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revision 1624, Wed Oct 11 15:00:11 2006 UTC revision 2227, Mon Jul 21 19:49:33 2008 UTC
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1    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
4            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
5            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
6            diagU2N().
7    
8    
9            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
10            .spDiagonal() and new .trDiagonal().
11    
12            * R/dtCMatrix.R (solve): make use of .trDiagonal()
13    
14    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
17            stumbled upon by Michael H.
18    
19            * tests/validObj.R: testing the bug-fix
20    
21            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
22            versions.
23    
24            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
25            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
26    
27            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
28              AS_CHM_SP() which includes diagU2N.
29    
30            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
31            adapt to 3 arguments.
32    
33    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
34    
35            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
36              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
37              new solve method
38            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
39              Csparse_diagU2N functionality into Matrix_as_cs
40    
41    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
42    
43            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
44              vignette
45            * [r2214] R/AllGeneric.R: cosmetic
46            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
47    
48    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
49    
50            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
51              argument with default TRUE
52            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
53              Csparse_diagU2N
54            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
55              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
56              parent array; new solve method for signature(a = "dtCMatrix", b =
57              "sparseMatrix")
58    
59    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/diagMatrix.R (.bdiag): also keep triangular
62            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
63              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
64              bdiag() improvements of last week
65    
66    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
67    
68            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
69              messages
70    
71    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
74            symmetric- or nsparse-Matrix, also fixing the bug introduced with
75            the new version (.999375-10).
76    
77            * tests/Simple.R: regression test for the bugs.
78    
79    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
80    
81            * R/sparseVector.R (spV2M): fix for "isparseVector".
82            Further, fix <diag> -> <sparseVector> coercion
83            (repSpV): add rep(<sparseVector>, .) method
84    
85            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
86            use as.vector(.).
87    
88            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
89    
90            * R/AllClass.R: new (hidden) class union "scarceMatrix"
91            * R/AllClass.R: sparseVector: add prototype
92    
93            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
94            Kasper Kristensen
95    
96    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * tests/other-pkgs.R: add more interesting Matrix -> graph
99    
100    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
103            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
104    
105    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * DESCRIPTION: release 0.999375-10 to CRAN
108    
109            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
110            .bdiag().
111            * man/bdiag.Rd: update, including test.
112    
113    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * tests/Simple.R: add minimal bdiag() checks
116    
117            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
118              factor out the Tsparse - internal computation into new .bdiag()
119    
120    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/nsparseMatrix.R: specific fast all() and any() methods.
123    
124            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
125            when trying to produce too large result.
126    
127            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
128            very large matrices.
129    
130            * R/sparseMatrix.R (printSpMatrix2): new function, used by
131            show(<sparseMatrix>).
132    
133            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
134    
135    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * src/Mutils.c (m_encodeInd, m_encodeInd2):
138            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
139    
140            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
141            big matrices): -> 2nd argument 'di' instead of 'nr' !
142    
143    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dtCMatrix.R: faster dgC* -> dtC* method
146            * tests/Simple.R: (hence removed "FIXME")
147    
148            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
149            which can be be turned off for possible speed gains.
150    
151    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
154    
155            * R/not.R: fix !<ldiMatrix>
156            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
157    
158            * R/diagMatrix.R (Ops): fix one-off thinko in
159            <diagonal> o <numeric> methods
160    
161            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
162    
163    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
166            * tests/Simple.R: testing the above
167    
168    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
171    
172    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
175            * NAMESPACE (unname): finally exported
176    
177    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/Auxiliaries.R (cholMat): possibly keep packed
180    
181            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
182            for R < 2.7.0.
183    
184            * R/Tsparse.R ([): for triangularMatrix, check if result may be
185            triangular.
186            * tests/indexing.R: regression test
187    
188    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
191            * R/Ops.R: more methods, for lMatrix/nMatrix
192    
193    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/expm.R: new file for all expm() methods; notably new ones for
196            diagonal*, triangular*, symmetric* and also simple "matrix".
197    
198    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
201    
202            * inst/test-tools.R (assert.EQ.mat): better message when not equal
203    
204            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
205    
206            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
207            [dl]denseMatrix {identical slots; but more logical method dispatch}
208    
209    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
212    
213            * R/diagMatrix.R (determinant): method
214    
215    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
218    
219            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
220    
221            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
222            its diagonal
223    
224    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
225    
226            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
227    
228            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
229    
230            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
231    
232            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
233    
234    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
237    
238            * R/Ops.R (.do.Logic.lsparse): fix NA case
239    
240            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
241    
242            * R/Auxiliaries.R (nnzero): fix special cases, using
243            * R/Auxiliaries.R (indDiag): new utility
244            * R/Auxiliaries.R (indTri): new argument 'diag'
245    
246            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
247    
248    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
249    
250            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
251    
252            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
253            ".tCMatrix" triangular matrix.
254    
255            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
256            'clx' can be class *or* class representation.
257            (nnzSparse): new.
258            (non0ind): new 'xtendSymm' argument; used in
259            * R/Ops.R:
260    
261            * R/pMatrix.R: more efficient determinant() method
262    
263    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
266            * [disactivated] NAMESPACE: export(det)
267    
268            * R/diagMatrix.R (mkDiag): new substitute for diag()
269    
270            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
271            (as0, as1): new utility.
272    
273            * R/Csparse.R (diag, band): need diagU2N()
274    
275            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
276    
277            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
278    
279            * R/Ops.R (Compare): fix <nsp> o <nsp> case
280    
281            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
282    
283    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Auxiliaries.R (signPerm): new utility for
286            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
287    
288            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
289            since we have our own error handler (and can use tryCatch() from R).
290    
291    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
294    
295            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
296            when not positive definite.
297    
298            * R/Auxiliaries.R (asTri): new auxiliary
299            (non0.i): make *much* faster for Tsparse with many non-zero
300            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
301    
302            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
303            test-tools.R , see below
304    
305            * R/dMatrix.R: fix "Summary" method: + diagU2N()
306    
307            * NAMESPACE, R/Matrix.R: add mean() method
308    
309    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
312            cold-hot colors; try *changed* default useAbs = FALSE
313            * man/image-methods.Rd:  nice examples
314    
315    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * inst/test-tools.R (checkMatrix): new function for modularizing part
318            of tstMatrixClass() in tests/Class+Meth.R
319    
320            * R/dsCMatrix.R: coercion from "matrix"
321            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
322    
323            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
324            add test for as(matrix(,0,0), <class>)
325    
326    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
329            work as determinant(matrix(,0,0)).
330    
331            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
332            * man/sparseLU-class.Rd: ditto
333    
334            * R/dgCMatrix.R (determinant): method building on lu()
335            * R/sparseMatrix.R, Matrix.R, ...: ditto
336    
337            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
338    
339    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
342            pattern matrices.
343    
344    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * src/dense.c (dense_to_Csparse): all declarations *before*
347            R_CheckStack(); needed e.g. for ancient gcc 2.96.
348    
349    
350    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
351    
352            * DESCRIPTION (Version): 0.999375-9 --- need to release
353            for R-devel (and R 2.7.0 alpha soon).
354    
355            * R/AllClass.R: drop "double" from "atomicVector" class union
356    
357            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
358            * R/dgeMatrix.R: ditto
359    
360            * R/sparseMatrix.R (summary): count NAs
361    
362            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
363    
364    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
367            order to become compatible to new R 2.7.0 base::rcond().
368    
369    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
370    
371            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
372    
373            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
374    
375            * inst/test-tools.R (isValid): new utility, used much in
376            * tests/simple.R:
377    
378            * man/BunchKaufman-methods.Rd: added too
379    
380    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/dsyMatrix.R: add BunchKaufman() methods.
383            * R/dspMatrix.R:
384    
385            * src/init.c: add dsyMatrix_trf
386    
387    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
388    
389            * DESCRIPTION (Version): release 0.999375-7
390            * src/CHMfactor.c (CHMfactor_update): fix
391    
392    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
395            internal_chm_factor().
396    
397            * R/AllGeneric.R: do *not* define a "chol" generic
398                    (but rather use the implicit one *without* making pivot
399                    part of the signature)
400            * R/*.R: drop the 'pivot' from chol's signature and make
401                    'pivot=FALSE' a default argument of method definitions.
402    
403            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
404            version of Matrix
405    
406    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
409    
410            * R/sparseMatrix.R (is.na): new simple method
411            * R/denseMatrix.R (is.na): ditto.
412    
413            * R/diagMatrix.R (.symDiagonal): newly exported utility.
414    
415            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
416    
417            * src/UFsparse_download.sh: -->
418            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
419    
420    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
423            functionality; barely tested in
424            * tests/factorizing.R
425    
426            * src/Csparse.c (diag_tC): new functionality to enable faster
427            determinant(<dsCMatrix>, .) in
428            * R/dsCMatrix.R
429    
430    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
431    
432            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
433              src/CHMfactor.c, src/CHMfactor.h,
434              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
435              Log-determinant of the parent matrix from a CHMfactor object as
436              chm_factor_ldetL2; documentation and support
437    
438    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
439    
440            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
441    
442    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
445            warning.
446    
447    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
448    
449            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
450    
451            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
452              <diagonal> o <sparse_triangular>
453              setAs(., "nMatrix") added.
454    
455            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
456    
457            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
458                    new argument 'checkDense = FALSE'.
459    
460    
461    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
462    
463            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
464            back-permutation of the matrix exponential.
465    
466            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
467    
468            * DESCRIPTION (Date,Version): ready to release 0.999375-5
469    
470            * tests/simple.R: testing diagN2U
471    
472    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/Auxiliaries.R (diagN2U): interface to
475    
476            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
477    
478            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
479    
480    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * src/chm_common.c (chm_diagN2U): new utility.
483    
484            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
485            make use of chm_diagN2U() and hence now preserve triangularity and
486            unit-triangularity.
487    
488            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
489    
490    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
491    
492            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
493    
494            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
495            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
496    
497            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
498    
499            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
500    
501            * src/chm_common.c (AS_CHM_FINISH): add note about problem
502            for triangular (diag = "U").
503    
504    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
505    
506            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
507            * R/bind.R:  .Call(dense_to_Csparse, *)
508    
509    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/Matrix.R (Matrix): no longer use coercions to specific classes
512                    (since we are discouraging them in user code).
513    
514            * tests/*.R: also replaces coercions to specific classes by
515            coercions to super classes.
516    
517            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
518    
519    
520    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
521    
522            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
523    
524            * src/dense.c (dense_band): generalized from ddense_band
525    
526            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
527              now for "denseMatrix" (instead of just "ddense*"); much
528              simplified setMethod()s for these.
529    
530            * src/dense.c (dense_to_symmetric): generalized from ddense_*
531    
532    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
533    
534            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
535            version of as(*, "symmetricMatric").
536    
537            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
538            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
539    
540    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/Matrix.R (subset.ij): utility, as first step to faster
543               M [ <ij-matrix> ] indexing.
544    
545            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
546    
547            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
548            for more efficient symmpart() and skewpart() methods.
549    
550            * src/Mutils.c (equal_string_vectors): utility
551    
552            * src/dense.c (ddense_to_symmetric): new function used in
553    
554            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
555    
556            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
557            order to match the generic (and evade .local(..)).
558    
559            * R/dsCMatrix.R: dgC -> dsC: use C code!
560    
561            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
562            as per TODO
563    
564            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
565    
566            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
567    
568    
569    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
572    
573            * R/Auxiliaries.R (non0.i): take out of non0ind
574    
575            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
576            make tril(), triu(), band() work for "matrix" and all "dense*"
577    
578            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
579            * tests/simple.R: test the fix above
580    
581            * R/sparseMatrix.R ([): simplification: no coerce to <general>
582                    before we use as(., <Tsparse>)[...] anyway
583    
584            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
585    
586            * R/triangularMatrix.R (isTriangular): methods for all subclasses
587            instead of "triangularMatrix" -- just to disambiguate
588    
589    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
590    
591            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
592            * tests/indexing.R: example that fails above
593    
594    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
597            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
598                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
599    
600            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
601            * src/Tsparse.h, init.c: ditto
602            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
603                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
604            * R/sparseMatrix.R (isTriangular): hence simplified
605    
606    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * R/Ops.R (.Arith.Csparse): new utility factored out of former
609              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
610    
611    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
614    
615            * inst/test-tools.R (isOrthogonal): new function; also file restructured
616    
617    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
620            coercion to "nMatrix" and "pMatrix"
621    
622            * R/AllClass.R: "Schur" class;  "number" class union
623            * man/number-class.Rd:
624            * man/Schur-class.Rd:
625    
626            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
627            (.simpleSchur): Schur() method for diagonal matrices
628            (.triSchur):    Schur() method for triangular matrices
629            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
630    
631    
632    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
635    
636    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
639                    in order to ensure 'system = *' is not lost;
640                    formals()$system instead of cut&paste.
641            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
642    
643    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * DESCRIPTION (Date): make ready for release --> 0.999375-4
646    
647            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
648    
649    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
652                    and hence does as.vector(.).
653            * man/pMatrix-class.Rd: docs
654            * R/sparseMatrix.R: fix for printing "integer sparse"
655    
656            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
657    
658            * R/Matrix.R and others: use "exact" function argument list for
659                    both "["   : (x, i,j, ..., drop)
660                    and  "[<-" : (x, i,j, ..., value)
661    
662            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
663            * R/Tsparse.R (replTmat):    ditto
664            * R/diagMatrix.R (replDiag): ditto
665            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
666            * tests/indexing.R: testing the above
667    
668    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * R/sparseMatrix.R (cov2cor): method for sparse matrices
671    
672            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
673    
674            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
675    
676            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
677    
678    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
679    
680            * R/Matrix.R: "generic" cov2cor() method
681    
682            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
683                    speed up Q %*% D %*% t(Q)
684            * tests/dpoMatrix.R: test nearPD()
685    
686    2007-12-05  Doug Bates and Martin Maechler
687    
688            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
689            stats::xtabs() allowing to create sparse matrices.
690    
691    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
692    
693            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
694    
695    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
698    
699    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
700    
701            * R/LU.R: solve() method for "denseLU"
702    
703    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * DESCRIPTION (Version): 0.999375-3 preparing for release
706    
707            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
708    
709            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
710    
711    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
712    
713            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
714              thanks to Kasper Kristensen.
715            * tests/matprod.R: regression test for that.
716    
717    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
718    
719            * [r4778] R/AllGeneric.R: Check R version before defining generics for
720              primitives
721    
722    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/denseMatrix.R (rcond): method
725            * R/sparseQR.R (rcond): method, use x or t(x)
726    
727    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
730            matrices.
731            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
732    
733            * man/rcond.Rd: mention the more general definition, and add
734            example for non-square matrices.
735    
736            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
737    
738    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
741    
742    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
745            * tests/indexing.R: add new regression for the above cases.
746    
747    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * src/Mutils.h (__sun): clause for alloca.h on Solaris
750    
751    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
752    
753            * DESCRIPTION (Date, Version): 0.999375-2
754    
755    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
756    
757            * R/HBMM.R (readMM): make work for pattern matrices as well
758    
759    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
760    
761            * [r4730] src/Mutils.h: declare alloca
762            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
763              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
764              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
765              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
766              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
767              methods; switch writeMM to use CHOLMOD code; repair readMM
768    
769    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
770    
771            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
772            Oehlschlaegel's ... result type still to be discussed!
773    
774    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * man/image-methods.Rd: new, combining all image() methods
777    
778    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
781            to work via dgC...
782    
783            * R/Matrix.R (Matrix): special treatment for "table" (S3)
784    
785    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/dgTMatrix.R (image): change defaults to
788                    aspect = "iso", colorkey = FALSE
789    
790    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
793            must copy its *expanded* x slot before LAPACK call.
794    
795            * tests/matprod.R: test the last days' changes.
796    
797    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
798    
799            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
800              as well as in sources
801            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
802              Lapack call
803    
804    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
807                    ("Matrix", "matrix") which is needed in some cases.
808            Ditto for solve().
809    
810            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
811            infinite recursion in dispatch for some cases.
812    
813    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
814    
815            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
816              so pointers match
817    
818    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * DESCRIPTION (Date): set ready for release -- 0.999375-1
821    
822    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
823    
824            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
825              src/chm_common.c, src/chm_common.h: Change API for
826              numeric_as_chm_dense and N_AS_CHM_DN
827    
828    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
831            * tests/matprod.R: regr.test for it
832    
833    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
836            * tests/group-methods.R: and regression-test it
837    
838    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
839    
840            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
841              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
842              triplet_to_sparse, documentation, use typedefs
843    
844    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * man/dpoMatrix-class.Rd: added 'corMatrix' example
847    
848            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
849            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
850            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
851    
852            * R/lsparseMatrix.R: bug fix in "all" method
853            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
854    
855            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
856            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
857                    + matrix |-> nMatrix coercion
858            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
859            * man/pMatrix-class.Rd: ditto
860    
861            * R/Matrix.R (Summary): method for non-dMatrix
862    
863            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
864            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
865                    test all Summary methods.
866    
867    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
868    
869            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
870    
871    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
872    
873            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
874    
875            * R/pMatrix.R (t?crossprod): methods for pMatrix
876    
877    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
878    
879            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
880    
881    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
882    
883            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
884              trying to fix a subtle bug - which has been somewhere else.
885    
886    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
887    
888            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
889              solve the bug
890    
891    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * src/dgCMatrix.c (compressed_to_TMatrix):
894    
895    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * src/Csparse.c (Rsparse_validate): new, to have some validity
898            checking for RsparseMatrix
899            * src/dgCMatrix.c (xRMatrix_validate): ditto
900            * src/dtCMatrix.c (tRMatrix_validate): ditto
901    
902    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
903    
904            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
905              lgRMatrix
906            * [r4568] DESCRIPTION: Prepare for bug-fix release
907            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
908              for declaration of cholmod_symmetry
909    
910    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
913            release.
914    
915    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
916    
917            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
918              functions - no longer used
919            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
920              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
921              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
922              Alloca
923    
924    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
925    
926            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
927              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
928              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
929              src/t_gCMatrix_colSums.c: more R_CheckStack()s
930    
931    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
932    
933            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
934              the required amount of memory then call M_numeric_as_chm_dense.
935            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
936              (like Calloc but calling alloca)
937    
938    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
941            and extended with more sophisticated 'col.names' option.
942            * NAMESPACE: export  printSparseMatrix()
943            * man/printSpMatrix.Rd: document, incl. examples
944    
945    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
946    
947            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
948              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
949              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
950    
951    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
952    
953            * DESCRIPTION (Version): 0.99875-4
954    
955            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
956            some dimnames perservation.
957    
958            * R/dsTMatrix.R (t-method): keep dimnames
959            * R/dtTMatrix.R:  ditto
960    
961            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
962            and ncol(.) < 10
963    
964            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
965            from Mutils.h
966    
967            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
968            e.g. in as(<ngCMatrix>, "matrix")
969    
970    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
971    
972            * [r4529] .: Create a branch for the API changes from the 0.99875
973              series to the 0.999375 series
974            * [r4530] DESCRIPTION, inst/include/Matrix.h,
975              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
976              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
977              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
978              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
979              as_cholmod_x functions
980    
981    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
982    
983            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
984              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
985              to Comparisons
986    
987    >>>>>>> .merge-right.r4561
988    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
989    
990            * DESCRIPTION (Version): 0.99875-3 ready to be released.
991    
992            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
993    
994            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
995            that should also work in a future version of R.
996    
997    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
998    
999            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1000    
1001            * R/sparseVector.R: more *sparseVector coercions, notably for
1002            non - double ones.
1003    
1004    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1007              notably the new ones building on the new .Call(.)s:
1008    
1009            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1010            all 4 of [dlin]gCMatrix_colSums().
1011    
1012    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1013    
1014            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1015            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1016              result
1017    
1018    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1019    
1020            * R/kronecker.R: fix typo (could lead to inf.recursion)
1021            * test/simple.R: testing that
1022    
1023            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1024            method as well (which can have arguments, show() can't).
1025    
1026    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1027    
1028            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1029              added dgCMatrix_colSums for [col,row][Sums,Means]
1030    
1031    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1032    
1033            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1034              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1035              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1036            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1037              class
1038            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1039              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1040              row names to store the levels - duh!  Added an example.
1041    
1042    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1045            thanks to example from Christian Buchta; with a test here:
1046            * tests/simple.R:
1047    
1048    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1049    
1050            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1051            of colSums(*, sparseResult = TRUE)
1052    
1053    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1054    
1055            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1056            'na.rm = FALSE' as "everywhere" else in R.
1057    
1058    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1059    
1060            * [r4421] src/CSparse_install.sh: Modify for new organization of
1061              CSparse package
1062            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1063              SuiteSparse
1064            * [r4426] src/Makefile: add ./UFconfig to the include path for
1065              compilation
1066            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1067            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1068              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1069    
1070    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1071    
1072            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1073            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1074            suppressed column names.
1075    
1076    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1077    
1078            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1079              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1080              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1081              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1082              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1083              Remove warnings after change to const char* CHAR
1084    
1085    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1086    
1087            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1088              type of M_cholmod_ssmult
1089    
1090    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1091    
1092            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1093              src/init.c: Yet another cholmod export - cholmod_ssmult
1094    
1095    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * NAMESPACE: exported drop0(), since
1098            * man/drop0.Rd: I have seen several cases, I really wanted to use
1099            it, so our users may want too.
1100    
1101    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1102    
1103            * man/colSums.Rd: separately document colSums() etc, since these
1104            have the extra argument 'sparseResult'.
1105    
1106    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1107    
1108            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1109            * man/spMatrix.Rd: docu., including examples
1110    
1111            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1112            in order to make colMeans() etc fast *and* correct.
1113            * R/sparseVector.R (replSPvec): "[<-" functionality for
1114            sparseVectors; tested in
1115            * tests/simple.R:
1116    
1117    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1118    
1119            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1120            (very) sparse Matrices; output similar to Matlab's print().
1121    
1122    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1123    
1124            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1125            0-based, indices (Jose Quesada <quesada@gmail.com>).
1126    
1127    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1128    
1129            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1130    
1131    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1132    
1133            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1134            tapply1() for large sparse matrices.
1135    
1136    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1137    
1138            * R/Matrix.R (dim<-): reshape now via sparseVector.
1139    
1140            * R/sparseVector.R: methods and function for
1141            * R/AllClass.R: new "sparseVector" class and daughters.
1142            * NAMESPACE: export new classes
1143    
1144    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1145    
1146            * DESCRIPTION (Version): 0.99875-1
1147            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1148    
1149    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1152            indexing
1153            * tests/indexing.R: test set for that.
1154    
1155    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1156    
1157            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1158            entries.
1159            * tests/indexing.R(out): add regression test for it
1160    
1161    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1162    
1163            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1164            name for "!" method definitions.
1165    
1166    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/Tsparse.R (intI): new utility, used for "[" :
1169                    Cleanup up there, and fixes for duplicated indices - more TODO!
1170    
1171            * tests/indexing.R(out): more tests
1172    
1173    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1174    
1175            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1176            code that is now part of the R Lapack library.
1177    
1178            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1179            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1180    
1181    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1182    
1183            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1184    
1185    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1186    
1187            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1188            up with extraneous names '0'...'<n-1>'
1189    
1190    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1191    
1192            * R/dgTMatrix.R (mat2dgT): care about NAs
1193    
1194    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1195    
1196            * R/kronecker.R: triangularity preserving methods
1197    
1198    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1199    
1200            * R/kronecker.R: new file collecting kronecker() methods in one
1201                    place.  Goal: become much faster!
1202    
1203    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1204    
1205            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1206            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1207            can be much faster.
1208    
1209            * tests/matprod.R: add regression tests for these (upper & lower).
1210    
1211    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1212    
1213            * R/Matrix.R (diff): method for our Matrices.
1214    
1215            * R/sparseMatrix.R (isDiagonal): check dim()!
1216    
1217    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1218    
1219            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1220            proposal from Tamas Papp.
1221    
1222    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1223    
1224            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1225    
1226            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1227            rather define and export  cBind() and rBind() only.
1228            --> useRs *must* change code that used to have cbind()/rbind() !!
1229    
1230            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1231            * R/bind.Rout.save: ditto
1232    
1233    2007-02-16  Douglas Bates  <bates@r-project.org>
1234    
1235            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1236            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1237            const modifier on declaration of the array 'valid'
1238    
1239    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1240    
1241            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1242    
1243    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1244    
1245            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1246    
1247            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1248            * tests/simple.R: test the above and some of these coercions:
1249    
1250            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1251                    be careful to avoid infinite recursion, using new coercions in
1252            * R/ngCMatrix.R and nsC... and ntC...
1253            * R/lsparseMatrix.R: ditto
1254    
1255            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1256    
1257            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1258            * R/Rsparse.R: reactivate .Call()s
1259    
1260            * tests/Class+Meth.R: a bit more on actual classes
1261    
1262    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1263    
1264            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1265    
1266    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1267    
1268            * DESCRIPTION (Version): 0.9975-10 to upload
1269    
1270            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1271            specific classes less unconditionally.
1272    
1273            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1274    
1275            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1276    
1277            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1278            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1279            R_to_CMatrix segfaults on one platform.
1280            Eliminate most coercion method to *specific* classes, and replace
1281            with virtual classes coercions.
1282    
1283    
1284    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1285    
1286            * src/init.c: export the CHM...._validate() placeholders, since
1287            they *are* called.
1288    
1289            * tests/Class+Meth.R (classCanCoerce): and starting to test
1290            all as(<from>, <to>)
1291    
1292    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1293    
1294            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1295            * tests/indexing.R: tested now
1296            * tests/indexing.Rout.save: updated
1297    
1298            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1299            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1300            appropriate.
1301    
1302            * NAMESPACE: export a trivial
1303            * R/Matrix.R: drop() Matrix-method
1304    
1305            * R/AllClass.R: moved all prototypes to virtual super classes.
1306    
1307            * R/Rsparse.R: many more coercions to have less exceptions in
1308            * tests/Class+Meth.R:
1309    
1310            * R/Ops.R (Compare): tweak for case with NA
1311            * tests/simpl.R: hence another 'FIXME' eliminated
1312    
1313    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1314    
1315            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1316            objects.
1317    
1318            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1319              and more of "!", "&", "|", all, any; coercions
1320    
1321            * R/Rsparse.R: many coercions (which enable quite a few other
1322            methods), thanks to enhancements in
1323            * src/dgCMatrix.c (R_to_CMatrix): new, and
1324            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1325            symmetric & triangular and ..RMatrix objects.
1326    
1327            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1328            renamed file from src/dsTMatrix.c;
1329            now dealing with symmetric and triangular Tsparse coercions, both
1330            to dense and general.
1331    
1332    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1333    
1334            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1335    
1336            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1337            where sensible when the <numeric> is of length > 1.
1338    
1339    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1340    
1341            * R/Matrix.R ([<-): for M[] <- value: fix length
1342    
1343    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1344    
1345            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1346            * R/ndenseMatrix.R: new coercions n* -> l*
1347    
1348    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1349    
1350            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1351    
1352            * R/Ops.R ("Logic"): and other "Ops", many updates
1353    
1354    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1355    
1356            * src/Mutils.h (SET_DimNames): new utility
1357    
1358            * R/Auxiliaries.R (nnzero): improved and now exported via
1359    
1360            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1361    
1362    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1363    
1364            * R/diagMatrix.R (!): fix typo.
1365    
1366    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1367    
1368            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1369                    allow to pass class definition --> speedup
1370            * R/sparseMatrix.R: apply the above
1371    
1372            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1373    
1374            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1375            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1376            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1377    
1378            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1379    
1380            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1381            and use it for "sparse*" as well, since it's faster than the
1382            as_Csparse(.) way.
1383    
1384    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1385    
1386            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1387    
1388    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1391            as method for   M[ ij ] <- v
1392            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1393    
1394            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1395            FALSE answer
1396    
1397            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1398            * tests/indexing.R: test it, and some of the above
1399    
1400    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1401    
1402            * R/Auxiliaries.R (is_duplicatedT): new utility
1403    
1404    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1405    
1406            * src/init.c (R_init_Matrix): export cholmod_scale
1407    
1408    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1409    
1410            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1411            base::as.matrix to (x, ...)
1412    
1413    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1414    
1415            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1416            file; start using "Logic", hence
1417    
1418            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1419            * NAMESPACE: import and export "Logic"
1420    
1421    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1422    
1423            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1424            only needed previously to R version 2.5.0.
1425    
1426    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1427    
1428            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1429    
1430            * R/Tsparse.R (replTmat): fix subassignment of triangular
1431            * R/Csparse.R (replCmat): ditto
1432            * tests/indexing.R: more tests, incl the above fix
1433    
1434    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1435    
1436            * R/Auxiliaries.R (drop0): extend for non CSparse
1437            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1438    
1439            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1440                    use uplo correctly (!); other places: use uplo_P() macro
1441    
1442            * R/Csparse.R (replCmat): call diagU2N() when needed
1443            * R/Tsparse.R (replTmat): ditto
1444    
1445            * src/dtCMatrix.c (tCMatrix_validate): new
1446            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1447            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1448    
1449            * R/diagMatrix.R (replDiag): to use in [<-
1450    
1451    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1452    
1453            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1454                    also more general diagU2N().
1455    
1456    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1457    
1458            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1459            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1460    
1461    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1462    
1463            * tests/bind.R: a few more cases
1464            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1465    
1466            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1467            * R/ddenseMatrix.R (cbind2/rbind2)
1468            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1469            * tests/indexing.R
1470            * tests/indexing.Rout.save: updated
1471    
1472    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1473    
1474            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1475            * tests/indexing.R
1476    
1477    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1478    
1479            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1480            align with proper position of "0", i.e., right for integers.
1481            argument 'align' by default is "fancy".
1482    
1483    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1484    
1485            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1486            * R/Csparse.R: and fix "Compare" for more cases.
1487            * tests/Class+Meth.R: test some of these (m == m, m != m)
1488    
1489    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1490    
1491            * R/lsparseMatrix.R: all() and any() methods
1492            * R/ldenseMatrix.R:      ditto
1493            * NAMESPACE, R/Matrix.R: ditto
1494    
1495            * man/all-methods.Rd: document them minimally
1496    
1497            * tests/simple.R: add a few examples for these
1498    
1499    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1500    
1501            * R/Tsparse.R ([): fix long standing typo in symmetric case
1502            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1503    
1504    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1505    
1506            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1507            to LL before converting to a sparse matrix. (The LDL form can be
1508            converted to a sparse matrix but it is implicitly a unit
1509            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1510    
1511    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1512    
1513            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1514    
1515    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1516    
1517            * DESCRIPTION (Version): updated -> release 0.9975-7
1518            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1519    
1520    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1521    
1522            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1523    
1524    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1525    
1526            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1527            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1528            is exactly singular.
1529    
1530    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1531    
1532            * DESCRIPTION (Date): updated -> release 0.9975-6
1533    
1534    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1535    
1536            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1537            now returns symmetric.
1538    
1539            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1540    
1541            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1542            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1543    
1544            * R/Auxiliaries.R (.type.kind): added
1545    
1546    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1547    
1548            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1549            running src/CSparse_install.sh
1550    
1551            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1552    
1553    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1554    
1555            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1556            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1557    
1558            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1559    
1560            * tests/Class+Meth.R (tstMatrixClass): now assure
1561            the (important in method programming) property :
1562    
1563                    ###>>  Every "Matrix" is either
1564                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1565    
1566                    (where "*" stands for "Matrix")
1567    
1568            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1569    
1570            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1571            * tests/validObj.R: checks for "comparison"
1572    
1573            * R/sparseMatrix.R ([): improved indexing for sparse;
1574                    trying to keep <symmetric>[ n, n] symmmetric
1575    
1576            * tests/indexing.R: indexing for logical sparse now ok
1577    
1578    
1579    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1580    
1581            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1582    
1583            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1584    
1585    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1586    
1587            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1588    
1589            * tests/simple.R: validObject() checking the above.
1590    
1591            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1592            replacing both dgCMatrix_validate and lgCM*.
1593    
1594            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1595            fix dimnames setting in other places.
1596            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1597    
1598    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1599    
1600            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1601    
1602            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1603            symmetry test, via
1604            * R/Auxiliaries.R (.as.dgC.0.factors):
1605    
1606    2006-11-01  Douglas Bates  <bates@r-project.org>
1607    
1608            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1609            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1610            <CsparseMatrix>) added
1611    
1612    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1613    
1614            * tests/matprod.R: add a variation of Harri's example
1615    
1616            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1617            recursive infinitely.
1618    
1619            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1620    
1621            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1622    
1623    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1624    
1625            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1626            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1627            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1628            satisfy the above test.
1629    
1630    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1631    
1632            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1633    
1634            * R/dgCMatrix.R: solve(a, b="missing") based on
1635            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1636            RHS = NULL.
1637    
1638            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1639            add more (needed) [t]crossprod() methods.
1640    
1641            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1642    
1643            * R/Auxiliaries.R (as_CspClass): cleanup
1644            (drop0): internal utility for "Csparse_drop(*, 0)"
1645            (.bail.out.2): encourage active feedback
1646    
1647    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1648    
1649            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1650    
1651            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1652            non-valid or 'sorted' case).
1653    
1654            * R/dsparseMatrix.R: add "chol" method.
1655            * R/ddenseMatrix.R: ditto
1656    
1657            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1658            * NAMESPACE (Ops)
1659            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1660            coercion; deprecating direct lower level coercions.
1661    
1662            * R/*.R (seq): use seq_len() and seq_along() where possible.
1663    
1664    
1665    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1666    
1667            * DESCRIPTION (Version): 0.9975-5 ready for release
1668    
1669    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1670    
1671            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1672    
1673    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1674    
1675            * R/AllClass.R (corMatrix): add 'validity' check;
1676                    comment out unused "LDL" class definition
1677            * NAMESPACE: mention, but do not export "LDL" class
1678            * R/corMatrix.R: new (simple), needed for R-devel with
1679            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1680              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1681    
1682    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1683    
1684            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1685            use Rprintf and R's error handling.
1686    
1687    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1688    
1689            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1690            * tests/matprod.R: add tests for the bug fixed.
1691    
1692  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>  2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1693    
1694          * src/HBMM.[ch]: remove HarwellBoeing format for writing.          * src/HBMM.[ch]: remove HarwellBoeing format for writing.
# Line 5  Line 1696 
1696    
1697  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>  2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1698    
1699          * R/dgCMatrix.R: deprecate the writeHB function.  Use writeMM instead.          * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1700    
1701  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1702    

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