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revision 1786, Fri Feb 16 17:37:56 2007 UTC revision 2226, Mon Jul 21 17:15:17 2008 UTC
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1    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
4            .spDiagonal() and new .trDiagonal().
5    
6            * R/dtCMatrix.R (solve): make use of .trDiagonal()
7    
8    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
9    
10            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
11            stumbled upon by Michael H.
12    
13            * tests/validObj.R: testing the bug-fix
14    
15            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
16            versions.
17    
18            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
19            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
20    
21            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
22              AS_CHM_SP() which includes diagU2N.
23    
24            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
25            adapt to 3 arguments.
26    
27    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
28    
29            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
30              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
31              new solve method
32            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
33              Csparse_diagU2N functionality into Matrix_as_cs
34    
35    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * [r2215] inst/doc/factor2sparse.Rnw: revive a year-old unfinished
38              vignette
39            * [r2214] R/AllGeneric.R: cosmetic
40            * [r2213] man/image-methods.Rd: typo ("non-number" :-\ )
41    
42    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
43    
44            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
45              argument with default TRUE
46            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
47              Csparse_diagU2N
48            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
49              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
50              parent array; new solve method for signature(a = "dtCMatrix", b =
51              "sparseMatrix")
52    
53    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/diagMatrix.R (.bdiag): also keep triangular
56            * [r2209] ChangeLog, DESCRIPTION, R/diagMatrix.R, inst/test-tools.R,
57              man/dsCMatrix-class.Rd, man/dsyMatrix-class.Rd, tests/Simple.R:
58              bdiag() improvements of last week
59    
60    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
61    
62            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
63              messages
64    
65    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
68            symmetric- or nsparse-Matrix, also fixing the bug introduced with
69            the new version (.999375-10).
70    
71            * tests/Simple.R: regression test for the bugs.
72    
73    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/sparseVector.R (spV2M): fix for "isparseVector".
76            Further, fix <diag> -> <sparseVector> coercion
77            (repSpV): add rep(<sparseVector>, .) method
78    
79            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
80            use as.vector(.).
81    
82            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
83    
84            * R/AllClass.R: new (hidden) class union "scarceMatrix"
85            * R/AllClass.R: sparseVector: add prototype
86    
87            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
88            Kasper Kristensen
89    
90    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * tests/other-pkgs.R: add more interesting Matrix -> graph
93    
94    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
97            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
98    
99    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
100    
101            * DESCRIPTION: release 0.999375-10 to CRAN
102    
103            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
104            .bdiag().
105            * man/bdiag.Rd: update, including test.
106    
107    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * tests/Simple.R: add minimal bdiag() checks
110    
111            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
112              factor out the Tsparse - internal computation into new .bdiag()
113    
114    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/nsparseMatrix.R: specific fast all() and any() methods.
117    
118            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
119            when trying to produce too large result.
120    
121            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
122            very large matrices.
123    
124            * R/sparseMatrix.R (printSpMatrix2): new function, used by
125            show(<sparseMatrix>).
126    
127            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
128    
129    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * src/Mutils.c (m_encodeInd, m_encodeInd2):
132            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
133    
134            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
135            big matrices): -> 2nd argument 'di' instead of 'nr' !
136    
137    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * R/dtCMatrix.R: faster dgC* -> dtC* method
140            * tests/Simple.R: (hence removed "FIXME")
141    
142            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
143            which can be be turned off for possible speed gains.
144    
145    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
148    
149            * R/not.R: fix !<ldiMatrix>
150            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
151    
152            * R/diagMatrix.R (Ops): fix one-off thinko in
153            <diagonal> o <numeric> methods
154    
155            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
156    
157    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
160            * tests/Simple.R: testing the above
161    
162    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
165    
166    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
169            * NAMESPACE (unname): finally exported
170    
171    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/Auxiliaries.R (cholMat): possibly keep packed
174    
175            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
176            for R < 2.7.0.
177    
178            * R/Tsparse.R ([): for triangularMatrix, check if result may be
179            triangular.
180            * tests/indexing.R: regression test
181    
182    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
185            * R/Ops.R: more methods, for lMatrix/nMatrix
186    
187    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/expm.R: new file for all expm() methods; notably new ones for
190            diagonal*, triangular*, symmetric* and also simple "matrix".
191    
192    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
195    
196            * inst/test-tools.R (assert.EQ.mat): better message when not equal
197    
198            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
199    
200            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
201            [dl]denseMatrix {identical slots; but more logical method dispatch}
202    
203    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
206    
207            * R/diagMatrix.R (determinant): method
208    
209    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
210    
211            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
212    
213            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
214    
215            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
216            its diagonal
217    
218    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
221    
222            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
223    
224            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
225    
226            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
227    
228    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
231    
232            * R/Ops.R (.do.Logic.lsparse): fix NA case
233    
234            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
235    
236            * R/Auxiliaries.R (nnzero): fix special cases, using
237            * R/Auxiliaries.R (indDiag): new utility
238            * R/Auxiliaries.R (indTri): new argument 'diag'
239    
240            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
241    
242    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
245    
246            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
247            ".tCMatrix" triangular matrix.
248    
249            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
250            'clx' can be class *or* class representation.
251            (nnzSparse): new.
252            (non0ind): new 'xtendSymm' argument; used in
253            * R/Ops.R:
254    
255            * R/pMatrix.R: more efficient determinant() method
256    
257    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
260            * [disactivated] NAMESPACE: export(det)
261    
262            * R/diagMatrix.R (mkDiag): new substitute for diag()
263    
264            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
265            (as0, as1): new utility.
266    
267            * R/Csparse.R (diag, band): need diagU2N()
268    
269            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
270    
271            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
272    
273            * R/Ops.R (Compare): fix <nsp> o <nsp> case
274    
275            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
276    
277    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
278    
279            * R/Auxiliaries.R (signPerm): new utility for
280            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
281    
282            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
283            since we have our own error handler (and can use tryCatch() from R).
284    
285    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
288    
289            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
290            when not positive definite.
291    
292            * R/Auxiliaries.R (asTri): new auxiliary
293            (non0.i): make *much* faster for Tsparse with many non-zero
294            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
295    
296            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
297            test-tools.R , see below
298    
299            * R/dMatrix.R: fix "Summary" method: + diagU2N()
300    
301            * NAMESPACE, R/Matrix.R: add mean() method
302    
303    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
306            cold-hot colors; try *changed* default useAbs = FALSE
307            * man/image-methods.Rd:  nice examples
308    
309    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * inst/test-tools.R (checkMatrix): new function for modularizing part
312            of tstMatrixClass() in tests/Class+Meth.R
313    
314            * R/dsCMatrix.R: coercion from "matrix"
315            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
316    
317            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
318            add test for as(matrix(,0,0), <class>)
319    
320    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
321    
322            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
323            work as determinant(matrix(,0,0)).
324    
325            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
326            * man/sparseLU-class.Rd: ditto
327    
328            * R/dgCMatrix.R (determinant): method building on lu()
329            * R/sparseMatrix.R, Matrix.R, ...: ditto
330    
331            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
332    
333    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
336            pattern matrices.
337    
338    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340            * src/dense.c (dense_to_Csparse): all declarations *before*
341            R_CheckStack(); needed e.g. for ancient gcc 2.96.
342    
343    
344    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * DESCRIPTION (Version): 0.999375-9 --- need to release
347            for R-devel (and R 2.7.0 alpha soon).
348    
349            * R/AllClass.R: drop "double" from "atomicVector" class union
350    
351            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
352            * R/dgeMatrix.R: ditto
353    
354            * R/sparseMatrix.R (summary): count NAs
355    
356            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
357    
358    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
361            order to become compatible to new R 2.7.0 base::rcond().
362    
363    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
366    
367            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
368    
369            * inst/test-tools.R (isValid): new utility, used much in
370            * tests/simple.R:
371    
372            * man/BunchKaufman-methods.Rd: added too
373    
374    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
375    
376            * R/dsyMatrix.R: add BunchKaufman() methods.
377            * R/dspMatrix.R:
378    
379            * src/init.c: add dsyMatrix_trf
380    
381    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
382    
383            * DESCRIPTION (Version): release 0.999375-7
384            * src/CHMfactor.c (CHMfactor_update): fix
385    
386    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
389            internal_chm_factor().
390    
391            * R/AllGeneric.R: do *not* define a "chol" generic
392                    (but rather use the implicit one *without* making pivot
393                    part of the signature)
394            * R/*.R: drop the 'pivot' from chol's signature and make
395                    'pivot=FALSE' a default argument of method definitions.
396    
397            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
398            version of Matrix
399    
400    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
401    
402            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
403    
404            * R/sparseMatrix.R (is.na): new simple method
405            * R/denseMatrix.R (is.na): ditto.
406    
407            * R/diagMatrix.R (.symDiagonal): newly exported utility.
408    
409            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
410    
411            * src/UFsparse_download.sh: -->
412            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
413    
414    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
417            functionality; barely tested in
418            * tests/factorizing.R
419    
420            * src/Csparse.c (diag_tC): new functionality to enable faster
421            determinant(<dsCMatrix>, .) in
422            * R/dsCMatrix.R
423    
424    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
425    
426            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
427              src/CHMfactor.c, src/CHMfactor.h,
428              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
429              Log-determinant of the parent matrix from a CHMfactor object as
430              chm_factor_ldetL2; documentation and support
431    
432    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
435    
436    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
439            warning.
440    
441    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
444    
445            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
446              <diagonal> o <sparse_triangular>
447              setAs(., "nMatrix") added.
448    
449            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
450    
451            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
452                    new argument 'checkDense = FALSE'.
453    
454    
455    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
456    
457            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
458            back-permutation of the matrix exponential.
459    
460            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
461    
462            * DESCRIPTION (Date,Version): ready to release 0.999375-5
463    
464            * tests/simple.R: testing diagN2U
465    
466    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/Auxiliaries.R (diagN2U): interface to
469    
470            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
471    
472            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
473    
474    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476            * src/chm_common.c (chm_diagN2U): new utility.
477    
478            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
479            make use of chm_diagN2U() and hence now preserve triangularity and
480            unit-triangularity.
481    
482            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
483    
484    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
485    
486            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
487    
488            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
489            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
490    
491            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
492    
493            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
494    
495            * src/chm_common.c (AS_CHM_FINISH): add note about problem
496            for triangular (diag = "U").
497    
498    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
501            * R/bind.R:  .Call(dense_to_Csparse, *)
502    
503    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * R/Matrix.R (Matrix): no longer use coercions to specific classes
506                    (since we are discouraging them in user code).
507    
508            * tests/*.R: also replaces coercions to specific classes by
509            coercions to super classes.
510    
511            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
512    
513    
514    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
517    
518            * src/dense.c (dense_band): generalized from ddense_band
519    
520            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
521              now for "denseMatrix" (instead of just "ddense*"); much
522              simplified setMethod()s for these.
523    
524            * src/dense.c (dense_to_symmetric): generalized from ddense_*
525    
526    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
527    
528            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
529            version of as(*, "symmetricMatric").
530    
531            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
532            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
533    
534    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/Matrix.R (subset.ij): utility, as first step to faster
537               M [ <ij-matrix> ] indexing.
538    
539            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
540    
541            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
542            for more efficient symmpart() and skewpart() methods.
543    
544            * src/Mutils.c (equal_string_vectors): utility
545    
546            * src/dense.c (ddense_to_symmetric): new function used in
547    
548            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
549    
550            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
551            order to match the generic (and evade .local(..)).
552    
553            * R/dsCMatrix.R: dgC -> dsC: use C code!
554    
555            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
556            as per TODO
557    
558            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
559    
560            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
561    
562    
563    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
566    
567            * R/Auxiliaries.R (non0.i): take out of non0ind
568    
569            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
570            make tril(), triu(), band() work for "matrix" and all "dense*"
571    
572            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
573            * tests/simple.R: test the fix above
574    
575            * R/sparseMatrix.R ([): simplification: no coerce to <general>
576                    before we use as(., <Tsparse>)[...] anyway
577    
578            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
579    
580            * R/triangularMatrix.R (isTriangular): methods for all subclasses
581            instead of "triangularMatrix" -- just to disambiguate
582    
583    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
586            * tests/indexing.R: example that fails above
587    
588    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
589    
590            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
591            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
592                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
593    
594            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
595            * src/Tsparse.h, init.c: ditto
596            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
597                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
598            * R/sparseMatrix.R (isTriangular): hence simplified
599    
600    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
601    
602            * R/Ops.R (.Arith.Csparse): new utility factored out of former
603              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
604    
605    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
608    
609            * inst/test-tools.R (isOrthogonal): new function; also file restructured
610    
611    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
612    
613            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
614            coercion to "nMatrix" and "pMatrix"
615    
616            * R/AllClass.R: "Schur" class;  "number" class union
617            * man/number-class.Rd:
618            * man/Schur-class.Rd:
619    
620            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
621            (.simpleSchur): Schur() method for diagonal matrices
622            (.triSchur):    Schur() method for triangular matrices
623            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
624    
625    
626    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
629    
630    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
633                    in order to ensure 'system = *' is not lost;
634                    formals()$system instead of cut&paste.
635            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
636    
637    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
638    
639            * DESCRIPTION (Date): make ready for release --> 0.999375-4
640    
641            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
642    
643    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
646                    and hence does as.vector(.).
647            * man/pMatrix-class.Rd: docs
648            * R/sparseMatrix.R: fix for printing "integer sparse"
649    
650            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
651    
652            * R/Matrix.R and others: use "exact" function argument list for
653                    both "["   : (x, i,j, ..., drop)
654                    and  "[<-" : (x, i,j, ..., value)
655    
656            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
657            * R/Tsparse.R (replTmat):    ditto
658            * R/diagMatrix.R (replDiag): ditto
659            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
660            * tests/indexing.R: testing the above
661    
662    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/sparseMatrix.R (cov2cor): method for sparse matrices
665    
666            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
667    
668            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
669    
670            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
671    
672    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Matrix.R: "generic" cov2cor() method
675    
676            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
677                    speed up Q %*% D %*% t(Q)
678            * tests/dpoMatrix.R: test nearPD()
679    
680    2007-12-05  Doug Bates and Martin Maechler
681    
682            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
683            stats::xtabs() allowing to create sparse matrices.
684    
685    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
688    
689    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
692    
693    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/LU.R: solve() method for "denseLU"
696    
697    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
698    
699            * DESCRIPTION (Version): 0.999375-3 preparing for release
700    
701            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
702    
703            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
704    
705    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
708              thanks to Kasper Kristensen.
709            * tests/matprod.R: regression test for that.
710    
711    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
712    
713            * [r4778] R/AllGeneric.R: Check R version before defining generics for
714              primitives
715    
716    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
717    
718            * R/denseMatrix.R (rcond): method
719            * R/sparseQR.R (rcond): method, use x or t(x)
720    
721    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
722    
723            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
724            matrices.
725            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
726    
727            * man/rcond.Rd: mention the more general definition, and add
728            example for non-square matrices.
729    
730            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
731    
732    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
735    
736    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
737    
738            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
739            * tests/indexing.R: add new regression for the above cases.
740    
741    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * src/Mutils.h (__sun): clause for alloca.h on Solaris
744    
745    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
746    
747            * DESCRIPTION (Date, Version): 0.999375-2
748    
749    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
750    
751            * R/HBMM.R (readMM): make work for pattern matrices as well
752    
753    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
754    
755            * [r4730] src/Mutils.h: declare alloca
756            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
757              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
758              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
759              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
760              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
761              methods; switch writeMM to use CHOLMOD code; repair readMM
762    
763    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
764    
765            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
766            Oehlschlaegel's ... result type still to be discussed!
767    
768    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * man/image-methods.Rd: new, combining all image() methods
771    
772    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
775            to work via dgC...
776    
777            * R/Matrix.R (Matrix): special treatment for "table" (S3)
778    
779    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * R/dgTMatrix.R (image): change defaults to
782                    aspect = "iso", colorkey = FALSE
783    
784    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
787            must copy its *expanded* x slot before LAPACK call.
788    
789            * tests/matprod.R: test the last days' changes.
790    
791    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
792    
793            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
794              as well as in sources
795            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
796              Lapack call
797    
798    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
801                    ("Matrix", "matrix") which is needed in some cases.
802            Ditto for solve().
803    
804            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
805            infinite recursion in dispatch for some cases.
806    
807    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
808    
809            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
810              so pointers match
811    
812    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
813    
814            * DESCRIPTION (Date): set ready for release -- 0.999375-1
815    
816    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
817    
818            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
819              src/chm_common.c, src/chm_common.h: Change API for
820              numeric_as_chm_dense and N_AS_CHM_DN
821    
822    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
823    
824            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
825            * tests/matprod.R: regr.test for it
826    
827    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
830            * tests/group-methods.R: and regression-test it
831    
832    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
833    
834            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
835              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
836              triplet_to_sparse, documentation, use typedefs
837    
838    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * man/dpoMatrix-class.Rd: added 'corMatrix' example
841    
842            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
843            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
844            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
845    
846            * R/lsparseMatrix.R: bug fix in "all" method
847            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
848    
849            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
850            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
851                    + matrix |-> nMatrix coercion
852            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
853            * man/pMatrix-class.Rd: ditto
854    
855            * R/Matrix.R (Summary): method for non-dMatrix
856    
857            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
858            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
859                    test all Summary methods.
860    
861    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
862    
863            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
864    
865    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
866    
867            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
868    
869            * R/pMatrix.R (t?crossprod): methods for pMatrix
870    
871    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
872    
873            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
874    
875    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
876    
877            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
878              trying to fix a subtle bug - which has been somewhere else.
879    
880    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
881    
882            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
883              solve the bug
884    
885    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
886    
887            * src/dgCMatrix.c (compressed_to_TMatrix):
888    
889    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * src/Csparse.c (Rsparse_validate): new, to have some validity
892            checking for RsparseMatrix
893            * src/dgCMatrix.c (xRMatrix_validate): ditto
894            * src/dtCMatrix.c (tRMatrix_validate): ditto
895    
896    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
897    
898            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
899              lgRMatrix
900            * [r4568] DESCRIPTION: Prepare for bug-fix release
901            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
902              for declaration of cholmod_symmetry
903    
904    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
905    
906            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
907            release.
908    
909    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
910    
911            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
912              functions - no longer used
913            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
914              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
915              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
916              Alloca
917    
918    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
919    
920            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
921              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
922              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
923              src/t_gCMatrix_colSums.c: more R_CheckStack()s
924    
925    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
926    
927            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
928              the required amount of memory then call M_numeric_as_chm_dense.
929            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
930              (like Calloc but calling alloca)
931    
932    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
935            and extended with more sophisticated 'col.names' option.
936            * NAMESPACE: export  printSparseMatrix()
937            * man/printSpMatrix.Rd: document, incl. examples
938    
939    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
940    
941            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
942              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
943              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
944    
945    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
946    
947            * DESCRIPTION (Version): 0.99875-4
948    
949            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
950            some dimnames perservation.
951    
952            * R/dsTMatrix.R (t-method): keep dimnames
953            * R/dtTMatrix.R:  ditto
954    
955            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
956            and ncol(.) < 10
957    
958            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
959            from Mutils.h
960    
961            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
962            e.g. in as(<ngCMatrix>, "matrix")
963    
964    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
965    
966            * [r4529] .: Create a branch for the API changes from the 0.99875
967              series to the 0.999375 series
968            * [r4530] DESCRIPTION, inst/include/Matrix.h,
969              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
970              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
971              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
972              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
973              as_cholmod_x functions
974    
975    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
976    
977            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
978              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
979              to Comparisons
980    
981    >>>>>>> .merge-right.r4561
982    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
983    
984            * DESCRIPTION (Version): 0.99875-3 ready to be released.
985    
986            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
987    
988            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
989            that should also work in a future version of R.
990    
991    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
992    
993            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
994    
995            * R/sparseVector.R: more *sparseVector coercions, notably for
996            non - double ones.
997    
998    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1001              notably the new ones building on the new .Call(.)s:
1002    
1003            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1004            all 4 of [dlin]gCMatrix_colSums().
1005    
1006    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1007    
1008            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1009            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1010              result
1011    
1012    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1013    
1014            * R/kronecker.R: fix typo (could lead to inf.recursion)
1015            * test/simple.R: testing that
1016    
1017            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1018            method as well (which can have arguments, show() can't).
1019    
1020    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1021    
1022            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1023              added dgCMatrix_colSums for [col,row][Sums,Means]
1024    
1025    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1026    
1027            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1028              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1029              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1030            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1031              class
1032            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1033              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1034              row names to store the levels - duh!  Added an example.
1035    
1036    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1037    
1038            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1039            thanks to example from Christian Buchta; with a test here:
1040            * tests/simple.R:
1041    
1042    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1043    
1044            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1045            of colSums(*, sparseResult = TRUE)
1046    
1047    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1048    
1049            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1050            'na.rm = FALSE' as "everywhere" else in R.
1051    
1052    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1053    
1054            * [r4421] src/CSparse_install.sh: Modify for new organization of
1055              CSparse package
1056            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1057              SuiteSparse
1058            * [r4426] src/Makefile: add ./UFconfig to the include path for
1059              compilation
1060            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1061            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1062              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1063    
1064    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1065    
1066            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1067            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1068            suppressed column names.
1069    
1070    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1071    
1072            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1073              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1074              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1075              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1076              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1077              Remove warnings after change to const char* CHAR
1078    
1079    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1080    
1081            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1082              type of M_cholmod_ssmult
1083    
1084    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1085    
1086            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1087              src/init.c: Yet another cholmod export - cholmod_ssmult
1088    
1089    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1090    
1091            * NAMESPACE: exported drop0(), since
1092            * man/drop0.Rd: I have seen several cases, I really wanted to use
1093            it, so our users may want too.
1094    
1095    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * man/colSums.Rd: separately document colSums() etc, since these
1098            have the extra argument 'sparseResult'.
1099    
1100    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1103            * man/spMatrix.Rd: docu., including examples
1104    
1105            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1106            in order to make colMeans() etc fast *and* correct.
1107            * R/sparseVector.R (replSPvec): "[<-" functionality for
1108            sparseVectors; tested in
1109            * tests/simple.R:
1110    
1111    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1112    
1113            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1114            (very) sparse Matrices; output similar to Matlab's print().
1115    
1116    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1117    
1118            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1119            0-based, indices (Jose Quesada <quesada@gmail.com>).
1120    
1121    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1122    
1123            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1124    
1125    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1126    
1127            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1128            tapply1() for large sparse matrices.
1129    
1130    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1131    
1132            * R/Matrix.R (dim<-): reshape now via sparseVector.
1133    
1134            * R/sparseVector.R: methods and function for
1135            * R/AllClass.R: new "sparseVector" class and daughters.
1136            * NAMESPACE: export new classes
1137    
1138    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1139    
1140            * DESCRIPTION (Version): 0.99875-1
1141            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1142    
1143    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1144    
1145            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1146            indexing
1147            * tests/indexing.R: test set for that.
1148    
1149    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1150    
1151            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1152            entries.
1153            * tests/indexing.R(out): add regression test for it
1154    
1155    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1156    
1157            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1158            name for "!" method definitions.
1159    
1160    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1161    
1162            * R/Tsparse.R (intI): new utility, used for "[" :
1163                    Cleanup up there, and fixes for duplicated indices - more TODO!
1164    
1165            * tests/indexing.R(out): more tests
1166    
1167    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1168    
1169            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1170            code that is now part of the R Lapack library.
1171    
1172            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1173            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1174    
1175    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1176    
1177            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1178    
1179    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1180    
1181            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1182            up with extraneous names '0'...'<n-1>'
1183    
1184    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/dgTMatrix.R (mat2dgT): care about NAs
1187    
1188    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * R/kronecker.R: triangularity preserving methods
1191    
1192    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1193    
1194            * R/kronecker.R: new file collecting kronecker() methods in one
1195                    place.  Goal: become much faster!
1196    
1197    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1198    
1199            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1200            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1201            can be much faster.
1202    
1203            * tests/matprod.R: add regression tests for these (upper & lower).
1204    
1205    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1206    
1207            * R/Matrix.R (diff): method for our Matrices.
1208    
1209            * R/sparseMatrix.R (isDiagonal): check dim()!
1210    
1211    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1212    
1213            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1214            proposal from Tamas Papp.
1215    
1216    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1217    
1218            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1219    
1220            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1221            rather define and export  cBind() and rBind() only.
1222            --> useRs *must* change code that used to have cbind()/rbind() !!
1223    
1224            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1225            * R/bind.Rout.save: ditto
1226    
1227    2007-02-16  Douglas Bates  <bates@r-project.org>
1228    
1229            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1230            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1231            const modifier on declaration of the array 'valid'
1232    
1233  2007-02-12  Douglas Bates  <bates@stat.wisc.edu>  2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1234    
1235          * R/CHMfactor.R: Add image method (coercion to sparseMatrix).          * R/CHMfactor.R: Add image method (coercion to sparseMatrix).

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