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revision 1847, Sat May 19 19:23:28 2007 UTC revision 2207, Mon Jul 7 22:34:52 2008 UTC
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1    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseVector.R (spV2M): fix for "isparseVector".
4            Further, fix <diag> -> <sparseVector> coercion
5            (repSpV): add rep(<sparseVector>, .) method
6    
7            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
8            use as.vector(.).
9    
10            * R/[TCR]sparse.R ([<-): methods for  value = "sparseVector"
11    
12            * R/AllClass.R: new (hidden) class union "scarceMatrix"
13            * R/AllClass.R: sparseVector: add prototype
14    
15            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to Kasper Kristensen
16    
17    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * tests/other-pkgs.R: add more interesting Matrix -> graph
20    
21    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
22    
23            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
24            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
25    
26    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
29            .bdiag().
30            * man/bdiag.Rd: update, including test.
31    
32    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * tests/Simple.R: add minimal bdiag() checks
35    
36            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
37              factor out the Tsparse - internal computation into new .bdiag()
38    
39    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * R/nsparseMatrix.R: specific fast all() and any() methods.
42    
43            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
44            when trying to produce too large result.
45    
46            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
47            very large matrices.
48    
49            * R/sparseMatrix.R (printSpMatrix2): new function, used by
50            show(<sparseMatrix>).
51    
52            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
53    
54    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * src/Mutils.c (m_encodeInd, m_encodeInd2):
57            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
58    
59            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
60            big matrices): -> 2nd argument 'di' instead of 'nr' !
61    
62    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/dtCMatrix.R: faster dgC* -> dtC* method
65            * tests/Simple.R: (hence removed "FIXME")
66    
67            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
68            which can be be turned off for possible speed gains.
69    
70    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
73    
74            * R/not.R: fix !<ldiMatrix>
75            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
76    
77            * R/diagMatrix.R (Ops): fix one-off thinko in
78            <diagonal> o <numeric> methods
79    
80            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
81    
82    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
83    
84            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
85            * tests/Simple.R: testing the above
86    
87    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
90    
91    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
94            * NAMESPACE (unname): finally exported
95    
96    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/Auxiliaries.R (cholMat): possibly keep packed
99    
100            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
101            for R < 2.7.0.
102    
103            * R/Tsparse.R ([): for triangularMatrix, check if result may be
104            triangular.
105            * tests/indexing.R: regression test
106    
107    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
110            * R/Ops.R: more methods, for lMatrix/nMatrix
111    
112    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/expm.R: new file for all expm() methods; notably new ones for
115            diagonal*, triangular*, symmetric* and also simple "matrix".
116    
117    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
120    
121            * inst/test-tools.R (assert.EQ.mat): better message when not equal
122    
123            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
124    
125            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
126            [dl]denseMatrix {identical slots; but more logical method dispatch}
127    
128    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
131    
132            * R/diagMatrix.R (determinant): method
133    
134    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
137    
138            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
139    
140            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
141            its diagonal
142    
143    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
146    
147            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
148    
149            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
150    
151            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
152    
153    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
156    
157            * R/Ops.R (.do.Logic.lsparse): fix NA case
158    
159            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
160    
161            * R/Auxiliaries.R (nnzero): fix special cases, using
162            * R/Auxiliaries.R (indDiag): new utility
163            * R/Auxiliaries.R (indTri): new argument 'diag'
164    
165            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
166    
167    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
170    
171            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
172            ".tCMatrix" triangular matrix.
173    
174            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
175            'clx' can be class *or* class representation.
176            (nnzSparse): new.
177            (non0ind): new 'xtendSymm' argument; used in
178            * R/Ops.R:
179    
180            * R/pMatrix.R: more efficient determinant() method
181    
182    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
185            * [disactivated] NAMESPACE: export(det)
186    
187            * R/diagMatrix.R (mkDiag): new substitute for diag()
188    
189            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
190            (as0, as1): new utility.
191    
192            * R/Csparse.R (diag, band): need diagU2N()
193    
194            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
195    
196            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
197    
198            * R/Ops.R (Compare): fix <nsp> o <nsp> case
199    
200            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
201    
202    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/Auxiliaries.R (signPerm): new utility for
205            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
206    
207            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
208            since we have our own error handler (and can use tryCatch() from R).
209    
210    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
213    
214            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
215            when not positive definite.
216    
217            * R/Auxiliaries.R (asTri): new auxiliary
218            (non0.i): make *much* faster for Tsparse with many non-zero
219            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
220    
221            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
222            test-tools.R , see below
223    
224            * R/dMatrix.R: fix "Summary" method: + diagU2N()
225    
226            * NAMESPACE, R/Matrix.R: add mean() method
227    
228    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
231            cold-hot colors; try *changed* default useAbs = FALSE
232            * man/image-methods.Rd:  nice examples
233    
234    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * inst/test-tools.R (checkMatrix): new function for modularizing part
237            of tstMatrixClass() in tests/Class+Meth.R
238    
239            * R/dsCMatrix.R: coercion from "matrix"
240            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
241    
242            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
243            add test for as(matrix(,0,0), <class>)
244    
245    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
248            work as determinant(matrix(,0,0)).
249    
250            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
251            * man/sparseLU-class.Rd: ditto
252    
253            * R/dgCMatrix.R (determinant): method building on lu()
254            * R/sparseMatrix.R, Matrix.R, ...: ditto
255    
256            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
257    
258    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
261            pattern matrices.
262    
263    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * src/dense.c (dense_to_Csparse): all declarations *before*
266            R_CheckStack(); needed e.g. for ancient gcc 2.96.
267    
268    
269    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
270    
271            * DESCRIPTION (Version): 0.999375-9 --- need to release
272            for R-devel (and R 2.7.0 alpha soon).
273    
274            * R/AllClass.R: drop "double" from "atomicVector" class union
275    
276            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
277            * R/dgeMatrix.R: ditto
278    
279            * R/sparseMatrix.R (summary): count NAs
280    
281            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
282    
283    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
286            order to become compatible to new R 2.7.0 base::rcond().
287    
288    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
289    
290            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
291    
292            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
293    
294            * inst/test-tools.R (isValid): new utility, used much in
295            * tests/simple.R:
296    
297            * man/BunchKaufman-methods.Rd: added too
298    
299    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/dsyMatrix.R: add BunchKaufman() methods.
302            * R/dspMatrix.R:
303    
304            * src/init.c: add dsyMatrix_trf
305    
306    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
307    
308            * DESCRIPTION (Version): release 0.999375-7
309            * src/CHMfactor.c (CHMfactor_update): fix
310    
311    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
312    
313            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
314            internal_chm_factor().
315    
316            * R/AllGeneric.R: do *not* define a "chol" generic
317                    (but rather use the implicit one *without* making pivot
318                    part of the signature)
319            * R/*.R: drop the 'pivot' from chol's signature and make
320                    'pivot=FALSE' a default argument of method definitions.
321    
322            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
323            version of Matrix
324    
325    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
328    
329            * R/sparseMatrix.R (is.na): new simple method
330            * R/denseMatrix.R (is.na): ditto.
331    
332            * R/diagMatrix.R (.symDiagonal): newly exported utility.
333    
334            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
335    
336            * src/UFsparse_download.sh: -->
337            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
338    
339    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
342            functionality; barely tested in
343            * tests/factorizing.R
344    
345            * src/Csparse.c (diag_tC): new functionality to enable faster
346            determinant(<dsCMatrix>, .) in
347            * R/dsCMatrix.R
348    
349    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
350    
351            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
352              src/CHMfactor.c, src/CHMfactor.h,
353              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
354              Log-determinant of the parent matrix from a CHMfactor object as
355              chm_factor_ldetL2; documentation and support
356    
357    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
360    
361    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
362    
363            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
364            warning.
365    
366    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
369    
370            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
371              <diagonal> o <sparse_triangular>
372              setAs(., "nMatrix") added.
373    
374            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
375    
376            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
377                    new argument 'checkDense = FALSE'.
378    
379    
380    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
383            back-permutation of the matrix exponential.
384    
385            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
386    
387            * DESCRIPTION (Date,Version): ready to release 0.999375-5
388    
389            * tests/simple.R: testing diagN2U
390    
391    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Auxiliaries.R (diagN2U): interface to
394    
395            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
396    
397            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
398    
399    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * src/chm_common.c (chm_diagN2U): new utility.
402    
403            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
404            make use of chm_diagN2U() and hence now preserve triangularity and
405            unit-triangularity.
406    
407            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
408    
409    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
410    
411            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
412    
413            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
414            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
415    
416            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
417    
418            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
419    
420            * src/chm_common.c (AS_CHM_FINISH): add note about problem
421            for triangular (diag = "U").
422    
423    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
426            * R/bind.R:  .Call(dense_to_Csparse, *)
427    
428    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * R/Matrix.R (Matrix): no longer use coercions to specific classes
431                    (since we are discouraging them in user code).
432    
433            * tests/*.R: also replaces coercions to specific classes by
434            coercions to super classes.
435    
436            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
437    
438    
439    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
442    
443            * src/dense.c (dense_band): generalized from ddense_band
444    
445            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
446              now for "denseMatrix" (instead of just "ddense*"); much
447              simplified setMethod()s for these.
448    
449            * src/dense.c (dense_to_symmetric): generalized from ddense_*
450    
451    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
454            version of as(*, "symmetricMatric").
455    
456            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
457            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
458    
459    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/Matrix.R (subset.ij): utility, as first step to faster
462               M [ <ij-matrix> ] indexing.
463    
464            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
465    
466            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
467            for more efficient symmpart() and skewpart() methods.
468    
469            * src/Mutils.c (equal_string_vectors): utility
470    
471            * src/dense.c (ddense_to_symmetric): new function used in
472    
473            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
474    
475            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
476            order to match the generic (and evade .local(..)).
477    
478            * R/dsCMatrix.R: dgC -> dsC: use C code!
479    
480            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
481            as per TODO
482    
483            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
484    
485            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
486    
487    
488    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
489    
490            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
491    
492            * R/Auxiliaries.R (non0.i): take out of non0ind
493    
494            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
495            make tril(), triu(), band() work for "matrix" and all "dense*"
496    
497            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
498            * tests/simple.R: test the fix above
499    
500            * R/sparseMatrix.R ([): simplification: no coerce to <general>
501                    before we use as(., <Tsparse>)[...] anyway
502    
503            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
504    
505            * R/triangularMatrix.R (isTriangular): methods for all subclasses
506            instead of "triangularMatrix" -- just to disambiguate
507    
508    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
511            * tests/indexing.R: example that fails above
512    
513    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
514    
515            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
516            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
517                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
518    
519            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
520            * src/Tsparse.h, init.c: ditto
521            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
522                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
523            * R/sparseMatrix.R (isTriangular): hence simplified
524    
525    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
526    
527            * R/Ops.R (.Arith.Csparse): new utility factored out of former
528              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
529    
530    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
531    
532            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
533    
534            * inst/test-tools.R (isOrthogonal): new function; also file restructured
535    
536    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
539            coercion to "nMatrix" and "pMatrix"
540    
541            * R/AllClass.R: "Schur" class;  "number" class union
542            * man/number-class.Rd:
543            * man/Schur-class.Rd:
544    
545            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
546            (.simpleSchur): Schur() method for diagonal matrices
547            (.triSchur):    Schur() method for triangular matrices
548            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
549    
550    
551    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
554    
555    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
558                    in order to ensure 'system = *' is not lost;
559                    formals()$system instead of cut&paste.
560            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
561    
562    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * DESCRIPTION (Date): make ready for release --> 0.999375-4
565    
566            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
567    
568    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
571                    and hence does as.vector(.).
572            * man/pMatrix-class.Rd: docs
573            * R/sparseMatrix.R: fix for printing "integer sparse"
574    
575            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
576    
577            * R/Matrix.R and others: use "exact" function argument list for
578                    both "["   : (x, i,j, ..., drop)
579                    and  "[<-" : (x, i,j, ..., value)
580    
581            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
582            * R/Tsparse.R (replTmat):    ditto
583            * R/diagMatrix.R (replDiag): ditto
584            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
585            * tests/indexing.R: testing the above
586    
587    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/sparseMatrix.R (cov2cor): method for sparse matrices
590    
591            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
592    
593            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
594    
595            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
596    
597    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Matrix.R: "generic" cov2cor() method
600    
601            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
602                    speed up Q %*% D %*% t(Q)
603            * tests/dpoMatrix.R: test nearPD()
604    
605    2007-12-05  Doug Bates and Martin Maechler
606    
607            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
608            stats::xtabs() allowing to create sparse matrices.
609    
610    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
613    
614    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
615    
616            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
617    
618    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
619    
620            * R/LU.R: solve() method for "denseLU"
621    
622    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * DESCRIPTION (Version): 0.999375-3 preparing for release
625    
626            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
627    
628            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
629    
630    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
633              thanks to Kasper Kristensen.
634            * tests/matprod.R: regression test for that.
635    
636    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
637    
638            * [r4778] R/AllGeneric.R: Check R version before defining generics for
639              primitives
640    
641    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
642    
643            * R/denseMatrix.R (rcond): method
644            * R/sparseQR.R (rcond): method, use x or t(x)
645    
646    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
649            matrices.
650            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
651    
652            * man/rcond.Rd: mention the more general definition, and add
653            example for non-square matrices.
654    
655            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
656    
657    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
658    
659            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
660    
661    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
662    
663            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
664            * tests/indexing.R: add new regression for the above cases.
665    
666    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * src/Mutils.h (__sun): clause for alloca.h on Solaris
669    
670    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * DESCRIPTION (Date, Version): 0.999375-2
673    
674    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
675    
676            * R/HBMM.R (readMM): make work for pattern matrices as well
677    
678    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
679    
680            * [r4730] src/Mutils.h: declare alloca
681            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
682              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
683              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
684              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
685              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
686              methods; switch writeMM to use CHOLMOD code; repair readMM
687    
688    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
689    
690            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
691            Oehlschlaegel's ... result type still to be discussed!
692    
693    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * man/image-methods.Rd: new, combining all image() methods
696    
697    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
700            to work via dgC...
701    
702            * R/Matrix.R (Matrix): special treatment for "table" (S3)
703    
704    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
705    
706            * R/dgTMatrix.R (image): change defaults to
707                    aspect = "iso", colorkey = FALSE
708    
709    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
712            must copy its *expanded* x slot before LAPACK call.
713    
714            * tests/matprod.R: test the last days' changes.
715    
716    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
717    
718            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
719              as well as in sources
720            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
721              Lapack call
722    
723    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
724    
725            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
726                    ("Matrix", "matrix") which is needed in some cases.
727            Ditto for solve().
728    
729            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
730            infinite recursion in dispatch for some cases.
731    
732    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
733    
734            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
735              so pointers match
736    
737    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * DESCRIPTION (Date): set ready for release -- 0.999375-1
740    
741    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
742    
743            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
744              src/chm_common.c, src/chm_common.h: Change API for
745              numeric_as_chm_dense and N_AS_CHM_DN
746    
747    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
750            * tests/matprod.R: regr.test for it
751    
752    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
755            * tests/group-methods.R: and regression-test it
756    
757    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
758    
759            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
760              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
761              triplet_to_sparse, documentation, use typedefs
762    
763    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * man/dpoMatrix-class.Rd: added 'corMatrix' example
766    
767            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
768            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
769            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
770    
771            * R/lsparseMatrix.R: bug fix in "all" method
772            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
773    
774            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
775            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
776                    + matrix |-> nMatrix coercion
777            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
778            * man/pMatrix-class.Rd: ditto
779    
780            * R/Matrix.R (Summary): method for non-dMatrix
781    
782            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
783            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
784                    test all Summary methods.
785    
786    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
787    
788            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
789    
790    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
791    
792            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
793    
794            * R/pMatrix.R (t?crossprod): methods for pMatrix
795    
796    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
797    
798            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
799    
800    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
801    
802            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
803              trying to fix a subtle bug - which has been somewhere else.
804    
805    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
806    
807            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
808              solve the bug
809    
810    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
811    
812            * src/dgCMatrix.c (compressed_to_TMatrix):
813    
814    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
815    
816            * src/Csparse.c (Rsparse_validate): new, to have some validity
817            checking for RsparseMatrix
818            * src/dgCMatrix.c (xRMatrix_validate): ditto
819            * src/dtCMatrix.c (tRMatrix_validate): ditto
820    
821    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
822    
823            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
824              lgRMatrix
825            * [r4568] DESCRIPTION: Prepare for bug-fix release
826            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
827              for declaration of cholmod_symmetry
828    
829    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
830    
831            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
832            release.
833    
834    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
835    
836            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
837              functions - no longer used
838            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
839              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
840              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
841              Alloca
842    
843    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
844    
845            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
846              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
847              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
848              src/t_gCMatrix_colSums.c: more R_CheckStack()s
849    
850    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
851    
852            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
853              the required amount of memory then call M_numeric_as_chm_dense.
854            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
855              (like Calloc but calling alloca)
856    
857    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
858    
859            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
860            and extended with more sophisticated 'col.names' option.
861            * NAMESPACE: export  printSparseMatrix()
862            * man/printSpMatrix.Rd: document, incl. examples
863    
864    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
865    
866            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
867              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
868              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
869    
870    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
871    
872            * DESCRIPTION (Version): 0.99875-4
873    
874            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
875            some dimnames perservation.
876    
877            * R/dsTMatrix.R (t-method): keep dimnames
878            * R/dtTMatrix.R:  ditto
879    
880            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
881            and ncol(.) < 10
882    
883            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
884            from Mutils.h
885    
886            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
887            e.g. in as(<ngCMatrix>, "matrix")
888    
889    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
890    
891            * [r4529] .: Create a branch for the API changes from the 0.99875
892              series to the 0.999375 series
893            * [r4530] DESCRIPTION, inst/include/Matrix.h,
894              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
895              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
896              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
897              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
898              as_cholmod_x functions
899    
900    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
901    
902            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
903              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
904              to Comparisons
905    
906    >>>>>>> .merge-right.r4561
907    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
908    
909            * DESCRIPTION (Version): 0.99875-3 ready to be released.
910    
911            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
912    
913            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
914            that should also work in a future version of R.
915    
916    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
917    
918            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
919    
920            * R/sparseVector.R: more *sparseVector coercions, notably for
921            non - double ones.
922    
923    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
926              notably the new ones building on the new .Call(.)s:
927    
928            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
929            all 4 of [dlin]gCMatrix_colSums().
930    
931    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
932    
933            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
934            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
935              result
936    
937    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
938    
939            * R/kronecker.R: fix typo (could lead to inf.recursion)
940            * test/simple.R: testing that
941    
942            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
943            method as well (which can have arguments, show() can't).
944    
945    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
946    
947            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
948              added dgCMatrix_colSums for [col,row][Sums,Means]
949    
950    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
951    
952            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
953              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
954              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
955            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
956              class
957            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
958              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
959              row names to store the levels - duh!  Added an example.
960    
961    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
962    
963            * src/Csparse.c (Csparse_validate): check for *repeated* entries
964            thanks to example from Christian Buchta; with a test here:
965            * tests/simple.R:
966    
967    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
968    
969            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
970            of colSums(*, sparseResult = TRUE)
971    
972    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
973    
974            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
975            'na.rm = FALSE' as "everywhere" else in R.
976    
977    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
978    
979            * [r4421] src/CSparse_install.sh: Modify for new organization of
980              CSparse package
981            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
982              SuiteSparse
983            * [r4426] src/Makefile: add ./UFconfig to the include path for
984              compilation
985            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
986            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
987              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
988    
989    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
990    
991            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
992            * R/sparseMatrix.R (prSpMatrix): now gives a message about
993            suppressed column names.
994    
995    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
996    
997            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
998              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
999              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1000              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1001              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1002              Remove warnings after change to const char* CHAR
1003    
1004    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1005    
1006            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1007              type of M_cholmod_ssmult
1008    
1009    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1010    
1011            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1012              src/init.c: Yet another cholmod export - cholmod_ssmult
1013    
1014    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * NAMESPACE: exported drop0(), since
1017            * man/drop0.Rd: I have seen several cases, I really wanted to use
1018            it, so our users may want too.
1019    
1020    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1021    
1022            * man/colSums.Rd: separately document colSums() etc, since these
1023            have the extra argument 'sparseResult'.
1024    
1025    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1026    
1027            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1028            * man/spMatrix.Rd: docu., including examples
1029    
1030            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1031            in order to make colMeans() etc fast *and* correct.
1032            * R/sparseVector.R (replSPvec): "[<-" functionality for
1033            sparseVectors; tested in
1034            * tests/simple.R:
1035    
1036    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1039            (very) sparse Matrices; output similar to Matlab's print().
1040    
1041  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>  2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1042    
1043          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not          * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not

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