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revision 1577, Mon Sep 18 21:01:45 2006 UTC revision 2244, Sat Aug 23 18:09:51 2008 UTC
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1    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
4              documentation for CHMfactor class
5            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
6              pMatrix
7    
8    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
11    
12    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
15            variable assignments {from "next version" codetools}.
16            * R/Csparse.R, R/Tsparse.R: ditto
17    
18    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/sparseVector.R (sp2vec, coerce to sparseVector):
21            make sure no integer overflows happen, and use double precision
22            (n, index) where appropriate.
23    
24            * tests/Simple.R: test "large" sparse vectors.
25    
26    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
29            just integer (allowing much longer length).
30    
31    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
34            "denseMatrix".  This renders "scarceMatrix" dispensable and
35            invalidates part of MM's presentations on "space of Matrix
36            classes", but seems cleaner overall.
37    
38            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
39            "sparseMatrix" in method signatures;
40            further, instead of coercing to "sparseMatrix", coerce to
41            "TsparseMatrix" now.
42    
43    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
46            .Call(.)
47            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
48    
49    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
52            recursion in new test in
53            * tests/matprod.R: testing the above and another solve() case, below
54    
55            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
56            e.g. triangular 'x'.
57    
58            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
59            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
60            correctly with unit-triangular x
61    
62            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
63            instead of not checking diagU.
64    
65            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
66            experiments where diagonalMatrix would extend sparse*.
67    
68    
69    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
72            "x@p[ncol(x)]" instead of length(x@i).
73            * R/Auxiliaries.R (nnzero): ditto
74    
75            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
76            since that fails for over-allocated i.
77    
78            * tests/validObj.R: more testing of over-allocated (i,x) slots
79    
80    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
83            'sort_in_place' and set it to TRUE in call from
84            * src/Csparse.c (Csparse_validate): sort in place, making sure that
85            validObject() continues sort the columns if needed.
86    
87            * tests/validObj.R: now tests that more thoroughly, and
88            * man/CsparseMatrix-class.Rd: documents it.
89    
90    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
91    
92            * [r2233] src/chm_common.c: sort columns more carefully in
93              as_cholmod_sparse
94            * [r2231] src/chm_common.c: check for sorted columns in
95              as_cholmod_sparse instead of assuming it
96            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
97              expanding diagonal
98    
99    
100    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
103            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
104            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
105            diagU2N().
106    
107            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
108            .spDiagonal() and new .trDiagonal().
109    
110            * R/dtCMatrix.R (solve): make use of .trDiagonal()
111    
112    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
115            stumbled upon by Michael H.
116    
117            * tests/validObj.R: testing the bug-fix
118    
119            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
120            versions.
121    
122            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
123            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
124    
125            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
126              AS_CHM_SP() which includes diagU2N.
127    
128            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
129            adapt to 3 arguments.
130    
131    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
132    
133            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
134              dtCMatrix_sparse_solve
135            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
136              storage
137            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
138              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
139              new solve method
140            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
141              Csparse_diagU2N functionality into Matrix_as_cs
142    
143    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
146    
147    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
148    
149            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
150              argument with default TRUE
151            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
152              Csparse_diagU2N
153            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
154              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
155              parent array; new solve method for signature(a = "dtCMatrix", b =
156              "sparseMatrix")
157    
158    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/diagMatrix.R (.bdiag): also keep result triangular
161    
162    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
163    
164            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
165              messages
166    
167    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
170            symmetric- or nsparse-Matrix, also fixing the bug introduced with
171            the new version (.999375-10).
172    
173            * tests/Simple.R: regression test for the bugs.
174    
175    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
176    
177            * R/sparseVector.R (spV2M): fix for "isparseVector".
178            Further, fix <diag> -> <sparseVector> coercion
179            (repSpV): add rep(<sparseVector>, .) method
180    
181            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
182            use as.vector(.).
183    
184            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
185    
186            * R/AllClass.R: new (hidden) class union "scarceMatrix"
187            * R/AllClass.R: sparseVector: add prototype
188    
189            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
190            Kasper Kristensen
191    
192    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * tests/other-pkgs.R: add more interesting Matrix -> graph
195    
196    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
197    
198            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
199            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
200    
201    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
202    
203            * DESCRIPTION: release 0.999375-10 to CRAN
204    
205            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
206            .bdiag().
207            * man/bdiag.Rd: update, including test.
208    
209    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * tests/Simple.R: add minimal bdiag() checks
212    
213            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
214              factor out the Tsparse - internal computation into new .bdiag()
215    
216    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/nsparseMatrix.R: specific fast all() and any() methods.
219    
220            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
221            when trying to produce too large result.
222    
223            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
224            very large matrices.
225    
226            * R/sparseMatrix.R (printSpMatrix2): new function, used by
227            show(<sparseMatrix>).
228    
229            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
230    
231    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
232    
233            * src/Mutils.c (m_encodeInd, m_encodeInd2):
234            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
235    
236            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
237            big matrices): -> 2nd argument 'di' instead of 'nr' !
238    
239    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dtCMatrix.R: faster dgC* -> dtC* method
242            * tests/Simple.R: (hence removed "FIXME")
243    
244            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
245            which can be be turned off for possible speed gains.
246    
247    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
248    
249            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
250    
251            * R/not.R: fix !<ldiMatrix>
252            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
253    
254            * R/diagMatrix.R (Ops): fix one-off thinko in
255            <diagonal> o <numeric> methods
256    
257            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
258    
259    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
262            * tests/Simple.R: testing the above
263    
264    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
267    
268    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
271            * NAMESPACE (unname): finally exported
272    
273    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/Auxiliaries.R (cholMat): possibly keep packed
276    
277            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
278            for R < 2.7.0.
279    
280            * R/Tsparse.R ([): for triangularMatrix, check if result may be
281            triangular.
282            * tests/indexing.R: regression test
283    
284    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
287            * R/Ops.R: more methods, for lMatrix/nMatrix
288    
289    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/expm.R: new file for all expm() methods; notably new ones for
292            diagonal*, triangular*, symmetric* and also simple "matrix".
293    
294    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
297    
298            * inst/test-tools.R (assert.EQ.mat): better message when not equal
299    
300            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
301    
302            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
303            [dl]denseMatrix {identical slots; but more logical method dispatch}
304    
305    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
308    
309            * R/diagMatrix.R (determinant): method
310    
311    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
314    
315            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
316    
317            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
318            its diagonal
319    
320    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
323    
324            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
325    
326            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
327    
328            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
329    
330    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
331    
332            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
333    
334            * R/Ops.R (.do.Logic.lsparse): fix NA case
335    
336            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
337    
338            * R/Auxiliaries.R (nnzero): fix special cases, using
339            * R/Auxiliaries.R (indDiag): new utility
340            * R/Auxiliaries.R (indTri): new argument 'diag'
341    
342            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
343    
344    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
347    
348            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
349            ".tCMatrix" triangular matrix.
350    
351            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
352            'clx' can be class *or* class representation.
353            (nnzSparse): new.
354            (non0ind): new 'xtendSymm' argument; used in
355            * R/Ops.R:
356    
357            * R/pMatrix.R: more efficient determinant() method
358    
359    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
362            * [disactivated] NAMESPACE: export(det)
363    
364            * R/diagMatrix.R (mkDiag): new substitute for diag()
365    
366            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
367            (as0, as1): new utility.
368    
369            * R/Csparse.R (diag, band): need diagU2N()
370    
371            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
372    
373            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
374    
375            * R/Ops.R (Compare): fix <nsp> o <nsp> case
376    
377            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
378    
379    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
380    
381            * R/Auxiliaries.R (signPerm): new utility for
382            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
383    
384            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
385            since we have our own error handler (and can use tryCatch() from R).
386    
387    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
390    
391            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
392            when not positive definite.
393    
394            * R/Auxiliaries.R (asTri): new auxiliary
395            (non0.i): make *much* faster for Tsparse with many non-zero
396            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
397    
398            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
399            test-tools.R , see below
400    
401            * R/dMatrix.R: fix "Summary" method: + diagU2N()
402    
403            * NAMESPACE, R/Matrix.R: add mean() method
404    
405    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
408            cold-hot colors; try *changed* default useAbs = FALSE
409            * man/image-methods.Rd:  nice examples
410    
411    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
412    
413            * inst/test-tools.R (checkMatrix): new function for modularizing part
414            of tstMatrixClass() in tests/Class+Meth.R
415    
416            * R/dsCMatrix.R: coercion from "matrix"
417            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
418    
419            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
420            add test for as(matrix(,0,0), <class>)
421    
422    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
423    
424            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
425            work as determinant(matrix(,0,0)).
426    
427            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
428            * man/sparseLU-class.Rd: ditto
429    
430            * R/dgCMatrix.R (determinant): method building on lu()
431            * R/sparseMatrix.R, Matrix.R, ...: ditto
432    
433            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
434    
435    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
436    
437            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
438            pattern matrices.
439    
440    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * src/dense.c (dense_to_Csparse): all declarations *before*
443            R_CheckStack(); needed e.g. for ancient gcc 2.96.
444    
445    
446    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
447    
448            * DESCRIPTION (Version): 0.999375-9 --- need to release
449            for R-devel (and R 2.7.0 alpha soon).
450    
451            * R/AllClass.R: drop "double" from "atomicVector" class union
452    
453            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
454            * R/dgeMatrix.R: ditto
455    
456            * R/sparseMatrix.R (summary): count NAs
457    
458            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
459    
460    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
461    
462            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
463            order to become compatible to new R 2.7.0 base::rcond().
464    
465    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
468    
469            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
470    
471            * inst/test-tools.R (isValid): new utility, used much in
472            * tests/simple.R:
473    
474            * man/BunchKaufman-methods.Rd: added too
475    
476    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/dsyMatrix.R: add BunchKaufman() methods.
479            * R/dspMatrix.R:
480    
481            * src/init.c: add dsyMatrix_trf
482    
483    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
484    
485            * DESCRIPTION (Version): release 0.999375-7
486            * src/CHMfactor.c (CHMfactor_update): fix
487    
488    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
491            internal_chm_factor().
492    
493            * R/AllGeneric.R: do *not* define a "chol" generic
494                    (but rather use the implicit one *without* making pivot
495                    part of the signature)
496            * R/*.R: drop the 'pivot' from chol's signature and make
497                    'pivot=FALSE' a default argument of method definitions.
498    
499            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
500            version of Matrix
501    
502    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
503    
504            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
505    
506            * R/sparseMatrix.R (is.na): new simple method
507            * R/denseMatrix.R (is.na): ditto.
508    
509            * R/diagMatrix.R (.symDiagonal): newly exported utility.
510    
511            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
512    
513            * src/UFsparse_download.sh: -->
514            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
515    
516    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
519            functionality; barely tested in
520            * tests/factorizing.R
521    
522            * src/Csparse.c (diag_tC): new functionality to enable faster
523            determinant(<dsCMatrix>, .) in
524            * R/dsCMatrix.R
525    
526    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
527    
528            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
529              src/CHMfactor.c, src/CHMfactor.h,
530              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
531              Log-determinant of the parent matrix from a CHMfactor object as
532              chm_factor_ldetL2; documentation and support
533    
534    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
537    
538    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
539    
540            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
541            warning.
542    
543    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
544    
545            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
546    
547            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
548              <diagonal> o <sparse_triangular>
549              setAs(., "nMatrix") added.
550    
551            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
552    
553            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
554                    new argument 'checkDense = FALSE'.
555    
556    
557    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
560            back-permutation of the matrix exponential.
561    
562            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
563    
564            * DESCRIPTION (Date,Version): ready to release 0.999375-5
565    
566            * tests/simple.R: testing diagN2U
567    
568    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/Auxiliaries.R (diagN2U): interface to
571    
572            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
573    
574            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
575    
576    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
577    
578            * src/chm_common.c (chm_diagN2U): new utility.
579    
580            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
581            make use of chm_diagN2U() and hence now preserve triangularity and
582            unit-triangularity.
583    
584            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
585    
586    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
589    
590            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
591            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
592    
593            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
594    
595            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
596    
597            * src/chm_common.c (AS_CHM_FINISH): add note about problem
598            for triangular (diag = "U").
599    
600    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
603            * R/bind.R:  .Call(dense_to_Csparse, *)
604    
605    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * R/Matrix.R (Matrix): no longer use coercions to specific classes
608                    (since we are discouraging them in user code).
609    
610            * tests/*.R: also replaces coercions to specific classes by
611            coercions to super classes.
612    
613            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
614    
615    
616    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
619    
620            * src/dense.c (dense_band): generalized from ddense_band
621    
622            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
623              now for "denseMatrix" (instead of just "ddense*"); much
624              simplified setMethod()s for these.
625    
626            * src/dense.c (dense_to_symmetric): generalized from ddense_*
627    
628    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
631            version of as(*, "symmetricMatric").
632    
633            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
634            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
635    
636    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
637    
638            * R/Matrix.R (subset.ij): utility, as first step to faster
639               M [ <ij-matrix> ] indexing.
640    
641            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
642    
643            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
644            for more efficient symmpart() and skewpart() methods.
645    
646            * src/Mutils.c (equal_string_vectors): utility
647    
648            * src/dense.c (ddense_to_symmetric): new function used in
649    
650            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
651    
652            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
653            order to match the generic (and evade .local(..)).
654    
655            * R/dsCMatrix.R: dgC -> dsC: use C code!
656    
657            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
658            as per TODO
659    
660            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
661    
662            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
663    
664    
665    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
666    
667            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
668    
669            * R/Auxiliaries.R (non0.i): take out of non0ind
670    
671            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
672            make tril(), triu(), band() work for "matrix" and all "dense*"
673    
674            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
675            * tests/simple.R: test the fix above
676    
677            * R/sparseMatrix.R ([): simplification: no coerce to <general>
678                    before we use as(., <Tsparse>)[...] anyway
679    
680            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
681    
682            * R/triangularMatrix.R (isTriangular): methods for all subclasses
683            instead of "triangularMatrix" -- just to disambiguate
684    
685    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
688            * tests/indexing.R: example that fails above
689    
690    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
693            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
694                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
695    
696            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
697            * src/Tsparse.h, init.c: ditto
698            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
699                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
700            * R/sparseMatrix.R (isTriangular): hence simplified
701    
702    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
703    
704            * R/Ops.R (.Arith.Csparse): new utility factored out of former
705              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
706    
707    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
710    
711            * inst/test-tools.R (isOrthogonal): new function; also file restructured
712    
713    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
716            coercion to "nMatrix" and "pMatrix"
717    
718            * R/AllClass.R: "Schur" class;  "number" class union
719            * man/number-class.Rd:
720            * man/Schur-class.Rd:
721    
722            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
723            (.simpleSchur): Schur() method for diagonal matrices
724            (.triSchur):    Schur() method for triangular matrices
725            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
726    
727    
728    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
731    
732    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
735                    in order to ensure 'system = *' is not lost;
736                    formals()$system instead of cut&paste.
737            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
738    
739    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * DESCRIPTION (Date): make ready for release --> 0.999375-4
742    
743            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
744    
745    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
748                    and hence does as.vector(.).
749            * man/pMatrix-class.Rd: docs
750            * R/sparseMatrix.R: fix for printing "integer sparse"
751    
752            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
753    
754            * R/Matrix.R and others: use "exact" function argument list for
755                    both "["   : (x, i,j, ..., drop)
756                    and  "[<-" : (x, i,j, ..., value)
757    
758            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
759            * R/Tsparse.R (replTmat):    ditto
760            * R/diagMatrix.R (replDiag): ditto
761            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
762            * tests/indexing.R: testing the above
763    
764    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
765    
766            * R/sparseMatrix.R (cov2cor): method for sparse matrices
767    
768            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
769    
770            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
771    
772            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
773    
774    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
775    
776            * R/Matrix.R: "generic" cov2cor() method
777    
778            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
779                    speed up Q %*% D %*% t(Q)
780            * tests/dpoMatrix.R: test nearPD()
781    
782    2007-12-05  Doug Bates and Martin Maechler
783    
784            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
785            stats::xtabs() allowing to create sparse matrices.
786    
787    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
788    
789            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
790    
791    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
792    
793            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
794    
795    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * R/LU.R: solve() method for "denseLU"
798    
799    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
800    
801            * DESCRIPTION (Version): 0.999375-3 preparing for release
802    
803            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
804    
805            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
806    
807    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
810              thanks to Kasper Kristensen.
811            * tests/matprod.R: regression test for that.
812    
813    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
814    
815            * [r4778] R/AllGeneric.R: Check R version before defining generics for
816              primitives
817    
818    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
819    
820            * R/denseMatrix.R (rcond): method
821            * R/sparseQR.R (rcond): method, use x or t(x)
822    
823    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
824    
825            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
826            matrices.
827            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
828    
829            * man/rcond.Rd: mention the more general definition, and add
830            example for non-square matrices.
831    
832            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
833    
834    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
835    
836            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
837    
838    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
841            * tests/indexing.R: add new regression for the above cases.
842    
843    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * src/Mutils.h (__sun): clause for alloca.h on Solaris
846    
847    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * DESCRIPTION (Date, Version): 0.999375-2
850    
851    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
852    
853            * R/HBMM.R (readMM): make work for pattern matrices as well
854    
855    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
856    
857            * [r4730] src/Mutils.h: declare alloca
858            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
859              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
860              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
861              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
862              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
863              methods; switch writeMM to use CHOLMOD code; repair readMM
864    
865    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
866    
867            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
868            Oehlschlaegel's ... result type still to be discussed!
869    
870    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * man/image-methods.Rd: new, combining all image() methods
873    
874    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
877            to work via dgC...
878    
879            * R/Matrix.R (Matrix): special treatment for "table" (S3)
880    
881    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/dgTMatrix.R (image): change defaults to
884                    aspect = "iso", colorkey = FALSE
885    
886    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
887    
888            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
889            must copy its *expanded* x slot before LAPACK call.
890    
891            * tests/matprod.R: test the last days' changes.
892    
893    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
894    
895            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
896              as well as in sources
897            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
898              Lapack call
899    
900    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
901    
902            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
903                    ("Matrix", "matrix") which is needed in some cases.
904            Ditto for solve().
905    
906            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
907            infinite recursion in dispatch for some cases.
908    
909    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
910    
911            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
912              so pointers match
913    
914    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * DESCRIPTION (Date): set ready for release -- 0.999375-1
917    
918    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
919    
920            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
921              src/chm_common.c, src/chm_common.h: Change API for
922              numeric_as_chm_dense and N_AS_CHM_DN
923    
924    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
927            * tests/matprod.R: regr.test for it
928    
929    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
932            * tests/group-methods.R: and regression-test it
933    
934    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
935    
936            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
937              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
938              triplet_to_sparse, documentation, use typedefs
939    
940    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942            * man/dpoMatrix-class.Rd: added 'corMatrix' example
943    
944            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
945            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
946            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
947    
948            * R/lsparseMatrix.R: bug fix in "all" method
949            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
950    
951            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
952            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
953                    + matrix |-> nMatrix coercion
954            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
955            * man/pMatrix-class.Rd: ditto
956    
957            * R/Matrix.R (Summary): method for non-dMatrix
958    
959            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
960            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
961                    test all Summary methods.
962    
963    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
966    
967    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
968    
969            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
970    
971            * R/pMatrix.R (t?crossprod): methods for pMatrix
972    
973    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
974    
975            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
976    
977    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
978    
979            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
980              trying to fix a subtle bug - which has been somewhere else.
981    
982    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
983    
984            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
985              solve the bug
986    
987    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
988    
989            * src/dgCMatrix.c (compressed_to_TMatrix):
990    
991    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * src/Csparse.c (Rsparse_validate): new, to have some validity
994            checking for RsparseMatrix
995            * src/dgCMatrix.c (xRMatrix_validate): ditto
996            * src/dtCMatrix.c (tRMatrix_validate): ditto
997    
998    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
999    
1000            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
1001              lgRMatrix
1002            * [r4568] DESCRIPTION: Prepare for bug-fix release
1003            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
1004              for declaration of cholmod_symmetry
1005    
1006    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1007    
1008            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
1009            release.
1010    
1011    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
1012    
1013            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
1014              functions - no longer used
1015            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
1016              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
1017              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
1018              Alloca
1019    
1020    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
1021    
1022            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
1023              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
1024              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
1025              src/t_gCMatrix_colSums.c: more R_CheckStack()s
1026    
1027    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
1028    
1029            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
1030              the required amount of memory then call M_numeric_as_chm_dense.
1031            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
1032              (like Calloc but calling alloca)
1033    
1034    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1035    
1036            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
1037            and extended with more sophisticated 'col.names' option.
1038            * NAMESPACE: export  printSparseMatrix()
1039            * man/printSpMatrix.Rd: document, incl. examples
1040    
1041    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
1042    
1043            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
1044              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
1045              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
1046    
1047    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * DESCRIPTION (Version): 0.99875-4
1050    
1051            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
1052            some dimnames perservation.
1053    
1054            * R/dsTMatrix.R (t-method): keep dimnames
1055            * R/dtTMatrix.R:  ditto
1056    
1057            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
1058            and ncol(.) < 10
1059    
1060            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
1061            from Mutils.h
1062    
1063            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
1064            e.g. in as(<ngCMatrix>, "matrix")
1065    
1066    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
1067    
1068            * [r4529] .: Create a branch for the API changes from the 0.99875
1069              series to the 0.999375 series
1070            * [r4530] DESCRIPTION, inst/include/Matrix.h,
1071              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
1072              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
1073              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
1074              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
1075              as_cholmod_x functions
1076    
1077    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
1078    
1079            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
1080              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
1081              to Comparisons
1082    
1083    >>>>>>> .merge-right.r4561
1084    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * DESCRIPTION (Version): 0.99875-3 ready to be released.
1087    
1088            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
1089    
1090            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
1091            that should also work in a future version of R.
1092    
1093    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1094    
1095            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1096    
1097            * R/sparseVector.R: more *sparseVector coercions, notably for
1098            non - double ones.
1099    
1100    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1103              notably the new ones building on the new .Call(.)s:
1104    
1105            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1106            all 4 of [dlin]gCMatrix_colSums().
1107    
1108    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1109    
1110            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1111            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1112              result
1113    
1114    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1115    
1116            * R/kronecker.R: fix typo (could lead to inf.recursion)
1117            * test/simple.R: testing that
1118    
1119            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1120            method as well (which can have arguments, show() can't).
1121    
1122    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1123    
1124            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1125              added dgCMatrix_colSums for [col,row][Sums,Means]
1126    
1127    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1128    
1129            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1130              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1131              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1132            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1133              class
1134            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1135              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1136              row names to store the levels - duh!  Added an example.
1137    
1138    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1139    
1140            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1141            thanks to example from Christian Buchta; with a test here:
1142            * tests/simple.R:
1143    
1144    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1145    
1146            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1147            of colSums(*, sparseResult = TRUE)
1148    
1149    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1152            'na.rm = FALSE' as "everywhere" else in R.
1153    
1154    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1155    
1156            * [r4421] src/CSparse_install.sh: Modify for new organization of
1157              CSparse package
1158            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1159              SuiteSparse
1160            * [r4426] src/Makefile: add ./UFconfig to the include path for
1161              compilation
1162            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1163            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1164              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1165    
1166    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1167    
1168            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1169            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1170            suppressed column names.
1171    
1172    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1173    
1174            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1175              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1176              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1177              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1178              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1179              Remove warnings after change to const char* CHAR
1180    
1181    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1182    
1183            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1184              type of M_cholmod_ssmult
1185    
1186    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1187    
1188            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1189              src/init.c: Yet another cholmod export - cholmod_ssmult
1190    
1191    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1192    
1193            * NAMESPACE: exported drop0(), since
1194            * man/drop0.Rd: I have seen several cases, I really wanted to use
1195            it, so our users may want too.
1196    
1197    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * man/colSums.Rd: separately document colSums() etc, since these
1200            have the extra argument 'sparseResult'.
1201    
1202    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1203    
1204            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1205            * man/spMatrix.Rd: docu., including examples
1206    
1207            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1208            in order to make colMeans() etc fast *and* correct.
1209            * R/sparseVector.R (replSPvec): "[<-" functionality for
1210            sparseVectors; tested in
1211            * tests/simple.R:
1212    
1213    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1214    
1215            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1216            (very) sparse Matrices; output similar to Matlab's print().
1217    
1218    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1219    
1220            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1221            0-based, indices (Jose Quesada <quesada@gmail.com>).
1222    
1223    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1224    
1225            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1226    
1227    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1228    
1229            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1230            tapply1() for large sparse matrices.
1231    
1232    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1233    
1234            * R/Matrix.R (dim<-): reshape now via sparseVector.
1235    
1236            * R/sparseVector.R: methods and function for
1237            * R/AllClass.R: new "sparseVector" class and daughters.
1238            * NAMESPACE: export new classes
1239    
1240    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1241    
1242            * DESCRIPTION (Version): 0.99875-1
1243            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1244    
1245    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1246    
1247            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1248            indexing
1249            * tests/indexing.R: test set for that.
1250    
1251    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1254            entries.
1255            * tests/indexing.R(out): add regression test for it
1256    
1257    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1258    
1259            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1260            name for "!" method definitions.
1261    
1262    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1263    
1264            * R/Tsparse.R (intI): new utility, used for "[" :
1265                    Cleanup up there, and fixes for duplicated indices - more TODO!
1266    
1267            * tests/indexing.R(out): more tests
1268    
1269    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1270    
1271            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1272            code that is now part of the R Lapack library.
1273    
1274            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1275            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1276    
1277    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1278    
1279            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1280    
1281    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1282    
1283            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1284            up with extraneous names '0'...'<n-1>'
1285    
1286    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1287    
1288            * R/dgTMatrix.R (mat2dgT): care about NAs
1289    
1290    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1291    
1292            * R/kronecker.R: triangularity preserving methods
1293    
1294    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1295    
1296            * R/kronecker.R: new file collecting kronecker() methods in one
1297                    place.  Goal: become much faster!
1298    
1299    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1300    
1301            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1302            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1303            can be much faster.
1304    
1305            * tests/matprod.R: add regression tests for these (upper & lower).
1306    
1307    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1308    
1309            * R/Matrix.R (diff): method for our Matrices.
1310    
1311            * R/sparseMatrix.R (isDiagonal): check dim()!
1312    
1313    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1314    
1315            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1316            proposal from Tamas Papp.
1317    
1318    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1319    
1320            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1321    
1322            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1323            rather define and export  cBind() and rBind() only.
1324            --> useRs *must* change code that used to have cbind()/rbind() !!
1325    
1326            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1327            * R/bind.Rout.save: ditto
1328    
1329    2007-02-16  Douglas Bates  <bates@r-project.org>
1330    
1331            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1332            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1333            const modifier on declaration of the array 'valid'
1334    
1335    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1336    
1337            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1338    
1339    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1340    
1341            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1342    
1343            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1344            * tests/simple.R: test the above and some of these coercions:
1345    
1346            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1347                    be careful to avoid infinite recursion, using new coercions in
1348            * R/ngCMatrix.R and nsC... and ntC...
1349            * R/lsparseMatrix.R: ditto
1350    
1351            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1352    
1353            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1354            * R/Rsparse.R: reactivate .Call()s
1355    
1356            * tests/Class+Meth.R: a bit more on actual classes
1357    
1358    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1359    
1360            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1361    
1362    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1363    
1364            * DESCRIPTION (Version): 0.9975-10 to upload
1365    
1366            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1367            specific classes less unconditionally.
1368    
1369            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1370    
1371            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1372    
1373            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1374            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1375            R_to_CMatrix segfaults on one platform.
1376            Eliminate most coercion method to *specific* classes, and replace
1377            with virtual classes coercions.
1378    
1379    
1380    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1381    
1382            * src/init.c: export the CHM...._validate() placeholders, since
1383            they *are* called.
1384    
1385            * tests/Class+Meth.R (classCanCoerce): and starting to test
1386            all as(<from>, <to>)
1387    
1388    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1389    
1390            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1391            * tests/indexing.R: tested now
1392            * tests/indexing.Rout.save: updated
1393    
1394            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1395            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1396            appropriate.
1397    
1398            * NAMESPACE: export a trivial
1399            * R/Matrix.R: drop() Matrix-method
1400    
1401            * R/AllClass.R: moved all prototypes to virtual super classes.
1402    
1403            * R/Rsparse.R: many more coercions to have less exceptions in
1404            * tests/Class+Meth.R:
1405    
1406            * R/Ops.R (Compare): tweak for case with NA
1407            * tests/simpl.R: hence another 'FIXME' eliminated
1408    
1409    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1410    
1411            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1412            objects.
1413    
1414            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1415              and more of "!", "&", "|", all, any; coercions
1416    
1417            * R/Rsparse.R: many coercions (which enable quite a few other
1418            methods), thanks to enhancements in
1419            * src/dgCMatrix.c (R_to_CMatrix): new, and
1420            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1421            symmetric & triangular and ..RMatrix objects.
1422    
1423            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1424            renamed file from src/dsTMatrix.c;
1425            now dealing with symmetric and triangular Tsparse coercions, both
1426            to dense and general.
1427    
1428    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1431    
1432            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1433            where sensible when the <numeric> is of length > 1.
1434    
1435    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1436    
1437            * R/Matrix.R ([<-): for M[] <- value: fix length
1438    
1439    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1440    
1441            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1442            * R/ndenseMatrix.R: new coercions n* -> l*
1443    
1444    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1445    
1446            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1447    
1448            * R/Ops.R ("Logic"): and other "Ops", many updates
1449    
1450    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1451    
1452            * src/Mutils.h (SET_DimNames): new utility
1453    
1454            * R/Auxiliaries.R (nnzero): improved and now exported via
1455    
1456            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1457    
1458    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1459    
1460            * R/diagMatrix.R (!): fix typo.
1461    
1462    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1463    
1464            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1465                    allow to pass class definition --> speedup
1466            * R/sparseMatrix.R: apply the above
1467    
1468            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1469    
1470            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1471            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1472            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1473    
1474            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1475    
1476            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1477            and use it for "sparse*" as well, since it's faster than the
1478            as_Csparse(.) way.
1479    
1480    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1481    
1482            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1483    
1484    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1485    
1486            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1487            as method for   M[ ij ] <- v
1488            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1489    
1490            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1491            FALSE answer
1492    
1493            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1494            * tests/indexing.R: test it, and some of the above
1495    
1496    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1497    
1498            * R/Auxiliaries.R (is_duplicatedT): new utility
1499    
1500    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1501    
1502            * src/init.c (R_init_Matrix): export cholmod_scale
1503    
1504    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1505    
1506            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1507            base::as.matrix to (x, ...)
1508    
1509    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1510    
1511            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1512            file; start using "Logic", hence
1513    
1514            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1515            * NAMESPACE: import and export "Logic"
1516    
1517    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1518    
1519            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1520            only needed previously to R version 2.5.0.
1521    
1522    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1523    
1524            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1525    
1526            * R/Tsparse.R (replTmat): fix subassignment of triangular
1527            * R/Csparse.R (replCmat): ditto
1528            * tests/indexing.R: more tests, incl the above fix
1529    
1530    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1531    
1532            * R/Auxiliaries.R (drop0): extend for non CSparse
1533            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1534    
1535            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1536                    use uplo correctly (!); other places: use uplo_P() macro
1537    
1538            * R/Csparse.R (replCmat): call diagU2N() when needed
1539            * R/Tsparse.R (replTmat): ditto
1540    
1541            * src/dtCMatrix.c (tCMatrix_validate): new
1542            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1543            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1544    
1545            * R/diagMatrix.R (replDiag): to use in [<-
1546    
1547    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1548    
1549            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1550                    also more general diagU2N().
1551    
1552    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1553    
1554            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1555            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1556    
1557    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1558    
1559            * tests/bind.R: a few more cases
1560            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1561    
1562            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1563            * R/ddenseMatrix.R (cbind2/rbind2)
1564            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1565            * tests/indexing.R
1566            * tests/indexing.Rout.save: updated
1567    
1568    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1569    
1570            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1571            * tests/indexing.R
1572    
1573    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1574    
1575            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1576            align with proper position of "0", i.e., right for integers.
1577            argument 'align' by default is "fancy".
1578    
1579    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1580    
1581            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1582            * R/Csparse.R: and fix "Compare" for more cases.
1583            * tests/Class+Meth.R: test some of these (m == m, m != m)
1584    
1585    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1586    
1587            * R/lsparseMatrix.R: all() and any() methods
1588            * R/ldenseMatrix.R:      ditto
1589            * NAMESPACE, R/Matrix.R: ditto
1590    
1591            * man/all-methods.Rd: document them minimally
1592    
1593            * tests/simple.R: add a few examples for these
1594    
1595    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1596    
1597            * R/Tsparse.R ([): fix long standing typo in symmetric case
1598            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1599    
1600    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1601    
1602            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1603            to LL before converting to a sparse matrix. (The LDL form can be
1604            converted to a sparse matrix but it is implicitly a unit
1605            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1606    
1607    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1608    
1609            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1610    
1611    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1612    
1613            * DESCRIPTION (Version): updated -> release 0.9975-7
1614            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1615    
1616    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1617    
1618            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1619    
1620    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1621    
1622            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1623            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1624            is exactly singular.
1625    
1626    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1627    
1628            * DESCRIPTION (Date): updated -> release 0.9975-6
1629    
1630    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1631    
1632            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1633            now returns symmetric.
1634    
1635            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1636    
1637            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1638            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1639    
1640            * R/Auxiliaries.R (.type.kind): added
1641    
1642    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1643    
1644            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1645            running src/CSparse_install.sh
1646    
1647            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1648    
1649    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1650    
1651            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1652            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1653    
1654            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1655    
1656            * tests/Class+Meth.R (tstMatrixClass): now assure
1657            the (important in method programming) property :
1658    
1659                    ###>>  Every "Matrix" is either
1660                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1661    
1662                    (where "*" stands for "Matrix")
1663    
1664            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1665    
1666            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1667            * tests/validObj.R: checks for "comparison"
1668    
1669            * R/sparseMatrix.R ([): improved indexing for sparse;
1670                    trying to keep <symmetric>[ n, n] symmmetric
1671    
1672            * tests/indexing.R: indexing for logical sparse now ok
1673    
1674    
1675    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1676    
1677            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1678    
1679            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1680    
1681    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1682    
1683            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1684    
1685            * tests/simple.R: validObject() checking the above.
1686    
1687            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1688            replacing both dgCMatrix_validate and lgCM*.
1689    
1690            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1691            fix dimnames setting in other places.
1692            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1693    
1694    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1695    
1696            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1697    
1698            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1699            symmetry test, via
1700            * R/Auxiliaries.R (.as.dgC.0.factors):
1701    
1702    2006-11-01  Douglas Bates  <bates@r-project.org>
1703    
1704            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1705            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1706            <CsparseMatrix>) added
1707    
1708    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1709    
1710            * tests/matprod.R: add a variation of Harri's example
1711    
1712            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1713            recursive infinitely.
1714    
1715            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1716    
1717            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1718    
1719    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1720    
1721            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1722            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1723            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1724            satisfy the above test.
1725    
1726    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1727    
1728            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1729    
1730            * R/dgCMatrix.R: solve(a, b="missing") based on
1731            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1732            RHS = NULL.
1733    
1734            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1735            add more (needed) [t]crossprod() methods.
1736    
1737            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1738    
1739            * R/Auxiliaries.R (as_CspClass): cleanup
1740            (drop0): internal utility for "Csparse_drop(*, 0)"
1741            (.bail.out.2): encourage active feedback
1742    
1743    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1744    
1745            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1746    
1747            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1748            non-valid or 'sorted' case).
1749    
1750            * R/dsparseMatrix.R: add "chol" method.
1751            * R/ddenseMatrix.R: ditto
1752    
1753            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1754            * NAMESPACE (Ops)
1755            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1756            coercion; deprecating direct lower level coercions.
1757    
1758            * R/*.R (seq): use seq_len() and seq_along() where possible.
1759    
1760    
1761    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1762    
1763            * DESCRIPTION (Version): 0.9975-5 ready for release
1764    
1765    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1766    
1767            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1768    
1769    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1770    
1771            * R/AllClass.R (corMatrix): add 'validity' check;
1772                    comment out unused "LDL" class definition
1773            * NAMESPACE: mention, but do not export "LDL" class
1774            * R/corMatrix.R: new (simple), needed for R-devel with
1775            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1776              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1777    
1778    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1779    
1780            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1781            use Rprintf and R's error handling.
1782    
1783    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1784    
1785            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1786            * tests/matprod.R: add tests for the bug fixed.
1787    
1788    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1789    
1790            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1791            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1792    
1793    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1794    
1795            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1796    
1797    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1798    
1799            * DESCRIPTION (Version): 0.9975-3
1800    
1801            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1802            (sparse) matrices.
1803            * man/bdiag.Rd: docu + examples
1804    
1805            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1806    
1807            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1808            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1809    
1810            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1811            that result is sparse or diagonal (and not dense).
1812    
1813            * man/Subassign-methods.Rd: fix examples
1814    
1815            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1816            should always return a sparse (and not sometimes a diagonal) matrix.
1817    
1818    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1819    
1820            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1821    
1822    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1823    
1824            * DESCRIPTION (Version): 0.9975-2
1825    
1826            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1827    
1828    2006-10-02  Douglas Bates  <bates@R-project.org>
1829    
1830            * tests/dg_Matrix.R: Simplify test taking into account new code.
1831    
1832    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1833    
1834            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1835    
1836            * R/lsTMatrix.R: new files w/ missing methods
1837            * R/nsTMatrix.R:  "  'for completeness'
1838    
1839            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1840    
1841            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1842    
1843    
1844    2006-09-28  Douglas Bates  <bates@R-project.org>
1845    
1846            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1847            included.
1848    
1849            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1850            Export C-callable functions used in Zt_create in lme4.
1851    
1852    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1853    
1854            * DESCRIPTION (Version): 0.9975-1
1855    
1856            * tests/simple.R: less checks fail; using NA, found that our
1857                    kronecker() is not base-compatible with NA's.
1858    
1859            * R/dMatrix.R: "Compare" method now implemented for all cases
1860    
1861            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1862    
1863            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1864    
1865            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1866            * src/dspMatrix.c (dspMatrix_validate): ditto
1867    
1868            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1869              including coercion to [nl]tTMatrix.
1870    
1871            * R/diagMatrix.R (show): print a header line as for other classes.
1872    
1873    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1874    
1875            * src/Makefile.win (SUBDIRS): fix typo
1876    
1877    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1878    
1879            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1880    
1881  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>  2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1882    
1883          * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x          * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
# Line 54  Line 1934 
1934          * tests/: adaptions          * tests/: adaptions
1935          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
1936                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1937          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
1938    
1939  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
1940    
# Line 73  Line 1953 
1953          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1954    
1955          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1956          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
1957    
1958  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1959    
# Line 116  Line 1996 
1996    
1997          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1998          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1999          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
2000          * R/Csparse.R: dito          * R/Csparse.R: ditto
2001    
2002  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2003    
# Line 133  Line 2013 
2013    
2014          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
2015          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
2016          (.is.diagonal): dito          (.is.diagonal): ditto
2017    
2018          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
2019    

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