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revision 1852, Mon May 21 16:42:35 2007 UTC revision 2209, Mon Jul 14 19:39:39 2008 UTC
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1    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (.bdiag): also keep triangular
4    
5    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
8            symmetric- or nsparse-Matrix, also fixing the bug introduced with
9            the new version (.999375-10).
10    
11            * tests/Simple.R: regression test for the bugs.
12    
13    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
14    
15            * R/sparseVector.R (spV2M): fix for "isparseVector".
16            Further, fix <diag> -> <sparseVector> coercion
17            (repSpV): add rep(<sparseVector>, .) method
18    
19            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
20            use as.vector(.).
21    
22            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
23    
24            * R/AllClass.R: new (hidden) class union "scarceMatrix"
25            * R/AllClass.R: sparseVector: add prototype
26    
27            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
28            Kasper Kristensen
29    
30    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * tests/other-pkgs.R: add more interesting Matrix -> graph
33    
34    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
37            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
38    
39    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * DESCRIPTION: release 0.999375-10 to CRAN
42    
43            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
44            .bdiag().
45            * man/bdiag.Rd: update, including test.
46    
47    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * tests/Simple.R: add minimal bdiag() checks
50    
51            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
52              factor out the Tsparse - internal computation into new .bdiag()
53    
54    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * R/nsparseMatrix.R: specific fast all() and any() methods.
57    
58            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
59            when trying to produce too large result.
60    
61            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
62            very large matrices.
63    
64            * R/sparseMatrix.R (printSpMatrix2): new function, used by
65            show(<sparseMatrix>).
66    
67            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
68    
69    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * src/Mutils.c (m_encodeInd, m_encodeInd2):
72            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
73    
74            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
75            big matrices): -> 2nd argument 'di' instead of 'nr' !
76    
77    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * R/dtCMatrix.R: faster dgC* -> dtC* method
80            * tests/Simple.R: (hence removed "FIXME")
81    
82            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
83            which can be be turned off for possible speed gains.
84    
85    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
88    
89            * R/not.R: fix !<ldiMatrix>
90            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
91    
92            * R/diagMatrix.R (Ops): fix one-off thinko in
93            <diagonal> o <numeric> methods
94    
95            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
96    
97    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
100            * tests/Simple.R: testing the above
101    
102    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
103    
104            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
105    
106    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
109            * NAMESPACE (unname): finally exported
110    
111    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Auxiliaries.R (cholMat): possibly keep packed
114    
115            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
116            for R < 2.7.0.
117    
118            * R/Tsparse.R ([): for triangularMatrix, check if result may be
119            triangular.
120            * tests/indexing.R: regression test
121    
122    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
125            * R/Ops.R: more methods, for lMatrix/nMatrix
126    
127    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * R/expm.R: new file for all expm() methods; notably new ones for
130            diagonal*, triangular*, symmetric* and also simple "matrix".
131    
132    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
135    
136            * inst/test-tools.R (assert.EQ.mat): better message when not equal
137    
138            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
139    
140            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
141            [dl]denseMatrix {identical slots; but more logical method dispatch}
142    
143    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
146    
147            * R/diagMatrix.R (determinant): method
148    
149    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
152    
153            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
154    
155            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
156            its diagonal
157    
158    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
161    
162            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
163    
164            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
165    
166            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
167    
168    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
171    
172            * R/Ops.R (.do.Logic.lsparse): fix NA case
173    
174            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
175    
176            * R/Auxiliaries.R (nnzero): fix special cases, using
177            * R/Auxiliaries.R (indDiag): new utility
178            * R/Auxiliaries.R (indTri): new argument 'diag'
179    
180            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
181    
182    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
185    
186            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
187            ".tCMatrix" triangular matrix.
188    
189            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
190            'clx' can be class *or* class representation.
191            (nnzSparse): new.
192            (non0ind): new 'xtendSymm' argument; used in
193            * R/Ops.R:
194    
195            * R/pMatrix.R: more efficient determinant() method
196    
197    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
200            * [disactivated] NAMESPACE: export(det)
201    
202            * R/diagMatrix.R (mkDiag): new substitute for diag()
203    
204            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
205            (as0, as1): new utility.
206    
207            * R/Csparse.R (diag, band): need diagU2N()
208    
209            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
210    
211            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
212    
213            * R/Ops.R (Compare): fix <nsp> o <nsp> case
214    
215            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
216    
217    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (signPerm): new utility for
220            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
221    
222            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
223            since we have our own error handler (and can use tryCatch() from R).
224    
225    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
228    
229            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
230            when not positive definite.
231    
232            * R/Auxiliaries.R (asTri): new auxiliary
233            (non0.i): make *much* faster for Tsparse with many non-zero
234            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
235    
236            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
237            test-tools.R , see below
238    
239            * R/dMatrix.R: fix "Summary" method: + diagU2N()
240    
241            * NAMESPACE, R/Matrix.R: add mean() method
242    
243    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
246            cold-hot colors; try *changed* default useAbs = FALSE
247            * man/image-methods.Rd:  nice examples
248    
249    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * inst/test-tools.R (checkMatrix): new function for modularizing part
252            of tstMatrixClass() in tests/Class+Meth.R
253    
254            * R/dsCMatrix.R: coercion from "matrix"
255            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
256    
257            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
258            add test for as(matrix(,0,0), <class>)
259    
260    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
263            work as determinant(matrix(,0,0)).
264    
265            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
266            * man/sparseLU-class.Rd: ditto
267    
268            * R/dgCMatrix.R (determinant): method building on lu()
269            * R/sparseMatrix.R, Matrix.R, ...: ditto
270    
271            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
272    
273    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
276            pattern matrices.
277    
278    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * src/dense.c (dense_to_Csparse): all declarations *before*
281            R_CheckStack(); needed e.g. for ancient gcc 2.96.
282    
283    
284    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * DESCRIPTION (Version): 0.999375-9 --- need to release
287            for R-devel (and R 2.7.0 alpha soon).
288    
289            * R/AllClass.R: drop "double" from "atomicVector" class union
290    
291            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
292            * R/dgeMatrix.R: ditto
293    
294            * R/sparseMatrix.R (summary): count NAs
295    
296            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
297    
298    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
301            order to become compatible to new R 2.7.0 base::rcond().
302    
303    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
306    
307            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
308    
309            * inst/test-tools.R (isValid): new utility, used much in
310            * tests/simple.R:
311    
312            * man/BunchKaufman-methods.Rd: added too
313    
314    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/dsyMatrix.R: add BunchKaufman() methods.
317            * R/dspMatrix.R:
318    
319            * src/init.c: add dsyMatrix_trf
320    
321    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
322    
323            * DESCRIPTION (Version): release 0.999375-7
324            * src/CHMfactor.c (CHMfactor_update): fix
325    
326    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
329            internal_chm_factor().
330    
331            * R/AllGeneric.R: do *not* define a "chol" generic
332                    (but rather use the implicit one *without* making pivot
333                    part of the signature)
334            * R/*.R: drop the 'pivot' from chol's signature and make
335                    'pivot=FALSE' a default argument of method definitions.
336    
337            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
338            version of Matrix
339    
340    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
343    
344            * R/sparseMatrix.R (is.na): new simple method
345            * R/denseMatrix.R (is.na): ditto.
346    
347            * R/diagMatrix.R (.symDiagonal): newly exported utility.
348    
349            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
350    
351            * src/UFsparse_download.sh: -->
352            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
353    
354    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
357            functionality; barely tested in
358            * tests/factorizing.R
359    
360            * src/Csparse.c (diag_tC): new functionality to enable faster
361            determinant(<dsCMatrix>, .) in
362            * R/dsCMatrix.R
363    
364    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
365    
366            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
367              src/CHMfactor.c, src/CHMfactor.h,
368              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
369              Log-determinant of the parent matrix from a CHMfactor object as
370              chm_factor_ldetL2; documentation and support
371    
372    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
375    
376    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
379            warning.
380    
381    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
384    
385            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
386              <diagonal> o <sparse_triangular>
387              setAs(., "nMatrix") added.
388    
389            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
390    
391            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
392                    new argument 'checkDense = FALSE'.
393    
394    
395    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
398            back-permutation of the matrix exponential.
399    
400            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
401    
402            * DESCRIPTION (Date,Version): ready to release 0.999375-5
403    
404            * tests/simple.R: testing diagN2U
405    
406    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * R/Auxiliaries.R (diagN2U): interface to
409    
410            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
411    
412            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
413    
414    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/chm_common.c (chm_diagN2U): new utility.
417    
418            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
419            make use of chm_diagN2U() and hence now preserve triangularity and
420            unit-triangularity.
421    
422            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
423    
424    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
425    
426            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
427    
428            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
429            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
430    
431            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
432    
433            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
434    
435            * src/chm_common.c (AS_CHM_FINISH): add note about problem
436            for triangular (diag = "U").
437    
438    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
439    
440            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
441            * R/bind.R:  .Call(dense_to_Csparse, *)
442    
443    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
444    
445            * R/Matrix.R (Matrix): no longer use coercions to specific classes
446                    (since we are discouraging them in user code).
447    
448            * tests/*.R: also replaces coercions to specific classes by
449            coercions to super classes.
450    
451            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
452    
453    
454    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
455    
456            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
457    
458            * src/dense.c (dense_band): generalized from ddense_band
459    
460            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
461              now for "denseMatrix" (instead of just "ddense*"); much
462              simplified setMethod()s for these.
463    
464            * src/dense.c (dense_to_symmetric): generalized from ddense_*
465    
466    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
469            version of as(*, "symmetricMatric").
470    
471            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
472            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
473    
474    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * R/Matrix.R (subset.ij): utility, as first step to faster
477               M [ <ij-matrix> ] indexing.
478    
479            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
480    
481            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
482            for more efficient symmpart() and skewpart() methods.
483    
484            * src/Mutils.c (equal_string_vectors): utility
485    
486            * src/dense.c (ddense_to_symmetric): new function used in
487    
488            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
489    
490            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
491            order to match the generic (and evade .local(..)).
492    
493            * R/dsCMatrix.R: dgC -> dsC: use C code!
494    
495            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
496            as per TODO
497    
498            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
499    
500            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
501    
502    
503    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
506    
507            * R/Auxiliaries.R (non0.i): take out of non0ind
508    
509            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
510            make tril(), triu(), band() work for "matrix" and all "dense*"
511    
512            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
513            * tests/simple.R: test the fix above
514    
515            * R/sparseMatrix.R ([): simplification: no coerce to <general>
516                    before we use as(., <Tsparse>)[...] anyway
517    
518            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
519    
520            * R/triangularMatrix.R (isTriangular): methods for all subclasses
521            instead of "triangularMatrix" -- just to disambiguate
522    
523    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
526            * tests/indexing.R: example that fails above
527    
528    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
531            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
532                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
533    
534            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
535            * src/Tsparse.h, init.c: ditto
536            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
537                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
538            * R/sparseMatrix.R (isTriangular): hence simplified
539    
540    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
541    
542            * R/Ops.R (.Arith.Csparse): new utility factored out of former
543              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
544    
545    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
546    
547            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
548    
549            * inst/test-tools.R (isOrthogonal): new function; also file restructured
550    
551    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
554            coercion to "nMatrix" and "pMatrix"
555    
556            * R/AllClass.R: "Schur" class;  "number" class union
557            * man/number-class.Rd:
558            * man/Schur-class.Rd:
559    
560            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
561            (.simpleSchur): Schur() method for diagonal matrices
562            (.triSchur):    Schur() method for triangular matrices
563            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
564    
565    
566    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
569    
570    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
571    
572            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
573                    in order to ensure 'system = *' is not lost;
574                    formals()$system instead of cut&paste.
575            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
576    
577    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
578    
579            * DESCRIPTION (Date): make ready for release --> 0.999375-4
580    
581            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
582    
583    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
586                    and hence does as.vector(.).
587            * man/pMatrix-class.Rd: docs
588            * R/sparseMatrix.R: fix for printing "integer sparse"
589    
590            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
591    
592            * R/Matrix.R and others: use "exact" function argument list for
593                    both "["   : (x, i,j, ..., drop)
594                    and  "[<-" : (x, i,j, ..., value)
595    
596            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
597            * R/Tsparse.R (replTmat):    ditto
598            * R/diagMatrix.R (replDiag): ditto
599            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
600            * tests/indexing.R: testing the above
601    
602    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/sparseMatrix.R (cov2cor): method for sparse matrices
605    
606            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
607    
608            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
609    
610            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
611    
612    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * R/Matrix.R: "generic" cov2cor() method
615    
616            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
617                    speed up Q %*% D %*% t(Q)
618            * tests/dpoMatrix.R: test nearPD()
619    
620    2007-12-05  Doug Bates and Martin Maechler
621    
622            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
623            stats::xtabs() allowing to create sparse matrices.
624    
625    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
626    
627            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
628    
629    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
632    
633    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
634    
635            * R/LU.R: solve() method for "denseLU"
636    
637    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * DESCRIPTION (Version): 0.999375-3 preparing for release
640    
641            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
642    
643            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
644    
645    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
648              thanks to Kasper Kristensen.
649            * tests/matprod.R: regression test for that.
650    
651    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
652    
653            * [r4778] R/AllGeneric.R: Check R version before defining generics for
654              primitives
655    
656    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/denseMatrix.R (rcond): method
659            * R/sparseQR.R (rcond): method, use x or t(x)
660    
661    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
664            matrices.
665            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
666    
667            * man/rcond.Rd: mention the more general definition, and add
668            example for non-square matrices.
669    
670            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
671    
672    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
675    
676    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
679            * tests/indexing.R: add new regression for the above cases.
680    
681    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * src/Mutils.h (__sun): clause for alloca.h on Solaris
684    
685    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * DESCRIPTION (Date, Version): 0.999375-2
688    
689    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/HBMM.R (readMM): make work for pattern matrices as well
692    
693    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
694    
695            * [r4730] src/Mutils.h: declare alloca
696            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
697              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
698              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
699              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
700              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
701              methods; switch writeMM to use CHOLMOD code; repair readMM
702    
703    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
706            Oehlschlaegel's ... result type still to be discussed!
707    
708    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * man/image-methods.Rd: new, combining all image() methods
711    
712    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
713    
714            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
715            to work via dgC...
716    
717            * R/Matrix.R (Matrix): special treatment for "table" (S3)
718    
719    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/dgTMatrix.R (image): change defaults to
722                    aspect = "iso", colorkey = FALSE
723    
724    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
725    
726            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
727            must copy its *expanded* x slot before LAPACK call.
728    
729            * tests/matprod.R: test the last days' changes.
730    
731    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
732    
733            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
734              as well as in sources
735            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
736              Lapack call
737    
738    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
739    
740            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
741                    ("Matrix", "matrix") which is needed in some cases.
742            Ditto for solve().
743    
744            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
745            infinite recursion in dispatch for some cases.
746    
747    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
748    
749            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
750              so pointers match
751    
752    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * DESCRIPTION (Date): set ready for release -- 0.999375-1
755    
756    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
757    
758            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
759              src/chm_common.c, src/chm_common.h: Change API for
760              numeric_as_chm_dense and N_AS_CHM_DN
761    
762    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
765            * tests/matprod.R: regr.test for it
766    
767    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
768    
769            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
770            * tests/group-methods.R: and regression-test it
771    
772    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
773    
774            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
775              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
776              triplet_to_sparse, documentation, use typedefs
777    
778    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
779    
780            * man/dpoMatrix-class.Rd: added 'corMatrix' example
781    
782            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
783            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
784            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
785    
786            * R/lsparseMatrix.R: bug fix in "all" method
787            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
788    
789            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
790            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
791                    + matrix |-> nMatrix coercion
792            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
793            * man/pMatrix-class.Rd: ditto
794    
795            * R/Matrix.R (Summary): method for non-dMatrix
796    
797            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
798            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
799                    test all Summary methods.
800    
801    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
802    
803            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
804    
805    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
806    
807            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
808    
809            * R/pMatrix.R (t?crossprod): methods for pMatrix
810    
811    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
812    
813            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
814    
815    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
816    
817            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
818              trying to fix a subtle bug - which has been somewhere else.
819    
820    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
821    
822            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
823              solve the bug
824    
825    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
826    
827            * src/dgCMatrix.c (compressed_to_TMatrix):
828    
829    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * src/Csparse.c (Rsparse_validate): new, to have some validity
832            checking for RsparseMatrix
833            * src/dgCMatrix.c (xRMatrix_validate): ditto
834            * src/dtCMatrix.c (tRMatrix_validate): ditto
835    
836    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
837    
838            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
839              lgRMatrix
840            * [r4568] DESCRIPTION: Prepare for bug-fix release
841            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
842              for declaration of cholmod_symmetry
843    
844    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
845    
846            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
847            release.
848    
849    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
850    
851            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
852              functions - no longer used
853            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
854              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
855              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
856              Alloca
857    
858    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
859    
860            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
861              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
862              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
863              src/t_gCMatrix_colSums.c: more R_CheckStack()s
864    
865    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
866    
867            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
868              the required amount of memory then call M_numeric_as_chm_dense.
869            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
870              (like Calloc but calling alloca)
871    
872    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
875            and extended with more sophisticated 'col.names' option.
876            * NAMESPACE: export  printSparseMatrix()
877            * man/printSpMatrix.Rd: document, incl. examples
878    
879    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
880    
881            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
882              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
883              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
884    
885    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * DESCRIPTION (Version): 0.99875-4
888    
889            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
890            some dimnames perservation.
891    
892            * R/dsTMatrix.R (t-method): keep dimnames
893            * R/dtTMatrix.R:  ditto
894    
895            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
896            and ncol(.) < 10
897    
898            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
899            from Mutils.h
900    
901            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
902            e.g. in as(<ngCMatrix>, "matrix")
903    
904    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
905    
906            * [r4529] .: Create a branch for the API changes from the 0.99875
907              series to the 0.999375 series
908            * [r4530] DESCRIPTION, inst/include/Matrix.h,
909              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
910              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
911              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
912              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
913              as_cholmod_x functions
914    
915    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
916    
917            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
918              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
919              to Comparisons
920    
921    >>>>>>> .merge-right.r4561
922    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
923    
924            * DESCRIPTION (Version): 0.99875-3 ready to be released.
925    
926            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
927    
928            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
929            that should also work in a future version of R.
930    
931    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
932    
933            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
934    
935            * R/sparseVector.R: more *sparseVector coercions, notably for
936            non - double ones.
937    
938    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
939    
940            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
941              notably the new ones building on the new .Call(.)s:
942    
943            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
944            all 4 of [dlin]gCMatrix_colSums().
945    
946    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
947    
948            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
949            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
950              result
951    
952    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
953    
954            * R/kronecker.R: fix typo (could lead to inf.recursion)
955            * test/simple.R: testing that
956    
957            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
958            method as well (which can have arguments, show() can't).
959    
960    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
961    
962            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
963              added dgCMatrix_colSums for [col,row][Sums,Means]
964    
965    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
966    
967            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
968              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
969              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
970            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
971              class
972            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
973              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
974              row names to store the levels - duh!  Added an example.
975    
976    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * src/Csparse.c (Csparse_validate): check for *repeated* entries
979            thanks to example from Christian Buchta; with a test here:
980            * tests/simple.R:
981    
982    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
985            of colSums(*, sparseResult = TRUE)
986    
987    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
988    
989            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
990            'na.rm = FALSE' as "everywhere" else in R.
991    
992    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
993    
994            * [r4421] src/CSparse_install.sh: Modify for new organization of
995              CSparse package
996            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
997              SuiteSparse
998            * [r4426] src/Makefile: add ./UFconfig to the include path for
999              compilation
1000            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1001            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1002              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1003    
1004    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1007            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1008            suppressed column names.
1009    
1010    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1011    
1012            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1013              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1014              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1015              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1016              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1017              Remove warnings after change to const char* CHAR
1018    
1019    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1020    
1021            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1022              type of M_cholmod_ssmult
1023    
1024    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1025    
1026            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1027              src/init.c: Yet another cholmod export - cholmod_ssmult
1028    
1029    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1030    
1031            * NAMESPACE: exported drop0(), since
1032            * man/drop0.Rd: I have seen several cases, I really wanted to use
1033            it, so our users may want too.
1034    
1035    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * man/colSums.Rd: separately document colSums() etc, since these
1038            have the extra argument 'sparseResult'.
1039    
1040  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1041    
1042          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;          * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;

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