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revision 1624, Wed Oct 11 15:00:11 2006 UTC revision 2237, Fri Jul 25 06:55:42 2008 UTC
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1    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
4            recursion in new test in
5            * tests/matprod.R: testing the above and another solve() case, below
6    
7            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
8            e.g. triangular 'x'.
9    
10            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
11            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
12            correctly with unit-triangular x
13    
14            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
15            instead of not checking diagU.
16    
17            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
18            experiments where diagonalMatrix would extend sparse*.
19    
20    
21    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
24            "x@p[ncol(x)]" instead of length(x@i).
25            * R/Auxiliaries.R (nnzero): ditto
26    
27            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
28            since that fails for over-allocated i.
29    
30            * tests/validObj.R: more testing of over-allocated (i,x) slots
31    
32    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
35            'sort_in_place' and set it to TRUE in call from
36            * src/Csparse.c (Csparse_validate): sort in place, making sure that
37            validObject() continues sort the columns if needed.
38    
39            * tests/validObj.R: now tests that more thoroughly, and
40            * man/CsparseMatrix-class.Rd: documents it.
41    
42    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
45            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
46            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
47            diagU2N().
48    
49            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
50            .spDiagonal() and new .trDiagonal().
51    
52            * R/dtCMatrix.R (solve): make use of .trDiagonal()
53    
54    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
57            stumbled upon by Michael H.
58    
59            * tests/validObj.R: testing the bug-fix
60    
61            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
62            versions.
63    
64            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
65            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
66    
67            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
68              AS_CHM_SP() which includes diagU2N.
69    
70            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
71            adapt to 3 arguments.
72    
73    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
76              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
77              new solve method
78            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
79              Csparse_diagU2N functionality into Matrix_as_cs
80    
81    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
84    
85    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
86    
87            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
88              argument with default TRUE
89            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
90              Csparse_diagU2N
91            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
92              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
93              parent array; new solve method for signature(a = "dtCMatrix", b =
94              "sparseMatrix")
95    
96    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/diagMatrix.R (.bdiag): also keep result triangular
99    
100    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
101    
102            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
103              messages
104    
105    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
108            symmetric- or nsparse-Matrix, also fixing the bug introduced with
109            the new version (.999375-10).
110    
111            * tests/Simple.R: regression test for the bugs.
112    
113    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/sparseVector.R (spV2M): fix for "isparseVector".
116            Further, fix <diag> -> <sparseVector> coercion
117            (repSpV): add rep(<sparseVector>, .) method
118    
119            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
120            use as.vector(.).
121    
122            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
123    
124            * R/AllClass.R: new (hidden) class union "scarceMatrix"
125            * R/AllClass.R: sparseVector: add prototype
126    
127            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
128            Kasper Kristensen
129    
130    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
131    
132            * tests/other-pkgs.R: add more interesting Matrix -> graph
133    
134    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
137            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
138    
139    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * DESCRIPTION: release 0.999375-10 to CRAN
142    
143            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
144            .bdiag().
145            * man/bdiag.Rd: update, including test.
146    
147    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * tests/Simple.R: add minimal bdiag() checks
150    
151            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
152              factor out the Tsparse - internal computation into new .bdiag()
153    
154    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * R/nsparseMatrix.R: specific fast all() and any() methods.
157    
158            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
159            when trying to produce too large result.
160    
161            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
162            very large matrices.
163    
164            * R/sparseMatrix.R (printSpMatrix2): new function, used by
165            show(<sparseMatrix>).
166    
167            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
168    
169    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
170    
171            * src/Mutils.c (m_encodeInd, m_encodeInd2):
172            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
173    
174            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
175            big matrices): -> 2nd argument 'di' instead of 'nr' !
176    
177    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/dtCMatrix.R: faster dgC* -> dtC* method
180            * tests/Simple.R: (hence removed "FIXME")
181    
182            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
183            which can be be turned off for possible speed gains.
184    
185    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
188    
189            * R/not.R: fix !<ldiMatrix>
190            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
191    
192            * R/diagMatrix.R (Ops): fix one-off thinko in
193            <diagonal> o <numeric> methods
194    
195            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
196    
197    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
200            * tests/Simple.R: testing the above
201    
202    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
205    
206    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
209            * NAMESPACE (unname): finally exported
210    
211    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * R/Auxiliaries.R (cholMat): possibly keep packed
214    
215            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
216            for R < 2.7.0.
217    
218            * R/Tsparse.R ([): for triangularMatrix, check if result may be
219            triangular.
220            * tests/indexing.R: regression test
221    
222    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
225            * R/Ops.R: more methods, for lMatrix/nMatrix
226    
227    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/expm.R: new file for all expm() methods; notably new ones for
230            diagonal*, triangular*, symmetric* and also simple "matrix".
231    
232    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
235    
236            * inst/test-tools.R (assert.EQ.mat): better message when not equal
237    
238            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
239    
240            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
241            [dl]denseMatrix {identical slots; but more logical method dispatch}
242    
243    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
246    
247            * R/diagMatrix.R (determinant): method
248    
249    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
252    
253            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
254    
255            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
256            its diagonal
257    
258    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
261    
262            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
263    
264            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
265    
266            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
267    
268    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
271    
272            * R/Ops.R (.do.Logic.lsparse): fix NA case
273    
274            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
275    
276            * R/Auxiliaries.R (nnzero): fix special cases, using
277            * R/Auxiliaries.R (indDiag): new utility
278            * R/Auxiliaries.R (indTri): new argument 'diag'
279    
280            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
281    
282    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
285    
286            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
287            ".tCMatrix" triangular matrix.
288    
289            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
290            'clx' can be class *or* class representation.
291            (nnzSparse): new.
292            (non0ind): new 'xtendSymm' argument; used in
293            * R/Ops.R:
294    
295            * R/pMatrix.R: more efficient determinant() method
296    
297    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
300            * [disactivated] NAMESPACE: export(det)
301    
302            * R/diagMatrix.R (mkDiag): new substitute for diag()
303    
304            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
305            (as0, as1): new utility.
306    
307            * R/Csparse.R (diag, band): need diagU2N()
308    
309            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
310    
311            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
312    
313            * R/Ops.R (Compare): fix <nsp> o <nsp> case
314    
315            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
316    
317    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * R/Auxiliaries.R (signPerm): new utility for
320            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
321    
322            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
323            since we have our own error handler (and can use tryCatch() from R).
324    
325    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
328    
329            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
330            when not positive definite.
331    
332            * R/Auxiliaries.R (asTri): new auxiliary
333            (non0.i): make *much* faster for Tsparse with many non-zero
334            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
335    
336            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
337            test-tools.R , see below
338    
339            * R/dMatrix.R: fix "Summary" method: + diagU2N()
340    
341            * NAMESPACE, R/Matrix.R: add mean() method
342    
343    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
346            cold-hot colors; try *changed* default useAbs = FALSE
347            * man/image-methods.Rd:  nice examples
348    
349    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * inst/test-tools.R (checkMatrix): new function for modularizing part
352            of tstMatrixClass() in tests/Class+Meth.R
353    
354            * R/dsCMatrix.R: coercion from "matrix"
355            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
356    
357            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
358            add test for as(matrix(,0,0), <class>)
359    
360    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
363            work as determinant(matrix(,0,0)).
364    
365            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
366            * man/sparseLU-class.Rd: ditto
367    
368            * R/dgCMatrix.R (determinant): method building on lu()
369            * R/sparseMatrix.R, Matrix.R, ...: ditto
370    
371            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
372    
373    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
376            pattern matrices.
377    
378    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * src/dense.c (dense_to_Csparse): all declarations *before*
381            R_CheckStack(); needed e.g. for ancient gcc 2.96.
382    
383    
384    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * DESCRIPTION (Version): 0.999375-9 --- need to release
387            for R-devel (and R 2.7.0 alpha soon).
388    
389            * R/AllClass.R: drop "double" from "atomicVector" class union
390    
391            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
392            * R/dgeMatrix.R: ditto
393    
394            * R/sparseMatrix.R (summary): count NAs
395    
396            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
397    
398    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
401            order to become compatible to new R 2.7.0 base::rcond().
402    
403    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
406    
407            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
408    
409            * inst/test-tools.R (isValid): new utility, used much in
410            * tests/simple.R:
411    
412            * man/BunchKaufman-methods.Rd: added too
413    
414    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/dsyMatrix.R: add BunchKaufman() methods.
417            * R/dspMatrix.R:
418    
419            * src/init.c: add dsyMatrix_trf
420    
421    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
422    
423            * DESCRIPTION (Version): release 0.999375-7
424            * src/CHMfactor.c (CHMfactor_update): fix
425    
426    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
427    
428            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
429            internal_chm_factor().
430    
431            * R/AllGeneric.R: do *not* define a "chol" generic
432                    (but rather use the implicit one *without* making pivot
433                    part of the signature)
434            * R/*.R: drop the 'pivot' from chol's signature and make
435                    'pivot=FALSE' a default argument of method definitions.
436    
437            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
438            version of Matrix
439    
440    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
443    
444            * R/sparseMatrix.R (is.na): new simple method
445            * R/denseMatrix.R (is.na): ditto.
446    
447            * R/diagMatrix.R (.symDiagonal): newly exported utility.
448    
449            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
450    
451            * src/UFsparse_download.sh: -->
452            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
453    
454    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
457            functionality; barely tested in
458            * tests/factorizing.R
459    
460            * src/Csparse.c (diag_tC): new functionality to enable faster
461            determinant(<dsCMatrix>, .) in
462            * R/dsCMatrix.R
463    
464    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
465    
466            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
467              src/CHMfactor.c, src/CHMfactor.h,
468              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
469              Log-determinant of the parent matrix from a CHMfactor object as
470              chm_factor_ldetL2; documentation and support
471    
472    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
475    
476    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
479            warning.
480    
481    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
484    
485            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
486              <diagonal> o <sparse_triangular>
487              setAs(., "nMatrix") added.
488    
489            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
490    
491            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
492                    new argument 'checkDense = FALSE'.
493    
494    
495    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
496    
497            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
498            back-permutation of the matrix exponential.
499    
500            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
501    
502            * DESCRIPTION (Date,Version): ready to release 0.999375-5
503    
504            * tests/simple.R: testing diagN2U
505    
506    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
507    
508            * R/Auxiliaries.R (diagN2U): interface to
509    
510            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
511    
512            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
513    
514    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * src/chm_common.c (chm_diagN2U): new utility.
517    
518            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
519            make use of chm_diagN2U() and hence now preserve triangularity and
520            unit-triangularity.
521    
522            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
523    
524    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
525    
526            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
527    
528            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
529            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
530    
531            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
532    
533            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
534    
535            * src/chm_common.c (AS_CHM_FINISH): add note about problem
536            for triangular (diag = "U").
537    
538    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
541            * R/bind.R:  .Call(dense_to_Csparse, *)
542    
543    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * R/Matrix.R (Matrix): no longer use coercions to specific classes
546                    (since we are discouraging them in user code).
547    
548            * tests/*.R: also replaces coercions to specific classes by
549            coercions to super classes.
550    
551            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
552    
553    
554    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
555    
556            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
557    
558            * src/dense.c (dense_band): generalized from ddense_band
559    
560            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
561              now for "denseMatrix" (instead of just "ddense*"); much
562              simplified setMethod()s for these.
563    
564            * src/dense.c (dense_to_symmetric): generalized from ddense_*
565    
566    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
569            version of as(*, "symmetricMatric").
570    
571            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
572            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
573    
574    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/Matrix.R (subset.ij): utility, as first step to faster
577               M [ <ij-matrix> ] indexing.
578    
579            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
580    
581            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
582            for more efficient symmpart() and skewpart() methods.
583    
584            * src/Mutils.c (equal_string_vectors): utility
585    
586            * src/dense.c (ddense_to_symmetric): new function used in
587    
588            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
589    
590            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
591            order to match the generic (and evade .local(..)).
592    
593            * R/dsCMatrix.R: dgC -> dsC: use C code!
594    
595            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
596            as per TODO
597    
598            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
599    
600            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
601    
602    
603    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
604    
605            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
606    
607            * R/Auxiliaries.R (non0.i): take out of non0ind
608    
609            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
610            make tril(), triu(), band() work for "matrix" and all "dense*"
611    
612            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
613            * tests/simple.R: test the fix above
614    
615            * R/sparseMatrix.R ([): simplification: no coerce to <general>
616                    before we use as(., <Tsparse>)[...] anyway
617    
618            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
619    
620            * R/triangularMatrix.R (isTriangular): methods for all subclasses
621            instead of "triangularMatrix" -- just to disambiguate
622    
623    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
624    
625            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
626            * tests/indexing.R: example that fails above
627    
628    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
631            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
632                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
633    
634            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
635            * src/Tsparse.h, init.c: ditto
636            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
637                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
638            * R/sparseMatrix.R (isTriangular): hence simplified
639    
640    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/Ops.R (.Arith.Csparse): new utility factored out of former
643              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
644    
645    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
648    
649            * inst/test-tools.R (isOrthogonal): new function; also file restructured
650    
651    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
654            coercion to "nMatrix" and "pMatrix"
655    
656            * R/AllClass.R: "Schur" class;  "number" class union
657            * man/number-class.Rd:
658            * man/Schur-class.Rd:
659    
660            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
661            (.simpleSchur): Schur() method for diagonal matrices
662            (.triSchur):    Schur() method for triangular matrices
663            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
664    
665    
666    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
669    
670    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
673                    in order to ensure 'system = *' is not lost;
674                    formals()$system instead of cut&paste.
675            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
676    
677    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * DESCRIPTION (Date): make ready for release --> 0.999375-4
680    
681            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
682    
683    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
684    
685            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
686                    and hence does as.vector(.).
687            * man/pMatrix-class.Rd: docs
688            * R/sparseMatrix.R: fix for printing "integer sparse"
689    
690            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
691    
692            * R/Matrix.R and others: use "exact" function argument list for
693                    both "["   : (x, i,j, ..., drop)
694                    and  "[<-" : (x, i,j, ..., value)
695    
696            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
697            * R/Tsparse.R (replTmat):    ditto
698            * R/diagMatrix.R (replDiag): ditto
699            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
700            * tests/indexing.R: testing the above
701    
702    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/sparseMatrix.R (cov2cor): method for sparse matrices
705    
706            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
707    
708            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
709    
710            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
711    
712    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * R/Matrix.R: "generic" cov2cor() method
715    
716            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
717                    speed up Q %*% D %*% t(Q)
718            * tests/dpoMatrix.R: test nearPD()
719    
720    2007-12-05  Doug Bates and Martin Maechler
721    
722            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
723            stats::xtabs() allowing to create sparse matrices.
724    
725    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
728    
729    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
730    
731            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
732    
733    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/LU.R: solve() method for "denseLU"
736    
737    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * DESCRIPTION (Version): 0.999375-3 preparing for release
740    
741            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
742    
743            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
744    
745    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
748              thanks to Kasper Kristensen.
749            * tests/matprod.R: regression test for that.
750    
751    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
752    
753            * [r4778] R/AllGeneric.R: Check R version before defining generics for
754              primitives
755    
756    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
757    
758            * R/denseMatrix.R (rcond): method
759            * R/sparseQR.R (rcond): method, use x or t(x)
760    
761    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
762    
763            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
764            matrices.
765            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
766    
767            * man/rcond.Rd: mention the more general definition, and add
768            example for non-square matrices.
769    
770            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
771    
772    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
775    
776    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
779            * tests/indexing.R: add new regression for the above cases.
780    
781    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * src/Mutils.h (__sun): clause for alloca.h on Solaris
784    
785    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * DESCRIPTION (Date, Version): 0.999375-2
788    
789    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
790    
791            * R/HBMM.R (readMM): make work for pattern matrices as well
792    
793    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
794    
795            * [r4730] src/Mutils.h: declare alloca
796            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
797              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
798              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
799              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
800              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
801              methods; switch writeMM to use CHOLMOD code; repair readMM
802    
803    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
806            Oehlschlaegel's ... result type still to be discussed!
807    
808    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
809    
810            * man/image-methods.Rd: new, combining all image() methods
811    
812    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
815            to work via dgC...
816    
817            * R/Matrix.R (Matrix): special treatment for "table" (S3)
818    
819    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * R/dgTMatrix.R (image): change defaults to
822                    aspect = "iso", colorkey = FALSE
823    
824    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
827            must copy its *expanded* x slot before LAPACK call.
828    
829            * tests/matprod.R: test the last days' changes.
830    
831    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
832    
833            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
834              as well as in sources
835            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
836              Lapack call
837    
838    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
841                    ("Matrix", "matrix") which is needed in some cases.
842            Ditto for solve().
843    
844            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
845            infinite recursion in dispatch for some cases.
846    
847    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
848    
849            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
850              so pointers match
851    
852    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
853    
854            * DESCRIPTION (Date): set ready for release -- 0.999375-1
855    
856    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
857    
858            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
859              src/chm_common.c, src/chm_common.h: Change API for
860              numeric_as_chm_dense and N_AS_CHM_DN
861    
862    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
863    
864            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
865            * tests/matprod.R: regr.test for it
866    
867    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
870            * tests/group-methods.R: and regression-test it
871    
872    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
873    
874            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
875              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
876              triplet_to_sparse, documentation, use typedefs
877    
878    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * man/dpoMatrix-class.Rd: added 'corMatrix' example
881    
882            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
883            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
884            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
885    
886            * R/lsparseMatrix.R: bug fix in "all" method
887            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
888    
889            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
890            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
891                    + matrix |-> nMatrix coercion
892            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
893            * man/pMatrix-class.Rd: ditto
894    
895            * R/Matrix.R (Summary): method for non-dMatrix
896    
897            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
898            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
899                    test all Summary methods.
900    
901    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
902    
903            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
904    
905    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
908    
909            * R/pMatrix.R (t?crossprod): methods for pMatrix
910    
911    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
912    
913            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
914    
915    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
916    
917            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
918              trying to fix a subtle bug - which has been somewhere else.
919    
920    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
921    
922            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
923              solve the bug
924    
925    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
926    
927            * src/dgCMatrix.c (compressed_to_TMatrix):
928    
929    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * src/Csparse.c (Rsparse_validate): new, to have some validity
932            checking for RsparseMatrix
933            * src/dgCMatrix.c (xRMatrix_validate): ditto
934            * src/dtCMatrix.c (tRMatrix_validate): ditto
935    
936    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
937    
938            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
939              lgRMatrix
940            * [r4568] DESCRIPTION: Prepare for bug-fix release
941            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
942              for declaration of cholmod_symmetry
943    
944    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
945    
946            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
947            release.
948    
949    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
950    
951            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
952              functions - no longer used
953            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
954              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
955              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
956              Alloca
957    
958    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
959    
960            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
961              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
962              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
963              src/t_gCMatrix_colSums.c: more R_CheckStack()s
964    
965    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
966    
967            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
968              the required amount of memory then call M_numeric_as_chm_dense.
969            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
970              (like Calloc but calling alloca)
971    
972    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
973    
974            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
975            and extended with more sophisticated 'col.names' option.
976            * NAMESPACE: export  printSparseMatrix()
977            * man/printSpMatrix.Rd: document, incl. examples
978    
979    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
980    
981            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
982              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
983              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
984    
985    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
986    
987            * DESCRIPTION (Version): 0.99875-4
988    
989            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
990            some dimnames perservation.
991    
992            * R/dsTMatrix.R (t-method): keep dimnames
993            * R/dtTMatrix.R:  ditto
994    
995            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
996            and ncol(.) < 10
997    
998            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
999            from Mutils.h
1000    
1001            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
1002            e.g. in as(<ngCMatrix>, "matrix")
1003    
1004    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
1005    
1006            * [r4529] .: Create a branch for the API changes from the 0.99875
1007              series to the 0.999375 series
1008            * [r4530] DESCRIPTION, inst/include/Matrix.h,
1009              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
1010              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
1011              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
1012              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
1013              as_cholmod_x functions
1014    
1015    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
1016    
1017            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
1018              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
1019              to Comparisons
1020    
1021    >>>>>>> .merge-right.r4561
1022    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1023    
1024            * DESCRIPTION (Version): 0.99875-3 ready to be released.
1025    
1026            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
1027    
1028            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
1029            that should also work in a future version of R.
1030    
1031    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1034    
1035            * R/sparseVector.R: more *sparseVector coercions, notably for
1036            non - double ones.
1037    
1038    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1039    
1040            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1041              notably the new ones building on the new .Call(.)s:
1042    
1043            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1044            all 4 of [dlin]gCMatrix_colSums().
1045    
1046    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1047    
1048            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1049            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1050              result
1051    
1052    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1053    
1054            * R/kronecker.R: fix typo (could lead to inf.recursion)
1055            * test/simple.R: testing that
1056    
1057            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1058            method as well (which can have arguments, show() can't).
1059    
1060    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1061    
1062            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1063              added dgCMatrix_colSums for [col,row][Sums,Means]
1064    
1065    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1066    
1067            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1068              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1069              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1070            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1071              class
1072            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1073              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1074              row names to store the levels - duh!  Added an example.
1075    
1076    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1077    
1078            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1079            thanks to example from Christian Buchta; with a test here:
1080            * tests/simple.R:
1081    
1082    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1083    
1084            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1085            of colSums(*, sparseResult = TRUE)
1086    
1087    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1088    
1089            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1090            'na.rm = FALSE' as "everywhere" else in R.
1091    
1092    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1093    
1094            * [r4421] src/CSparse_install.sh: Modify for new organization of
1095              CSparse package
1096            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1097              SuiteSparse
1098            * [r4426] src/Makefile: add ./UFconfig to the include path for
1099              compilation
1100            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1101            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1102              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1103    
1104    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1105    
1106            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1107            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1108            suppressed column names.
1109    
1110    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1111    
1112            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1113              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1114              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1115              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1116              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1117              Remove warnings after change to const char* CHAR
1118    
1119    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1120    
1121            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1122              type of M_cholmod_ssmult
1123    
1124    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1125    
1126            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1127              src/init.c: Yet another cholmod export - cholmod_ssmult
1128    
1129    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1130    
1131            * NAMESPACE: exported drop0(), since
1132            * man/drop0.Rd: I have seen several cases, I really wanted to use
1133            it, so our users may want too.
1134    
1135    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1136    
1137            * man/colSums.Rd: separately document colSums() etc, since these
1138            have the extra argument 'sparseResult'.
1139    
1140    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1143            * man/spMatrix.Rd: docu., including examples
1144    
1145            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1146            in order to make colMeans() etc fast *and* correct.
1147            * R/sparseVector.R (replSPvec): "[<-" functionality for
1148            sparseVectors; tested in
1149            * tests/simple.R:
1150    
1151    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1152    
1153            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1154            (very) sparse Matrices; output similar to Matlab's print().
1155    
1156    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1157    
1158            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1159            0-based, indices (Jose Quesada <quesada@gmail.com>).
1160    
1161    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1162    
1163            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1164    
1165    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1166    
1167            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1168            tapply1() for large sparse matrices.
1169    
1170    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1171    
1172            * R/Matrix.R (dim<-): reshape now via sparseVector.
1173    
1174            * R/sparseVector.R: methods and function for
1175            * R/AllClass.R: new "sparseVector" class and daughters.
1176            * NAMESPACE: export new classes
1177    
1178    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * DESCRIPTION (Version): 0.99875-1
1181            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1182    
1183    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1184    
1185            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1186            indexing
1187            * tests/indexing.R: test set for that.
1188    
1189    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1190    
1191            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1192            entries.
1193            * tests/indexing.R(out): add regression test for it
1194    
1195    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1196    
1197            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1198            name for "!" method definitions.
1199    
1200    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1201    
1202            * R/Tsparse.R (intI): new utility, used for "[" :
1203                    Cleanup up there, and fixes for duplicated indices - more TODO!
1204    
1205            * tests/indexing.R(out): more tests
1206    
1207    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1208    
1209            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1210            code that is now part of the R Lapack library.
1211    
1212            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1213            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1214    
1215    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1216    
1217            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1218    
1219    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1220    
1221            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1222            up with extraneous names '0'...'<n-1>'
1223    
1224    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1225    
1226            * R/dgTMatrix.R (mat2dgT): care about NAs
1227    
1228    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1229    
1230            * R/kronecker.R: triangularity preserving methods
1231    
1232    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * R/kronecker.R: new file collecting kronecker() methods in one
1235                    place.  Goal: become much faster!
1236    
1237    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1240            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1241            can be much faster.
1242    
1243            * tests/matprod.R: add regression tests for these (upper & lower).
1244    
1245    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * R/Matrix.R (diff): method for our Matrices.
1248    
1249            * R/sparseMatrix.R (isDiagonal): check dim()!
1250    
1251    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1254            proposal from Tamas Papp.
1255    
1256    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1257    
1258            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1259    
1260            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1261            rather define and export  cBind() and rBind() only.
1262            --> useRs *must* change code that used to have cbind()/rbind() !!
1263    
1264            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1265            * R/bind.Rout.save: ditto
1266    
1267    2007-02-16  Douglas Bates  <bates@r-project.org>
1268    
1269            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1270            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1271            const modifier on declaration of the array 'valid'
1272    
1273    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1274    
1275            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1276    
1277    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1278    
1279            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1280    
1281            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1282            * tests/simple.R: test the above and some of these coercions:
1283    
1284            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1285                    be careful to avoid infinite recursion, using new coercions in
1286            * R/ngCMatrix.R and nsC... and ntC...
1287            * R/lsparseMatrix.R: ditto
1288    
1289            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1290    
1291            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1292            * R/Rsparse.R: reactivate .Call()s
1293    
1294            * tests/Class+Meth.R: a bit more on actual classes
1295    
1296    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1297    
1298            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1299    
1300    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1301    
1302            * DESCRIPTION (Version): 0.9975-10 to upload
1303    
1304            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1305            specific classes less unconditionally.
1306    
1307            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1308    
1309            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1310    
1311            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1312            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1313            R_to_CMatrix segfaults on one platform.
1314            Eliminate most coercion method to *specific* classes, and replace
1315            with virtual classes coercions.
1316    
1317    
1318    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1319    
1320            * src/init.c: export the CHM...._validate() placeholders, since
1321            they *are* called.
1322    
1323            * tests/Class+Meth.R (classCanCoerce): and starting to test
1324            all as(<from>, <to>)
1325    
1326    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1327    
1328            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1329            * tests/indexing.R: tested now
1330            * tests/indexing.Rout.save: updated
1331    
1332            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1333            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1334            appropriate.
1335    
1336            * NAMESPACE: export a trivial
1337            * R/Matrix.R: drop() Matrix-method
1338    
1339            * R/AllClass.R: moved all prototypes to virtual super classes.
1340    
1341            * R/Rsparse.R: many more coercions to have less exceptions in
1342            * tests/Class+Meth.R:
1343    
1344            * R/Ops.R (Compare): tweak for case with NA
1345            * tests/simpl.R: hence another 'FIXME' eliminated
1346    
1347    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1348    
1349            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1350            objects.
1351    
1352            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1353              and more of "!", "&", "|", all, any; coercions
1354    
1355            * R/Rsparse.R: many coercions (which enable quite a few other
1356            methods), thanks to enhancements in
1357            * src/dgCMatrix.c (R_to_CMatrix): new, and
1358            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1359            symmetric & triangular and ..RMatrix objects.
1360    
1361            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1362            renamed file from src/dsTMatrix.c;
1363            now dealing with symmetric and triangular Tsparse coercions, both
1364            to dense and general.
1365    
1366    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1367    
1368            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1369    
1370            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1371            where sensible when the <numeric> is of length > 1.
1372    
1373    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1374    
1375            * R/Matrix.R ([<-): for M[] <- value: fix length
1376    
1377    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1378    
1379            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1380            * R/ndenseMatrix.R: new coercions n* -> l*
1381    
1382    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1383    
1384            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1385    
1386            * R/Ops.R ("Logic"): and other "Ops", many updates
1387    
1388    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * src/Mutils.h (SET_DimNames): new utility
1391    
1392            * R/Auxiliaries.R (nnzero): improved and now exported via
1393    
1394            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1395    
1396    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1397    
1398            * R/diagMatrix.R (!): fix typo.
1399    
1400    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1401    
1402            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1403                    allow to pass class definition --> speedup
1404            * R/sparseMatrix.R: apply the above
1405    
1406            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1407    
1408            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1409            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1410            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1411    
1412            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1413    
1414            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1415            and use it for "sparse*" as well, since it's faster than the
1416            as_Csparse(.) way.
1417    
1418    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1419    
1420            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1421    
1422    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1423    
1424            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1425            as method for   M[ ij ] <- v
1426            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1427    
1428            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1429            FALSE answer
1430    
1431            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1432            * tests/indexing.R: test it, and some of the above
1433    
1434    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1435    
1436            * R/Auxiliaries.R (is_duplicatedT): new utility
1437    
1438    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1439    
1440            * src/init.c (R_init_Matrix): export cholmod_scale
1441    
1442    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1443    
1444            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1445            base::as.matrix to (x, ...)
1446    
1447    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1448    
1449            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1450            file; start using "Logic", hence
1451    
1452            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1453            * NAMESPACE: import and export "Logic"
1454    
1455    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1456    
1457            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1458            only needed previously to R version 2.5.0.
1459    
1460    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1461    
1462            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1463    
1464            * R/Tsparse.R (replTmat): fix subassignment of triangular
1465            * R/Csparse.R (replCmat): ditto
1466            * tests/indexing.R: more tests, incl the above fix
1467    
1468    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1469    
1470            * R/Auxiliaries.R (drop0): extend for non CSparse
1471            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1472    
1473            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1474                    use uplo correctly (!); other places: use uplo_P() macro
1475    
1476            * R/Csparse.R (replCmat): call diagU2N() when needed
1477            * R/Tsparse.R (replTmat): ditto
1478    
1479            * src/dtCMatrix.c (tCMatrix_validate): new
1480            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1481            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1482    
1483            * R/diagMatrix.R (replDiag): to use in [<-
1484    
1485    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1486    
1487            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1488                    also more general diagU2N().
1489    
1490    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1491    
1492            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1493            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1494    
1495    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1496    
1497            * tests/bind.R: a few more cases
1498            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1499    
1500            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1501            * R/ddenseMatrix.R (cbind2/rbind2)
1502            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1503            * tests/indexing.R
1504            * tests/indexing.Rout.save: updated
1505    
1506    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1507    
1508            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1509            * tests/indexing.R
1510    
1511    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1512    
1513            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1514            align with proper position of "0", i.e., right for integers.
1515            argument 'align' by default is "fancy".
1516    
1517    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1518    
1519            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1520            * R/Csparse.R: and fix "Compare" for more cases.
1521            * tests/Class+Meth.R: test some of these (m == m, m != m)
1522    
1523    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1524    
1525            * R/lsparseMatrix.R: all() and any() methods
1526            * R/ldenseMatrix.R:      ditto
1527            * NAMESPACE, R/Matrix.R: ditto
1528    
1529            * man/all-methods.Rd: document them minimally
1530    
1531            * tests/simple.R: add a few examples for these
1532    
1533    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1534    
1535            * R/Tsparse.R ([): fix long standing typo in symmetric case
1536            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1537    
1538    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1539    
1540            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1541            to LL before converting to a sparse matrix. (The LDL form can be
1542            converted to a sparse matrix but it is implicitly a unit
1543            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1544    
1545    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1546    
1547            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1548    
1549    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1550    
1551            * DESCRIPTION (Version): updated -> release 0.9975-7
1552            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1553    
1554    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1555    
1556            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1557    
1558    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1559    
1560            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1561            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1562            is exactly singular.
1563    
1564    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1565    
1566            * DESCRIPTION (Date): updated -> release 0.9975-6
1567    
1568    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1569    
1570            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1571            now returns symmetric.
1572    
1573            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1574    
1575            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1576            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1577    
1578            * R/Auxiliaries.R (.type.kind): added
1579    
1580    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1581    
1582            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1583            running src/CSparse_install.sh
1584    
1585            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1586    
1587    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1588    
1589            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1590            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1591    
1592            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1593    
1594            * tests/Class+Meth.R (tstMatrixClass): now assure
1595            the (important in method programming) property :
1596    
1597                    ###>>  Every "Matrix" is either
1598                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1599    
1600                    (where "*" stands for "Matrix")
1601    
1602            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1603    
1604            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1605            * tests/validObj.R: checks for "comparison"
1606    
1607            * R/sparseMatrix.R ([): improved indexing for sparse;
1608                    trying to keep <symmetric>[ n, n] symmmetric
1609    
1610            * tests/indexing.R: indexing for logical sparse now ok
1611    
1612    
1613    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1614    
1615            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1616    
1617            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1618    
1619    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1620    
1621            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1622    
1623            * tests/simple.R: validObject() checking the above.
1624    
1625            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1626            replacing both dgCMatrix_validate and lgCM*.
1627    
1628            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1629            fix dimnames setting in other places.
1630            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1631    
1632    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1633    
1634            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1635    
1636            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1637            symmetry test, via
1638            * R/Auxiliaries.R (.as.dgC.0.factors):
1639    
1640    2006-11-01  Douglas Bates  <bates@r-project.org>
1641    
1642            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1643            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1644            <CsparseMatrix>) added
1645    
1646    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1647    
1648            * tests/matprod.R: add a variation of Harri's example
1649    
1650            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1651            recursive infinitely.
1652    
1653            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1654    
1655            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1656    
1657    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1658    
1659            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1660            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1661            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1662            satisfy the above test.
1663    
1664    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1665    
1666            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1667    
1668            * R/dgCMatrix.R: solve(a, b="missing") based on
1669            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1670            RHS = NULL.
1671    
1672            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1673            add more (needed) [t]crossprod() methods.
1674    
1675            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1676    
1677            * R/Auxiliaries.R (as_CspClass): cleanup
1678            (drop0): internal utility for "Csparse_drop(*, 0)"
1679            (.bail.out.2): encourage active feedback
1680    
1681    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1682    
1683            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1684    
1685            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1686            non-valid or 'sorted' case).
1687    
1688            * R/dsparseMatrix.R: add "chol" method.
1689            * R/ddenseMatrix.R: ditto
1690    
1691            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1692            * NAMESPACE (Ops)
1693            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1694            coercion; deprecating direct lower level coercions.
1695    
1696            * R/*.R (seq): use seq_len() and seq_along() where possible.
1697    
1698    
1699    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1700    
1701            * DESCRIPTION (Version): 0.9975-5 ready for release
1702    
1703    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1704    
1705            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1706    
1707    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1708    
1709            * R/AllClass.R (corMatrix): add 'validity' check;
1710                    comment out unused "LDL" class definition
1711            * NAMESPACE: mention, but do not export "LDL" class
1712            * R/corMatrix.R: new (simple), needed for R-devel with
1713            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1714              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1715    
1716    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1717    
1718            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1719            use Rprintf and R's error handling.
1720    
1721    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1722    
1723            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1724            * tests/matprod.R: add tests for the bug fixed.
1725    
1726  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1727    
1728          * src/HBMM.[ch]: remove HarwellBoeing format for writing.          * src/HBMM.[ch]: remove HarwellBoeing format for writing.
# Line 5  Line 1730 
1730    
1731  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1732    
1733          * R/dgCMatrix.R: deprecate the writeHB function.  Use writeMM instead.          * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1734    
1735  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1736    

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