SCM

SCM Repository

[matrix] Diff of /pkg/ChangeLog
ViewVC logotype

Diff of /pkg/ChangeLog

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1405, Mon Aug 21 14:43:00 2006 UTC revision 2255, Sat Aug 30 07:20:33 2008 UTC
# Line 1  Line 1 
1    2008-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version): 0.999375-13 released to CRAN
4    
5    2008-08-29  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (attrSlotNames, attrSlots, attr.all_Mat): new
8            utilities, for now to be used in all.equal() methods.
9    
10            * R/Matrix.R (all.equal_Mat): be more careful (less tolerant) in
11            all.equal() methods.
12            * R/sparseMatrix.R: ditto
13    
14    2008-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
15    
16            * DESCRIPTION (Version): 0.999375-12 released to CRAN
17    
18            * R/Ops.R (Compare(<Csparse>,<Csparse>): fix for nsparseMatrix
19    
20    2008-08-27  Douglas Bates <bates@stat.wisc.edu>
21    
22            * R/sparseMatrix.R: fac2sparse() for NA's
23    
24    2008-08-26  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/sparseVector.R (all.equal.sparseV): make work for nsparseVector's
27    
28    2008-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * src/dgCMatrix.c (dgCMatrix_LU): partially revert change
31            r2175 (2008-04-23) and do give an error for a singular matrix.
32            * man/lu.Rd, R/Auxiliaries.R (detSparseLU): adapt to that.
33    
34            * R/LU.R: expand( <sparseLU> )
35    
36            * NAMESPACE, man/all.equal-methods.Rd:
37            * R/Matrix.R (all.equal): methods for Matrices,
38            * R/sparseMatrix.R, R/sparseVector.R: sparseMatrices and -Vectors
39    
40    
41    2008-08-23  Douglas Bates <bates@stat.wisc.edu>
42    
43            * [r2243] R/CHMfactor.R, man/CHMfactor-class.Rd: Added expand method and
44              documentation for CHMfactor class
45            * [r2241] R/CHMfactor.R: Added trivial coercion method for CHMfactor ->
46              pMatrix
47    
48    2008-08-19  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/nsCMatrix.R (setAs(., dgTMatrix))): remove unused method
51    
52    2008-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
53    
54            * R/Ops.R (.Ops2dge.via.x, and many others): eliminate never-used
55            variable assignments {from "next version" codetools}.
56            * R/Csparse.R, R/Tsparse.R: ditto
57    
58    2008-08-17  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/sparseVector.R (sp2vec, coerce to sparseVector):
61            make sure no integer overflows happen, and use double precision
62            (n, index) where appropriate.
63    
64            * tests/Simple.R: test "large" sparse vectors.
65    
66    2008-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
67    
68            * R/AllClass.R (sparseVector): 'length' and 'i' are "numeric", not
69            just integer (allowing much longer length).
70    
71    2008-07-28  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * R/AllClass.R (diagonalMatrix): extend  "sparseMatrix" instead of
74            "denseMatrix".  This renders "scarceMatrix" dispensable and
75            invalidates part of MM's presentations on "space of Matrix
76            classes", but seems cleaner overall.
77    
78            * R/diagMatrix.R, etc: eliminate "scarceMatrix", replacing it by
79            "sparseMatrix" in method signatures;
80            further, instead of coercing to "sparseMatrix", coerce to
81            "TsparseMatrix" now.
82    
83    2008-07-26  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * src/dgCMatrix.c (dgCMatrix_qrsol): allow third argument 'order' in
86            .Call(.)
87            * R/sparseMatrix.R (lm.fit.sparse), src/dgCMatrix.h, src/init.c: ditto
88    
89    2008-07-24  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/dgeMatrix.R: need solve(<dge>, <sparse>) against infinite
92            recursion in new test in
93            * tests/matprod.R: testing the above and another solve() case, below
94    
95            * R/sparseMatrix.R (lm.fit.sparse): slightly more efficient for
96            e.g. triangular 'x'.
97    
98            * src/dgCMatrix.c (dgCMatrix_qrsol): use AS_CSP() hence allowing dtC*
99            * src/dgCMatrix.c (dgCMatrix_cholsol): use AS_CHM_SP() to work
100            correctly with unit-triangular x
101    
102            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): use AS_CHM_SP()
103            instead of not checking diagU.
104    
105            * R/diagMatrix.R, R/Auxiliaries.R: tweaks to allow later
106            experiments where diagonalMatrix would extend sparse*.
107    
108    
109    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * src/dgCMatrix.c (compressed_non_0_ij): for nnzero(), use
112            "x@p[ncol(x)]" instead of length(x@i).
113            * R/Auxiliaries.R (nnzero): ditto
114    
115            * src/chm_common.c (as_cholmod_sparse): Do not use LENGTH(islot)
116            since that fails for over-allocated i.
117    
118            * tests/validObj.R: more testing of over-allocated (i,x) slots
119    
120    2008-07-23  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * src/chm_common.c (as_cholmod_sparse): Add 4th argument
123            'sort_in_place' and set it to TRUE in call from
124            * src/Csparse.c (Csparse_validate): sort in place, making sure that
125            validObject() continues sort the columns if needed.
126    
127            * tests/validObj.R: now tests that more thoroughly, and
128            * man/CsparseMatrix-class.Rd: documents it.
129    
130    2008-07-22  Douglas Bates <bates@stat.wisc.edu>
131    
132            * [r2233] src/chm_common.c: sort columns more carefully in
133              as_cholmod_sparse
134            * [r2231] src/chm_common.c: check for sorted columns in
135              as_cholmod_sparse instead of assuming it
136            * [r2228] src/cs_utils.c: Use R_alloc for semi-permanent storage when
137              expanding diagonal
138    
139    
140    2008-07-21  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * src/cs_utils.c (Matrix_as_cs): add check_Udiag switch
143            * src/cs_utils.h (AS_CSP & AS_CSP__): two versions
144            * src/dtCMatrix.c (dtCMatrix_sparse_solve): no longer needs
145            diagU2N().
146    
147            * R/diagMatrix.R (.sparseDiagonal): new utility, used in "old"
148            .spDiagonal() and new .trDiagonal().
149    
150            * R/dtCMatrix.R (solve): make use of .trDiagonal()
151    
152    2008-07-19  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Auxiliaries.R (dimNamesCheck): fix very long standing buglet,
155            stumbled upon by Michael H.
156    
157            * tests/validObj.R: testing the bug-fix
158    
159            * src/chm_common.h (AS_CHM_SP__, AS_CHM_TR__): the non-diagU2N
160            versions.
161    
162            * src/chm_common.c (as_cholmod_sparse, as_cholmod_triplet): new
163            boolean argument 'check_Udiag' (formerly implicitly was FALSE).
164    
165            * src/Csparse.c (Csparse_Csparse_prod, ...): etc: use the new
166              AS_CHM_SP() which includes diagU2N.
167    
168            * inst/include/Matrix_stubs.c (M_as_cholmod_sparse): similarly
169            adapt to 3 arguments.
170    
171    2008-07-17  Douglas Bates <bates@stat.wisc.edu>
172    
173            * [r2220] src/dtCMatrix.c: Correct number of columns for rhs in
174              dtCMatrix_sparse_solve
175            * [r2219] src/cs_utils.c: eye->nz should be -1 for compressed column
176              storage
177            * [r2217] R/dtCMatrix.R, src/dtCMatrix.c, src/dtCMatrix.h, src/init.c:
178              Replace dtCMatrix_solve by more general dtCMatrix_sparse_solve and add
179              new solve method
180            * [r2216] src/cs_utils.c: Utility csp_eye in case we want to fold
181              Csparse_diagU2N functionality into Matrix_as_cs
182    
183    2008-07-17  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * inst/doc/factor2sparse.Rnw: revive a year-old unfinished vignette
186    
187    2008-07-16  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r2212] R/sparseMatrix.R: fac2sparse gets a drop.unused.levels
190              argument with default TRUE
191            * [r2211] inst/include/Matrix.h, inst/include/Matrix_stubs.c: Export
192              Csparse_diagU2N
193            * [r2210] R/dtCMatrix.R, man/dtCMatrix-class.Rd, src/dtCMatrix.c,
194              src/dtCMatrix.h, src/init.c: Remove vestigial methods based on the
195              parent array; new solve method for signature(a = "dtCMatrix", b =
196              "sparseMatrix")
197    
198    2008-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * R/diagMatrix.R (.bdiag): also keep result triangular
201    
202    2008-07-13  Douglas Bates <bates@stat.wisc.edu>
203    
204            * [r2208] src/dtCMatrix.c, src/dtTMatrix.c: Revise wording in error
205              messages
206    
207    2008-07-12  Martin Maechler  <maechler@stat.math.ethz.ch>
208    
209            * R/diagMatrix.R (.bdiag): make more sophisticated, keeping
210            symmetric- or nsparse-Matrix, also fixing the bug introduced with
211            the new version (.999375-10).
212    
213            * tests/Simple.R: regression test for the bugs.
214    
215    2008-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * R/sparseVector.R (spV2M): fix for "isparseVector".
218            Further, fix <diag> -> <sparseVector> coercion
219            (repSpV): add rep(<sparseVector>, .) method
220    
221            * R/sparseMatrix.R ([<-): when the RHS is a "scarce"Matrix, do *not*
222            use as.vector(.).
223    
224            * R/Tsparse.R ([<-): & [CR]sparse.R: methods for value = "sparseVector"
225    
226            * R/AllClass.R: new (hidden) class union "scarceMatrix"
227            * R/AllClass.R: sparseVector: add prototype
228    
229            * src/dsCMatrix.c (chk_nm): fix "Cholesky" check, thanks to
230            Kasper Kristensen
231    
232    2008-06-28  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * tests/other-pkgs.R: add more interesting Matrix -> graph
235    
236    2008-06-27  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/sparseMatrix.R (Tsp2grNEL): add 'need.uniq' argument for speed
239            improvement in "[CR]sparseMatrix" -> "graphNEL" coercion.
240    
241    2008-06-25  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION: release 0.999375-10 to CRAN
244    
245            * R/diagMatrix.R (.bdiag): use more efficient Bates-algorithm for
246            .bdiag().
247            * man/bdiag.Rd: update, including test.
248    
249    2008-06-24  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * tests/Simple.R: add minimal bdiag() checks
252    
253            * R/diagMatrix.R (bdiag): fix bdiag(diag(4:5)) case;
254              factor out the Tsparse - internal computation into new .bdiag()
255    
256    2008-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
257    
258            * R/nsparseMatrix.R: specific fast all() and any() methods.
259    
260            * src/dgTMatrix.c (MAKE_gTMatrix_to_geMatrix): better error message
261            when trying to produce too large result.
262    
263            * inst/test-tools.R (checkMatrix): add 'do.matrix' with a check for
264            very large matrices.
265    
266            * R/sparseMatrix.R (printSpMatrix2): new function, used by
267            show(<sparseMatrix>).
268    
269            * R/diagMatrix.R (show): print only diagonal entries when nrow(.) >= 50.
270    
271    2008-06-13  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * src/Mutils.c (m_encodeInd, m_encodeInd2):
274            * R/*.R: .Call(m_encodeInd2?, ..) instead of encodeInd2?(..).
275    
276            * R/Auxiliaries.R (encodeInd2?): care against integer overflow (for
277            big matrices): -> 2nd argument 'di' instead of 'nr' !
278    
279    2008-06-09  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/dtCMatrix.R: faster dgC* -> dtC* method
282            * tests/Simple.R: (hence removed "FIXME")
283    
284            * R/Auxiliaries.R (copyClass): add 'check = .copyClass.check'
285            which can be be turned off for possible speed gains.
286    
287    2008-06-02  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/dMatrix.R, R/Tsparse.R: get rid of some disambiguation warnings
290    
291            * R/not.R: fix !<ldiMatrix>
292            implement two old "FIXME"s:  !<ldenseMatrix> & !<ndenseMatrix>
293    
294            * R/diagMatrix.R (Ops): fix one-off thinko in
295            <diagonal> o <numeric> methods
296    
297            * inst/test-tools.R: checkMatrix(): drop0(m12) unconditionally
298    
299    2008-05-30  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * R/diagMatrix.R (Ops): more <diagonal> o <Matrix> methods
302            * tests/Simple.R: testing the above
303    
304    2008-05-07  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * NAMESPACE: also import "Ops" {found via new tools:::get_S4_generics_with_methods()}
307    
308    2008-05-03  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Matrix.R (dimnames<-): dimnames(.) <- NULL works with a message;
311            * NAMESPACE (unname): finally exported
312    
313    2008-04-28  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Auxiliaries.R (cholMat): possibly keep packed
316    
317            * inst/test-tools.R (checkMatrix): add fixed determinant.matrix()
318            for R < 2.7.0.
319    
320            * R/Tsparse.R ([): for triangularMatrix, check if result may be
321            triangular.
322            * tests/indexing.R: regression test
323    
324    2008-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * inst/test-tools.R (checkMatrix): test <Ops> not only for dMatrix
327            * R/Ops.R: more methods, for lMatrix/nMatrix
328    
329    2008-04-24  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/expm.R: new file for all expm() methods; notably new ones for
332            diagonal*, triangular*, symmetric* and also simple "matrix".
333    
334    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/dsyMatrix.R: setAs(.) rather than setIs(.)  "to dpoMatrix"
337    
338            * inst/test-tools.R (assert.EQ.mat): better message when not equal
339    
340            * src/dgeMatrix.c (dgeMatrix_matrix_crossprod): allow integer RHS.
341    
342            * R/AllClass.R (ddiMatrix,ldiMatrix): extend [dl]Matrix instead of
343            [dl]denseMatrix {identical slots; but more logical method dispatch}
344    
345    2008-04-23  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/sparseMatrix.R (summary): use length(<i-slot>) instead of nnzero()
348    
349            * R/diagMatrix.R (determinant): method
350    
351    2008-04-22  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * src/dsCMatrix.c (dsCMatrix_Cholesky): suppress CHOLMOD printing too
354    
355            * R/Rsparse.R (.viaC.to.R): uplo fix for symmetric & triangular
356    
357            * R/dsCMatrix.R (determinant): switch to use Cholesky( 'LDL' ) and
358            its diagonal
359    
360    2008-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
361    
362            * R/dMatrix.R (Summary): short-cut for prod(<sparse>)
363    
364            * R/not.R: fix !<"U"-diag-ltrMatrix> ; drop {R < 2.6.0}-branch
365    
366            * R/Auxiliaries.R (tT2gT): fix for "U"-diag-ltTMatrix
367    
368            * R/AllClass.R: ltTMatrix validity: call (more stringent) tTMatrix_validate
369    
370    2008-04-19  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/Ops.R (Ops.x.x): aux.function, not just for (dMatrix,dMatrix)
373    
374            * R/Ops.R (.do.Logic.lsparse): fix NA case
375    
376            * R/Tsparse.R (replTmat): fix r.sym case, using indTri()
377    
378            * R/Auxiliaries.R (nnzero): fix special cases, using
379            * R/Auxiliaries.R (indDiag): new utility
380            * R/Auxiliaries.R (indTri): new argument 'diag'
381    
382            * R/dMatrix.R: Summmary(<ddenseMatrix>): different branch for dsy*
383    
384    2008-04-18  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/diagMatrix.R: "Summary" methods, and more "Arith" / "Ops"
387    
388            * src/Csparse.c (Csparse_drop): preserve (uplo,diag) for
389            ".tCMatrix" triangular matrix.
390    
391            * R/Auxiliaries.R (drop0): use diagU2N(); according to helpfile,
392            'clx' can be class *or* class representation.
393            (nnzSparse): new.
394            (non0ind): new 'xtendSymm' argument; used in
395            * R/Ops.R:
396    
397            * R/pMatrix.R: more efficient determinant() method
398    
399    2008-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * [disactivated] R/Matrix.R (det): det() as base::det(), but with Matrix environment
402            * [disactivated] NAMESPACE: export(det)
403    
404            * R/diagMatrix.R (mkDiag): new substitute for diag()
405    
406            * R/Auxiliaries.R (nnzero): fix for "diagU2N"-case
407            (as0, as1): new utility.
408    
409            * R/Csparse.R (diag, band): need diagU2N()
410    
411            * src/dgeMatrix.c (get_norm): return NA when 'x' slot has NA/NaN.
412    
413            * R/lMatrix.R: coerce(nMatrix |-> lMatrix) fix
414    
415            * R/Ops.R (Compare): fix <nsp> o <nsp> case
416    
417            * R/nsparseMatrix.R, R/pMatrix.R: is.na() method
418    
419    2008-04-16  Martin Maechler  <maechler@stat.math.ethz.ch>
420    
421            * R/Auxiliaries.R (signPerm): new utility for
422            * R/Auxiliaries.R (detSparseLU): determinant() via sparseLU
423    
424            * src/dsCMatrix.c (dsCMatrix_LDL_D): suppress 'CHOLMOD warning';
425            since we have our own error handler (and can use tryCatch() from R).
426    
427    2008-04-15  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/dgTMatrix.R (image): ha! set col=NA if lwd is small -- very nice!
430    
431            * R/dsCMatrix.R (determinant): use tryCatch() and switch to lu()
432            when not positive definite.
433    
434            * R/Auxiliaries.R (asTri): new auxiliary
435            (non0.i): make *much* faster for Tsparse with many non-zero
436            entries; add 'uniqT = TRUE' argument to be used when sorting is undesired.
437    
438            * tests/Class+Meth.R (dotestMat): now build on checkMatrix() from
439            test-tools.R , see below
440    
441            * R/dMatrix.R: fix "Summary" method: + diagU2N()
442    
443            * NAMESPACE, R/Matrix.R: add mean() method
444    
445    2008-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/dgTMatrix.R (image): allow to *not* take abs(), and use
448            cold-hot colors; try *changed* default useAbs = FALSE
449            * man/image-methods.Rd:  nice examples
450    
451    2008-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * inst/test-tools.R (checkMatrix): new function for modularizing part
454            of tstMatrixClass() in tests/Class+Meth.R
455    
456            * R/dsCMatrix.R: coercion from "matrix"
457            * R/ltTMatrix.R, R/ntTMatrix.R: ditto (change it).
458    
459            * tests/Class+Meth.R (tstMatrixClass): some cleanup;
460            add test for as(matrix(,0,0), <class>)
461    
462    2008-04-09  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * src/dgeMatrix.c (dgeMatrix_determinant): for n == 0,
465            work as determinant(matrix(,0,0)).
466    
467            * src/dgCMatrix.c (dgCMatrix_LU): return {L,U} as dtCMatrix
468            * man/sparseLU-class.Rd: ditto
469    
470            * R/dgCMatrix.R (determinant): method building on lu()
471            * R/sparseMatrix.R, Matrix.R, ...: ditto
472    
473            * R/Auxiliaries.R (mkDet): auxiliary for determinant()
474    
475    2008-04-07  Martin Maechler  <maechler@stat.math.ethz.ch>
476    
477            * R/sparseMatrix.R (summary<sparseMatrix>): no 'x' column for
478            pattern matrices.
479    
480    2008-04-02  Martin Maechler  <maechler@stat.math.ethz.ch>
481    
482            * src/dense.c (dense_to_Csparse): all declarations *before*
483            R_CheckStack(); needed e.g. for ancient gcc 2.96.
484    
485    
486    2008-03-29  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * DESCRIPTION (Version): 0.999375-9 --- need to release
489            for R-devel (and R 2.7.0 alpha soon).
490    
491            * R/AllClass.R: drop "double" from "atomicVector" class union
492    
493            * R/AllGeneric.R (rcond): check for base::rcond instead of R version
494            * R/dgeMatrix.R: ditto
495    
496            * R/sparseMatrix.R (summary): count NAs
497    
498            * inst/doc/Intro2Matrix.Rnw: changes, aim for *one* introduction.
499    
500    2008-03-28  Martin Maechler  <maechler@stat.math.ethz.ch>
501    
502            * R/AllGeneric.R: rcond(., norm) instead of rcond(., type), in
503            order to become compatible to new R 2.7.0 base::rcond().
504    
505    2008-03-25  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * DESCRIPTION (Version,Date): 0.999375-8 --- released to CRAN
508    
509            * R/diagMatrix.R (Ops): fix newly introduce bug in <.di> o <numeric>
510    
511            * inst/test-tools.R (isValid): new utility, used much in
512            * tests/simple.R:
513    
514            * man/BunchKaufman-methods.Rd: added too
515    
516    2008-03-24  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/dsyMatrix.R: add BunchKaufman() methods.
519            * R/dspMatrix.R:
520    
521            * src/init.c: add dsyMatrix_trf
522    
523    2008-03-23  Douglas Bates <bates@stat.wisc.edu>
524    
525            * DESCRIPTION (Version): release 0.999375-7
526            * src/CHMfactor.c (CHMfactor_update): fix
527    
528    2008-03-22  Martin Maechler  <maechler@stat.math.ethz.ch>
529    
530            * src/dsCMatrix.c (dsCMatrix_LDL_D): cleanup, also using
531            internal_chm_factor().
532    
533            * R/AllGeneric.R: do *not* define a "chol" generic
534                    (but rather use the implicit one *without* making pivot
535                    part of the signature)
536            * R/*.R: drop the 'pivot' from chol's signature and make
537                    'pivot=FALSE' a default argument of method definitions.
538    
539            * .Rbuildignore: add 'wrld_1deg': I.e. do not put it into released
540            version of Matrix
541    
542    2008-03-18  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * R/Tsparse.R (.T.2.n): drop 0's before coercion to "nMatrix"
545    
546            * R/sparseMatrix.R (is.na): new simple method
547            * R/denseMatrix.R (is.na): ditto.
548    
549            * R/diagMatrix.R (.symDiagonal): newly exported utility.
550    
551            * R/diagMatrix.R (Ops): <diag> * <numeric> should not become dgeMatrix!
552    
553            * src/UFsparse_download.sh: -->
554            * src/CHOLMOD/: update to CHOLMOD version 1.6 (Nov.2007)
555    
556    2008-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * src/dsCMatrix.c (dsCMatrix_LDL_D): even faster utility with same
559            functionality; barely tested in
560            * tests/factorizing.R
561    
562            * src/Csparse.c (diag_tC): new functionality to enable faster
563            determinant(<dsCMatrix>, .) in
564            * R/dsCMatrix.R
565    
566    2008-03-17 18:53  Douglas Bates <bates@stat.wisc.edu>
567    
568            * R/CHMfactor.R, inst/include/Matrix.h, inst/include/Matrix_stubs.c,
569              src/CHMfactor.c, src/CHMfactor.h,
570              man/CHMfactor-class.Rd, src/init.c, tests/factorizing.R:
571              Log-determinant of the parent matrix from a CHMfactor object as
572              chm_factor_ldetL2; documentation and support
573    
574    2008-03-15  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/dsCMatrix.R: enable determinant(<dsCMatrix>, .) via chol(.)
577    
578    2008-03-14  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/dsCMatrix.R: setAs(., "dsCMatrix") but with a deprecation
581            warning.
582    
583    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
584    
585            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
586    
587            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
588              <diagonal> o <sparse_triangular>
589              setAs(., "nMatrix") added.
590    
591            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
592    
593            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
594                    new argument 'checkDense = FALSE'.
595    
596    
597    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
600            back-permutation of the matrix exponential.
601    
602            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
603    
604            * DESCRIPTION (Date,Version): ready to release 0.999375-5
605    
606            * tests/simple.R: testing diagN2U
607    
608    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * R/Auxiliaries.R (diagN2U): interface to
611    
612            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
613    
614            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
615    
616    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * src/chm_common.c (chm_diagN2U): new utility.
619    
620            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
621            make use of chm_diagN2U() and hence now preserve triangularity and
622            unit-triangularity.
623    
624            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
625    
626    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
629    
630            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
631            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
632    
633            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
634    
635            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
636    
637            * src/chm_common.c (AS_CHM_FINISH): add note about problem
638            for triangular (diag = "U").
639    
640    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
643            * R/bind.R:  .Call(dense_to_Csparse, *)
644    
645    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/Matrix.R (Matrix): no longer use coercions to specific classes
648                    (since we are discouraging them in user code).
649    
650            * tests/*.R: also replaces coercions to specific classes by
651            coercions to super classes.
652    
653            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
654    
655    
656    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
659    
660            * src/dense.c (dense_band): generalized from ddense_band
661    
662            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
663              now for "denseMatrix" (instead of just "ddense*"); much
664              simplified setMethod()s for these.
665    
666            * src/dense.c (dense_to_symmetric): generalized from ddense_*
667    
668    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
671            version of as(*, "symmetricMatric").
672    
673            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
674            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
675    
676    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/Matrix.R (subset.ij): utility, as first step to faster
679               M [ <ij-matrix> ] indexing.
680    
681            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
682    
683            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
684            for more efficient symmpart() and skewpart() methods.
685    
686            * src/Mutils.c (equal_string_vectors): utility
687    
688            * src/dense.c (ddense_to_symmetric): new function used in
689    
690            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
691    
692            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
693            order to match the generic (and evade .local(..)).
694    
695            * R/dsCMatrix.R: dgC -> dsC: use C code!
696    
697            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
698            as per TODO
699    
700            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
701    
702            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
703    
704    
705    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
708    
709            * R/Auxiliaries.R (non0.i): take out of non0ind
710    
711            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
712            make tril(), triu(), band() work for "matrix" and all "dense*"
713    
714            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
715            * tests/simple.R: test the fix above
716    
717            * R/sparseMatrix.R ([): simplification: no coerce to <general>
718                    before we use as(., <Tsparse>)[...] anyway
719    
720            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
721    
722            * R/triangularMatrix.R (isTriangular): methods for all subclasses
723            instead of "triangularMatrix" -- just to disambiguate
724    
725    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
728            * tests/indexing.R: example that fails above
729    
730    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
731    
732            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
733            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
734                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
735    
736            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
737            * src/Tsparse.h, init.c: ditto
738            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
739                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
740            * R/sparseMatrix.R (isTriangular): hence simplified
741    
742    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
743    
744            * R/Ops.R (.Arith.Csparse): new utility factored out of former
745              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
746    
747    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
748    
749            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
750    
751            * inst/test-tools.R (isOrthogonal): new function; also file restructured
752    
753    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
754    
755            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
756            coercion to "nMatrix" and "pMatrix"
757    
758            * R/AllClass.R: "Schur" class;  "number" class union
759            * man/number-class.Rd:
760            * man/Schur-class.Rd:
761    
762            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
763            (.simpleSchur): Schur() method for diagonal matrices
764            (.triSchur):    Schur() method for triangular matrices
765            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
766    
767    
768    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
769    
770            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
771    
772    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
775                    in order to ensure 'system = *' is not lost;
776                    formals()$system instead of cut&paste.
777            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
778    
779    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
780    
781            * DESCRIPTION (Date): make ready for release --> 0.999375-4
782    
783            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
784    
785    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
788                    and hence does as.vector(.).
789            * man/pMatrix-class.Rd: docs
790            * R/sparseMatrix.R: fix for printing "integer sparse"
791    
792            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
793    
794            * R/Matrix.R and others: use "exact" function argument list for
795                    both "["   : (x, i,j, ..., drop)
796                    and  "[<-" : (x, i,j, ..., value)
797    
798            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
799            * R/Tsparse.R (replTmat):    ditto
800            * R/diagMatrix.R (replDiag): ditto
801            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
802            * tests/indexing.R: testing the above
803    
804    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
805    
806            * R/sparseMatrix.R (cov2cor): method for sparse matrices
807    
808            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
809    
810            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
811    
812            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
813    
814    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
815    
816            * R/Matrix.R: "generic" cov2cor() method
817    
818            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
819                    speed up Q %*% D %*% t(Q)
820            * tests/dpoMatrix.R: test nearPD()
821    
822    2007-12-05  Doug Bates and Martin Maechler
823    
824            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
825            stats::xtabs() allowing to create sparse matrices.
826    
827    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
830    
831    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
832    
833            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
834    
835    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
836    
837            * R/LU.R: solve() method for "denseLU"
838    
839    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
840    
841            * DESCRIPTION (Version): 0.999375-3 preparing for release
842    
843            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
844    
845            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
846    
847    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
850              thanks to Kasper Kristensen.
851            * tests/matprod.R: regression test for that.
852    
853    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
854    
855            * [r4778] R/AllGeneric.R: Check R version before defining generics for
856              primitives
857    
858    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * R/denseMatrix.R (rcond): method
861            * R/sparseQR.R (rcond): method, use x or t(x)
862    
863    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
866            matrices.
867            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
868    
869            * man/rcond.Rd: mention the more general definition, and add
870            example for non-square matrices.
871    
872            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
873    
874    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
877    
878    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
881            * tests/indexing.R: add new regression for the above cases.
882    
883    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
884    
885            * src/Mutils.h (__sun): clause for alloca.h on Solaris
886    
887    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * DESCRIPTION (Date, Version): 0.999375-2
890    
891    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * R/HBMM.R (readMM): make work for pattern matrices as well
894    
895    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
896    
897            * [r4730] src/Mutils.h: declare alloca
898            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
899              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
900              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
901              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
902              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
903              methods; switch writeMM to use CHOLMOD code; repair readMM
904    
905    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
908            Oehlschlaegel's ... result type still to be discussed!
909    
910    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
911    
912            * man/image-methods.Rd: new, combining all image() methods
913    
914    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
915    
916            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
917            to work via dgC...
918    
919            * R/Matrix.R (Matrix): special treatment for "table" (S3)
920    
921    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
922    
923            * R/dgTMatrix.R (image): change defaults to
924                    aspect = "iso", colorkey = FALSE
925    
926    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
927    
928            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
929            must copy its *expanded* x slot before LAPACK call.
930    
931            * tests/matprod.R: test the last days' changes.
932    
933    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
934    
935            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
936              as well as in sources
937            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
938              Lapack call
939    
940    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
941    
942            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
943                    ("Matrix", "matrix") which is needed in some cases.
944            Ditto for solve().
945    
946            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
947            infinite recursion in dispatch for some cases.
948    
949    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
950    
951            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
952              so pointers match
953    
954    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956            * DESCRIPTION (Date): set ready for release -- 0.999375-1
957    
958    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
959    
960            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
961              src/chm_common.c, src/chm_common.h: Change API for
962              numeric_as_chm_dense and N_AS_CHM_DN
963    
964    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
967            * tests/matprod.R: regr.test for it
968    
969    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
970    
971            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
972            * tests/group-methods.R: and regression-test it
973    
974    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
975    
976            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
977              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
978              triplet_to_sparse, documentation, use typedefs
979    
980    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
981    
982            * man/dpoMatrix-class.Rd: added 'corMatrix' example
983    
984            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
985            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
986            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
987    
988            * R/lsparseMatrix.R: bug fix in "all" method
989            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
990    
991            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
992            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
993                    + matrix |-> nMatrix coercion
994            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
995            * man/pMatrix-class.Rd: ditto
996    
997            * R/Matrix.R (Summary): method for non-dMatrix
998    
999            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
1000            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
1001                    test all Summary methods.
1002    
1003    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
1005            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
1006    
1007    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1008    
1009            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
1010    
1011            * R/pMatrix.R (t?crossprod): methods for pMatrix
1012    
1013    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
1014    
1015            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
1016    
1017    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
1018    
1019            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
1020              trying to fix a subtle bug - which has been somewhere else.
1021    
1022    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
1023    
1024            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
1025              solve the bug
1026    
1027    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1028    
1029            * src/dgCMatrix.c (compressed_to_TMatrix):
1030    
1031    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1032    
1033            * src/Csparse.c (Rsparse_validate): new, to have some validity
1034            checking for RsparseMatrix
1035            * src/dgCMatrix.c (xRMatrix_validate): ditto
1036            * src/dtCMatrix.c (tRMatrix_validate): ditto
1037    
1038    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
1039    
1040            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
1041              lgRMatrix
1042            * [r4568] DESCRIPTION: Prepare for bug-fix release
1043            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
1044              for declaration of cholmod_symmetry
1045    
1046    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1047    
1048            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
1049            release.
1050    
1051    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
1052    
1053            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
1054              functions - no longer used
1055            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
1056              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
1057              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
1058              Alloca
1059    
1060    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
1061    
1062            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
1063              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
1064              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
1065              src/t_gCMatrix_colSums.c: more R_CheckStack()s
1066    
1067    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
1068    
1069            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
1070              the required amount of memory then call M_numeric_as_chm_dense.
1071            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
1072              (like Calloc but calling alloca)
1073    
1074    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
1077            and extended with more sophisticated 'col.names' option.
1078            * NAMESPACE: export  printSparseMatrix()
1079            * man/printSpMatrix.Rd: document, incl. examples
1080    
1081    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
1082    
1083            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
1084              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
1085              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
1086    
1087    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1088    
1089            * DESCRIPTION (Version): 0.99875-4
1090    
1091            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
1092            some dimnames perservation.
1093    
1094            * R/dsTMatrix.R (t-method): keep dimnames
1095            * R/dtTMatrix.R:  ditto
1096    
1097            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
1098            and ncol(.) < 10
1099    
1100            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
1101            from Mutils.h
1102    
1103            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
1104            e.g. in as(<ngCMatrix>, "matrix")
1105    
1106    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
1107    
1108            * [r4529] .: Create a branch for the API changes from the 0.99875
1109              series to the 0.999375 series
1110            * [r4530] DESCRIPTION, inst/include/Matrix.h,
1111              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
1112              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
1113              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
1114              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
1115              as_cholmod_x functions
1116    
1117    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
1118    
1119            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
1120              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
1121              to Comparisons
1122    
1123    >>>>>>> .merge-right.r4561
1124    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1125    
1126            * DESCRIPTION (Version): 0.99875-3 ready to be released.
1127    
1128            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
1129    
1130            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
1131            that should also work in a future version of R.
1132    
1133    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1134    
1135            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
1136    
1137            * R/sparseVector.R: more *sparseVector coercions, notably for
1138            non - double ones.
1139    
1140    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1141    
1142            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
1143              notably the new ones building on the new .Call(.)s:
1144    
1145            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
1146            all 4 of [dlin]gCMatrix_colSums().
1147    
1148    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
1149    
1150            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
1151            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
1152              result
1153    
1154    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1155    
1156            * R/kronecker.R: fix typo (could lead to inf.recursion)
1157            * test/simple.R: testing that
1158    
1159            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
1160            method as well (which can have arguments, show() can't).
1161    
1162    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
1163    
1164            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
1165              added dgCMatrix_colSums for [col,row][Sums,Means]
1166    
1167    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
1168    
1169            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
1170              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
1171              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
1172            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
1173              class
1174            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
1175              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
1176              row names to store the levels - duh!  Added an example.
1177    
1178    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * src/Csparse.c (Csparse_validate): check for *repeated* entries
1181            thanks to example from Christian Buchta; with a test here:
1182            * tests/simple.R:
1183    
1184    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1185    
1186            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
1187            of colSums(*, sparseResult = TRUE)
1188    
1189    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1190    
1191            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
1192            'na.rm = FALSE' as "everywhere" else in R.
1193    
1194    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
1195    
1196            * [r4421] src/CSparse_install.sh: Modify for new organization of
1197              CSparse package
1198            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
1199              SuiteSparse
1200            * [r4426] src/Makefile: add ./UFconfig to the include path for
1201              compilation
1202            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
1203            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
1204              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
1205    
1206    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1207    
1208            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
1209            * R/sparseMatrix.R (prSpMatrix): now gives a message about
1210            suppressed column names.
1211    
1212    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
1213    
1214            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
1215              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
1216              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
1217              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
1218              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
1219              Remove warnings after change to const char* CHAR
1220    
1221    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
1222    
1223            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
1224              type of M_cholmod_ssmult
1225    
1226    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
1227    
1228            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
1229              src/init.c: Yet another cholmod export - cholmod_ssmult
1230    
1231    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1232    
1233            * NAMESPACE: exported drop0(), since
1234            * man/drop0.Rd: I have seen several cases, I really wanted to use
1235            it, so our users may want too.
1236    
1237    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * man/colSums.Rd: separately document colSums() etc, since these
1240            have the extra argument 'sparseResult'.
1241    
1242    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1243    
1244            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
1245            * man/spMatrix.Rd: docu., including examples
1246    
1247            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
1248            in order to make colMeans() etc fast *and* correct.
1249            * R/sparseVector.R (replSPvec): "[<-" functionality for
1250            sparseVectors; tested in
1251            * tests/simple.R:
1252    
1253    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1254    
1255            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
1256            (very) sparse Matrices; output similar to Matlab's print().
1257    
1258    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
1259    
1260            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
1261            0-based, indices (Jose Quesada <quesada@gmail.com>).
1262    
1263    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
1264    
1265            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
1266    
1267    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1268    
1269            * R/Auxiliaries.R (sparsapply): new utility, much faster than
1270            tapply1() for large sparse matrices.
1271    
1272    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1273    
1274            * R/Matrix.R (dim<-): reshape now via sparseVector.
1275    
1276            * R/sparseVector.R: methods and function for
1277            * R/AllClass.R: new "sparseVector" class and daughters.
1278            * NAMESPACE: export new classes
1279    
1280    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1281    
1282            * DESCRIPTION (Version): 0.99875-1
1283            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
1284    
1285    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1286    
1287            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
1288            indexing
1289            * tests/indexing.R: test set for that.
1290    
1291    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
1292    
1293            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
1294            entries.
1295            * tests/indexing.R(out): add regression test for it
1296    
1297    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1298    
1299            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
1300            name for "!" method definitions.
1301    
1302    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1303    
1304            * R/Tsparse.R (intI): new utility, used for "[" :
1305                    Cleanup up there, and fixes for duplicated indices - more TODO!
1306    
1307            * tests/indexing.R(out): more tests
1308    
1309    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
1310    
1311            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
1312            code that is now part of the R Lapack library.
1313    
1314            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
1315            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
1316    
1317    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1318    
1319            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
1320    
1321    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1322    
1323            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
1324            up with extraneous names '0'...'<n-1>'
1325    
1326    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1327    
1328            * R/dgTMatrix.R (mat2dgT): care about NAs
1329    
1330    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1331    
1332            * R/kronecker.R: triangularity preserving methods
1333    
1334    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1335    
1336            * R/kronecker.R: new file collecting kronecker() methods in one
1337                    place.  Goal: become much faster!
1338    
1339    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1340    
1341            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
1342            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
1343            can be much faster.
1344    
1345            * tests/matprod.R: add regression tests for these (upper & lower).
1346    
1347    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1348    
1349            * R/Matrix.R (diff): method for our Matrices.
1350    
1351            * R/sparseMatrix.R (isDiagonal): check dim()!
1352    
1353    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1354    
1355            * R/Matrix.R (dim<-): new method for "reshape()" built on a
1356            proposal from Tamas Papp.
1357    
1358    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1359    
1360            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
1361    
1362            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
1363            rather define and export  cBind() and rBind() only.
1364            --> useRs *must* change code that used to have cbind()/rbind() !!
1365    
1366            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
1367            * R/bind.Rout.save: ditto
1368    
1369    2007-02-16  Douglas Bates  <bates@r-project.org>
1370    
1371            * DESCRIPTION (Date, Version): 0.9975-11 with new date
1372            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
1373            const modifier on declaration of the array 'valid'
1374    
1375    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
1376    
1377            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
1378    
1379    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1380    
1381            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
1382    
1383            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
1384            * tests/simple.R: test the above and some of these coercions:
1385    
1386            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
1387                    be careful to avoid infinite recursion, using new coercions in
1388            * R/ngCMatrix.R and nsC... and ntC...
1389            * R/lsparseMatrix.R: ditto
1390    
1391            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
1392    
1393            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
1394            * R/Rsparse.R: reactivate .Call()s
1395    
1396            * tests/Class+Meth.R: a bit more on actual classes
1397    
1398    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
1399    
1400            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
1401    
1402    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1403    
1404            * DESCRIPTION (Version): 0.9975-10 to upload
1405    
1406            * tests/Class+Meth.R (tstMatrixClass): require coercions to
1407            specific classes less unconditionally.
1408    
1409            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
1410    
1411            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
1412    
1413            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
1414            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
1415            R_to_CMatrix segfaults on one platform.
1416            Eliminate most coercion method to *specific* classes, and replace
1417            with virtual classes coercions.
1418    
1419    
1420    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
1421    
1422            * src/init.c: export the CHM...._validate() placeholders, since
1423            they *are* called.
1424    
1425            * tests/Class+Meth.R (classCanCoerce): and starting to test
1426            all as(<from>, <to>)
1427    
1428    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1429    
1430            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
1431            * tests/indexing.R: tested now
1432            * tests/indexing.Rout.save: updated
1433    
1434            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
1435            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
1436            appropriate.
1437    
1438            * NAMESPACE: export a trivial
1439            * R/Matrix.R: drop() Matrix-method
1440    
1441            * R/AllClass.R: moved all prototypes to virtual super classes.
1442    
1443            * R/Rsparse.R: many more coercions to have less exceptions in
1444            * tests/Class+Meth.R:
1445    
1446            * R/Ops.R (Compare): tweak for case with NA
1447            * tests/simpl.R: hence another 'FIXME' eliminated
1448    
1449    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1450    
1451            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
1452            objects.
1453    
1454            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
1455              and more of "!", "&", "|", all, any; coercions
1456    
1457            * R/Rsparse.R: many coercions (which enable quite a few other
1458            methods), thanks to enhancements in
1459            * src/dgCMatrix.c (R_to_CMatrix): new, and
1460            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
1461            symmetric & triangular and ..RMatrix objects.
1462    
1463            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
1464            renamed file from src/dsTMatrix.c;
1465            now dealing with symmetric and triangular Tsparse coercions, both
1466            to dense and general.
1467    
1468    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1469    
1470            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
1471    
1472            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
1473            where sensible when the <numeric> is of length > 1.
1474    
1475    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1476    
1477            * R/Matrix.R ([<-): for M[] <- value: fix length
1478    
1479    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1480    
1481            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
1482            * R/ndenseMatrix.R: new coercions n* -> l*
1483    
1484    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1485    
1486            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
1487    
1488            * R/Ops.R ("Logic"): and other "Ops", many updates
1489    
1490    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1491    
1492            * src/Mutils.h (SET_DimNames): new utility
1493    
1494            * R/Auxiliaries.R (nnzero): improved and now exported via
1495    
1496            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
1497    
1498    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1499    
1500            * R/diagMatrix.R (!): fix typo.
1501    
1502    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1503    
1504            * R/Auxiliaries.R (as_Csparse): and quite a few others:
1505                    allow to pass class definition --> speedup
1506            * R/sparseMatrix.R: apply the above
1507    
1508            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
1509    
1510            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
1511            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
1512            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
1513    
1514            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
1515    
1516            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
1517            and use it for "sparse*" as well, since it's faster than the
1518            as_Csparse(.) way.
1519    
1520    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1521    
1522            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
1523    
1524    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
1525    
1526            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
1527            as method for   M[ ij ] <- v
1528            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
1529    
1530            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
1531            FALSE answer
1532    
1533            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
1534            * tests/indexing.R: test it, and some of the above
1535    
1536    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1537    
1538            * R/Auxiliaries.R (is_duplicatedT): new utility
1539    
1540    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
1541    
1542            * src/init.c (R_init_Matrix): export cholmod_scale
1543    
1544    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1545    
1546            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
1547            base::as.matrix to (x, ...)
1548    
1549    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1550    
1551            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
1552            file; start using "Logic", hence
1553    
1554            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
1555            * NAMESPACE: import and export "Logic"
1556    
1557    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1558    
1559            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
1560            only needed previously to R version 2.5.0.
1561    
1562    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1563    
1564            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
1565    
1566            * R/Tsparse.R (replTmat): fix subassignment of triangular
1567            * R/Csparse.R (replCmat): ditto
1568            * tests/indexing.R: more tests, incl the above fix
1569    
1570    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1571    
1572            * R/Auxiliaries.R (drop0): extend for non CSparse
1573            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
1574    
1575            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
1576                    use uplo correctly (!); other places: use uplo_P() macro
1577    
1578            * R/Csparse.R (replCmat): call diagU2N() when needed
1579            * R/Tsparse.R (replTmat): ditto
1580    
1581            * src/dtCMatrix.c (tCMatrix_validate): new
1582            * src/dtTMatrix.c (tTMatrix_validate): new, used in
1583            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
1584    
1585            * R/diagMatrix.R (replDiag): to use in [<-
1586    
1587    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
1588    
1589            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
1590                    also more general diagU2N().
1591    
1592    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
1593    
1594            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
1595            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
1596    
1597    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1598    
1599            * tests/bind.R: a few more cases
1600            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
1601    
1602            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
1603            * R/ddenseMatrix.R (cbind2/rbind2)
1604            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
1605            * tests/indexing.R
1606            * tests/indexing.Rout.save: updated
1607    
1608    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1609    
1610            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
1611            * tests/indexing.R
1612    
1613    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1614    
1615            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
1616            align with proper position of "0", i.e., right for integers.
1617            argument 'align' by default is "fancy".
1618    
1619    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
1620    
1621            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1622            * R/Csparse.R: and fix "Compare" for more cases.
1623            * tests/Class+Meth.R: test some of these (m == m, m != m)
1624    
1625    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1626    
1627            * R/lsparseMatrix.R: all() and any() methods
1628            * R/ldenseMatrix.R:      ditto
1629            * NAMESPACE, R/Matrix.R: ditto
1630    
1631            * man/all-methods.Rd: document them minimally
1632    
1633            * tests/simple.R: add a few examples for these
1634    
1635    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1636    
1637            * R/Tsparse.R ([): fix long standing typo in symmetric case
1638            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1639    
1640    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1641    
1642            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1643            to LL before converting to a sparse matrix. (The LDL form can be
1644            converted to a sparse matrix but it is implicitly a unit
1645            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1646    
1647    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1648    
1649            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1650    
1651    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1652    
1653            * DESCRIPTION (Version): updated -> release 0.9975-7
1654            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1655    
1656    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1657    
1658            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1659    
1660    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1661    
1662            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1663            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1664            is exactly singular.
1665    
1666    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1667    
1668            * DESCRIPTION (Date): updated -> release 0.9975-6
1669    
1670    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1671    
1672            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1673            now returns symmetric.
1674    
1675            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1676    
1677            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1678            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1679    
1680            * R/Auxiliaries.R (.type.kind): added
1681    
1682    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1683    
1684            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1685            running src/CSparse_install.sh
1686    
1687            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1688    
1689    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1690    
1691            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1692            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1693    
1694            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1695    
1696            * tests/Class+Meth.R (tstMatrixClass): now assure
1697            the (important in method programming) property :
1698    
1699                    ###>>  Every "Matrix" is either
1700                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1701    
1702                    (where "*" stands for "Matrix")
1703    
1704            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1705    
1706            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1707            * tests/validObj.R: checks for "comparison"
1708    
1709            * R/sparseMatrix.R ([): improved indexing for sparse;
1710                    trying to keep <symmetric>[ n, n] symmmetric
1711    
1712            * tests/indexing.R: indexing for logical sparse now ok
1713    
1714    
1715    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1716    
1717            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1718    
1719            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1720    
1721    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1722    
1723            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1724    
1725            * tests/simple.R: validObject() checking the above.
1726    
1727            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1728            replacing both dgCMatrix_validate and lgCM*.
1729    
1730            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1731            fix dimnames setting in other places.
1732            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1733    
1734    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1735    
1736            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1737    
1738            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1739            symmetry test, via
1740            * R/Auxiliaries.R (.as.dgC.0.factors):
1741    
1742    2006-11-01  Douglas Bates  <bates@r-project.org>
1743    
1744            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1745            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1746            <CsparseMatrix>) added
1747    
1748    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1749    
1750            * tests/matprod.R: add a variation of Harri's example
1751    
1752            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1753            recursive infinitely.
1754    
1755            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1756    
1757            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1758    
1759    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1760    
1761            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1762            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1763            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1764            satisfy the above test.
1765    
1766    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1767    
1768            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1769    
1770            * R/dgCMatrix.R: solve(a, b="missing") based on
1771            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1772            RHS = NULL.
1773    
1774            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1775            add more (needed) [t]crossprod() methods.
1776    
1777            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1778    
1779            * R/Auxiliaries.R (as_CspClass): cleanup
1780            (drop0): internal utility for "Csparse_drop(*, 0)"
1781            (.bail.out.2): encourage active feedback
1782    
1783    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1784    
1785            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1786    
1787            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1788            non-valid or 'sorted' case).
1789    
1790            * R/dsparseMatrix.R: add "chol" method.
1791            * R/ddenseMatrix.R: ditto
1792    
1793            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1794            * NAMESPACE (Ops)
1795            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1796            coercion; deprecating direct lower level coercions.
1797    
1798            * R/*.R (seq): use seq_len() and seq_along() where possible.
1799    
1800    
1801    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1802    
1803            * DESCRIPTION (Version): 0.9975-5 ready for release
1804    
1805    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1806    
1807            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1808    
1809    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1810    
1811            * R/AllClass.R (corMatrix): add 'validity' check;
1812                    comment out unused "LDL" class definition
1813            * NAMESPACE: mention, but do not export "LDL" class
1814            * R/corMatrix.R: new (simple), needed for R-devel with
1815            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1816              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1817    
1818    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1819    
1820            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1821            use Rprintf and R's error handling.
1822    
1823    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1824    
1825            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1826            * tests/matprod.R: add tests for the bug fixed.
1827    
1828    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1829    
1830            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1831            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1832    
1833    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1834    
1835            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1836    
1837    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1838    
1839            * DESCRIPTION (Version): 0.9975-3
1840    
1841            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1842            (sparse) matrices.
1843            * man/bdiag.Rd: docu + examples
1844    
1845            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1846    
1847            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1848            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1849    
1850            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1851            that result is sparse or diagonal (and not dense).
1852    
1853            * man/Subassign-methods.Rd: fix examples
1854    
1855            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1856            should always return a sparse (and not sometimes a diagonal) matrix.
1857    
1858    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1859    
1860            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1861    
1862    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1863    
1864            * DESCRIPTION (Version): 0.9975-2
1865    
1866            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1867    
1868    2006-10-02  Douglas Bates  <bates@R-project.org>
1869    
1870            * tests/dg_Matrix.R: Simplify test taking into account new code.
1871    
1872    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1873    
1874            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1875    
1876            * R/lsTMatrix.R: new files w/ missing methods
1877            * R/nsTMatrix.R:  "  'for completeness'
1878    
1879            * tests/Class+Meth.R: a bit less 'not.ok.classes'
1880    
1881            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
1882    
1883    
1884    2006-09-28  Douglas Bates  <bates@R-project.org>
1885    
1886            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
1887            included.
1888    
1889            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
1890            Export C-callable functions used in Zt_create in lme4.
1891    
1892    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1893    
1894            * DESCRIPTION (Version): 0.9975-1
1895    
1896            * tests/simple.R: less checks fail; using NA, found that our
1897                    kronecker() is not base-compatible with NA's.
1898    
1899            * R/dMatrix.R: "Compare" method now implemented for all cases
1900    
1901            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1902    
1903            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1904    
1905            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1906            * src/dspMatrix.c (dspMatrix_validate): ditto
1907    
1908            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1909              including coercion to [nl]tTMatrix.
1910    
1911            * R/diagMatrix.R (show): print a header line as for other classes.
1912    
1913    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1914    
1915            * src/Makefile.win (SUBDIRS): fix typo
1916    
1917    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1918    
1919            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1920    
1921    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1922    
1923            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1924            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1925            accept a symmetric matrix).
1926            * tests/group-methods.R: Uncomment test of crossprod applied to
1927            lsCMatrix objects.
1928    
1929    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1930    
1931            * R/AllClass.R (symmetricMatrix): add validity method (available
1932            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1933    
1934            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1935    
1936            * tests/indexing.Rout.save:
1937            * tests/indexing.R: additions, mainly for 'lsparse'
1938    
1939            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1940            case.
1941    
1942            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1943    
1944    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1945    
1946            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1947                    as 'N' (1-letter - Ok?)
1948    
1949            * tests/group-methods.R: add test for logical + NAs
1950    
1951            * R/dMatrix.R ("Compare"): fix to work with NA's
1952    
1953            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1954    
1955            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1956                    which is implemented.
1957    
1958    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1959    
1960            * src/chm_common.c: coerce logical <-> double instead of
1961            typecasting;  needed for "l" matrix handling in cholmod.
1962    
1963            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1964    
1965            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1966            (Tsp2grNEL): other fixes needed
1967    
1968    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1969    
1970            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1971                    Matrices, since "lMatrix", also "lsparseM" can have NA
1972            * R/ndenseMatrix.R, etc: new source files
1973            * man/nsparseMatrix-classes.Rd, etc: new help files
1974            * tests/: adaptions
1975            * src/chm_common.c (chm_dense_to_SEXP): and others:
1976                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1977            * src/Csparse.c, etc: ditto
1978    
1979    2006-09-11  Douglas Bates  <bates@R-project.org>
1980    
1981            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1982            alloc_d**Matrix functions to the lme4 package.
1983    
1984    2006-09-09  Douglas Bates  <bates@R-project.org>
1985    
1986            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1987            fixed
1988    
1989    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1990    
1991            * R/lMatrix.R: new
1992    
1993            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1994    
1995            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1996            * man/tcrossprod.Rd: ditto
1997    
1998    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1999    
2000            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
2001            for exported functions
2002            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
2003            Remove partitioning algorithms for sparse matrix reordering.  The
2004            copyright on the Metis code was problematic and the methods were
2005            rarely used.
2006            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
2007            operations are now done entirely in CHOLMOD code.
2008    
2009    2006-09-06  Douglas Bates  <bates@R-project.org>
2010    
2011            * src/Mutils.h: Remove functions that are no longer used.
2012    
2013    2006-09-04  Douglas Bates  <bates@R-project.org>
2014    
2015            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
2016            * src/DEPS.mkf: update
2017    
2018    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
2019    
2020            * created branches/Matrix-for-R-2.3.x;  on trunk: do
2021            * DESCRIPTION (Version): 0.9975-0
2022            (Depends): R (>= 2.4.0)
2023    
2024    2006-09-01  Douglas Bates  <bates@R-project.org>
2025    
2026            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
2027    
2028    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2029    
2030            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
2031            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
2032    
2033            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
2034    
2035    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2036    
2037            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
2038            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
2039            * R/dsparseMatrix.R: ditto
2040            * R/Csparse.R: ditto
2041    
2042    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
2043    
2044            * R/dMatrix.R (Compare): improve availability of "<", etc
2045            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
2046    
2047    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
2048    
2049            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
2050            of a 0-index which was used as 1-index (..hmm)
2051    
2052            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
2053    
2054            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
2055            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
2056            (.is.diagonal): ditto
2057    
2058            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
2059    
2060            * R/Matrix.R (Matrix): also work for NA data
2061    
2062    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
2063    
2064            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
2065            in all cases.
2066    
2067    2006-08-27  Douglas Bates  <bates@R-project.org>
2068    
2069            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
2070            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
2071    
2072    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
2073    
2074            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
2075            subclasses of "ddenseMatrix"
2076            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
2077            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
2078            instead of half dozen specialized ones.
2079    
2080    2006-08-25  Douglas Bates  <bates@R-project.org>
2081    
2082            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
2083            <tillard@cirad.fr> - ordering standard errors to match effects.
2084    
2085    2006-08-24  Douglas Bates  <bates@R-project.org>
2086    
2087            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
2088            on R_ldl.
2089            * R/lCholCMatrix.R,
2090            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
2091            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
2092            * many files in ./R and ./src: Use more general version of
2093            dup_mMatrix_as_dgeMatrix to simplify method definitions.
2094            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
2095            dtpMatrix, dspMatrix and dppMatrix conversions.
2096    
2097    
2098    2006-08-23  Douglas Bates  <bates@R-project.org>
2099    
2100            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
2101            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
2102            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
2103            dgeMatrix_crossprod (may need to do this in other places).
2104            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
2105            generic and method for dsCMatrix.  Use CHOLMOD for chol().
2106    
2107    2006-08-22  Douglas Bates  <bates@R-project.org>
2108    
2109            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
2110            types of classed Matrices, matrices or numeric or logical vectors.
2111            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
2112            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
2113            to Mutils.h (as an inline) and change name to Matrix_check_class;
2114            fixes in as_cholmod_factor and chm_factor_to_SEXP.
2115            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
2116            dsCMatrix_matrix_solve.  Comment out vestigial functions.
2117            * src/Csparse.c: use diag_P and uplo_P macros.
2118    
2119  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
2120    
2121          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by          * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
2122          valgrind.          valgrind.
2123            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
2124            inverses.
2125            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
2126            -Wall warnings.
2127            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
2128            Use dup_mMatrix_as_dgeMatrix.
2129    
2130  2006-08-20  Douglas Bates  <bates@R-project.org>  2006-08-20  Douglas Bates  <bates@R-project.org>
2131    

Legend:
Removed from v.1405  
changed lines
  Added in v.2255

root@r-forge.r-project.org
ViewVC Help
Powered by ViewVC 1.0.0  
Thanks to:
Vienna University of Economics and Business Powered By FusionForge