
1634    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1635    
1636            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1637    
1638            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1639            non-valid or 'sorted' case).
1640    
1641            * R/dsparseMatrix.R: add "chol" method.
1642            * R/ddenseMatrix.R: ditto
1643    
1644            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1645            * NAMESPACE (Ops)
1646            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1647            coercion; deprecating direct lower level coercions.
1648    
1649            * R/*.R (seq): use seq_len() and seq_along() where possible.
1650    
1651    
1652    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1653    
1654            * DESCRIPTION (Version): 0.9975-5 ready for release
1655    
1656  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>  2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1657    
1658          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.          * src/init.c (R_init_Matrix): export more cholmod CCallable functions.

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