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revision 1599, Fri Sep 29 09:39:50 2006 UTC revision 2123, Wed Mar 5 08:44:52 2008 UTC
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1    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
4    
5    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
8    
9            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
10            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
11    
12            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
13    
14            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
15    
16            * src/chm_common.c (AS_CHM_FINISH): add note about problem
17            for triangular (diag = "U").
18    
19    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
20    
21            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
22            * R/bind.R:  .Call(dense_to_Csparse, *)
23    
24    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
25    
26            * R/Matrix.R (Matrix): no longer use coercions to specific classes
27                    (since we are discouraging them in user code).
28    
29            * tests/*.R: also replaces coercions to specific classes by
30            coercions to super classes.
31    
32            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
33    
34    
35    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
38    
39            * src/dense.c (dense_band): generalized from ddense_band
40    
41            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
42              now for "denseMatrix" (instead of just "ddense*"); much
43              simplified setMethod()s for these.
44    
45            * src/dense.c (dense_to_symmetric): generalized from ddense_*
46    
47    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
48    
49            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
50            version of as(*, "symmetricMatric").
51    
52            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
53            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
54    
55    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (subset.ij): utility, as first step to faster
58               M [ <ij-matrix> ] indexing.
59    
60            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
61    
62            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
63            for more efficient symmpart() and skewpart() methods.
64    
65            * src/Mutils.c (equal_string_vectors): utility
66    
67            * src/dense.c (ddense_to_symmetric): new function used in
68    
69            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
70    
71            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
72            order to match the generic (and evade .local(..)).
73    
74            * R/dsCMatrix.R: dgC -> dsC: use C code!
75    
76            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
77            as per TODO
78    
79            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
80    
81            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
82    
83    
84    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
87    
88            * R/Auxiliaries.R (non0.i): take out of non0ind
89    
90            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
91            make tril(), triu(), band() work for "matrix" and all "dense*"
92    
93            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
94            * tests/simple.R: test the fix above
95    
96            * R/sparseMatrix.R ([): simplification: no coerce to <general>
97                    before we use as(., <Tsparse>)[...] anyway
98    
99            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
100    
101            * R/triangularMatrix.R (isTriangular): methods for all subclasses
102            instead of "triangularMatrix" -- just to disambiguate
103    
104    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
107            * tests/indexing.R: example that fails above
108    
109    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
112            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
113                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
114    
115            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
116            * src/Tsparse.h, init.c: ditto
117            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
118                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
119            * R/sparseMatrix.R (isTriangular): hence simplified
120    
121    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/Ops.R (.Arith.Csparse): new utility factored out of former
124              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
125    
126    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
127    
128            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
129    
130            * inst/test-tools.R (isOrthogonal): new function; also file restructured
131    
132    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
135            coercion to "nMatrix" and "pMatrix"
136    
137            * R/AllClass.R: "Schur" class;  "number" class union
138            * man/number-class.Rd:
139            * man/Schur-class.Rd:
140    
141            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
142            (.simpleSchur): Schur() method for diagonal matrices
143            (.triSchur):    Schur() method for triangular matrices
144            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
145    
146    
147    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
150    
151    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
154                    in order to ensure 'system = *' is not lost;
155                    formals()$system instead of cut&paste.
156            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
157    
158    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * DESCRIPTION (Date): make ready for release --> 0.999375-4
161    
162            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
163    
164    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
167                    and hence does as.vector(.).
168            * man/pMatrix-class.Rd: docs
169            * R/sparseMatrix.R: fix for printing "integer sparse"
170    
171            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
172    
173            * R/Matrix.R and others: use "exact" function argument list for
174                    both "["   : (x, i,j, ..., drop)
175                    and  "[<-" : (x, i,j, ..., value)
176    
177            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
178            * R/Tsparse.R (replTmat):    ditto
179            * R/diagMatrix.R (replDiag): ditto
180            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
181            * tests/indexing.R: testing the above
182    
183    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/sparseMatrix.R (cov2cor): method for sparse matrices
186    
187            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
188    
189            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
190    
191            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
192    
193    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * R/Matrix.R: "generic" cov2cor() method
196    
197            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
198                    speed up Q %*% D %*% t(Q)
199            * tests/dpoMatrix.R: test nearPD()
200    
201    2007-12-05  Doug Bates and Martin Maechler
202    
203            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
204            stats::xtabs() allowing to create sparse matrices.
205    
206    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
209    
210    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
213    
214    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/LU.R: solve() method for "denseLU"
217    
218    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
219    
220            * DESCRIPTION (Version): 0.999375-3 preparing for release
221    
222            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
223    
224            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
225    
226    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
229              thanks to Kasper Kristensen.
230            * tests/matprod.R: regression test for that.
231    
232    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
233    
234            * [r4778] R/AllGeneric.R: Check R version before defining generics for
235              primitives
236    
237    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
238    
239            * R/denseMatrix.R (rcond): method
240            * R/sparseQR.R (rcond): method, use x or t(x)
241    
242    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
243    
244            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
245            matrices.
246            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
247    
248            * man/rcond.Rd: mention the more general definition, and add
249            example for non-square matrices.
250    
251            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
252    
253    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
256    
257    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
260            * tests/indexing.R: add new regression for the above cases.
261    
262    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * src/Mutils.h (__sun): clause for alloca.h on Solaris
265    
266    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * DESCRIPTION (Date, Version): 0.999375-2
269    
270    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/HBMM.R (readMM): make work for pattern matrices as well
273    
274    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
275    
276            * [r4730] src/Mutils.h: declare alloca
277            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
278              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
279              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
280              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
281              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
282              methods; switch writeMM to use CHOLMOD code; repair readMM
283    
284    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
287            Oehlschlaegel's ... result type still to be discussed!
288    
289    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * man/image-methods.Rd: new, combining all image() methods
292    
293    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
296            to work via dgC...
297    
298            * R/Matrix.R (Matrix): special treatment for "table" (S3)
299    
300    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgTMatrix.R (image): change defaults to
303                    aspect = "iso", colorkey = FALSE
304    
305    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
308            must copy its *expanded* x slot before LAPACK call.
309    
310            * tests/matprod.R: test the last days' changes.
311    
312    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
313    
314            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
315              as well as in sources
316            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
317              Lapack call
318    
319    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
322                    ("Matrix", "matrix") which is needed in some cases.
323            Ditto for solve().
324    
325            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
326            infinite recursion in dispatch for some cases.
327    
328    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
329    
330            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
331              so pointers match
332    
333    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * DESCRIPTION (Date): set ready for release -- 0.999375-1
336    
337    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
338    
339            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
340              src/chm_common.c, src/chm_common.h: Change API for
341              numeric_as_chm_dense and N_AS_CHM_DN
342    
343    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
346            * tests/matprod.R: regr.test for it
347    
348    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
351            * tests/group-methods.R: and regression-test it
352    
353    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
354    
355            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
356              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
357              triplet_to_sparse, documentation, use typedefs
358    
359    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * man/dpoMatrix-class.Rd: added 'corMatrix' example
362    
363            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
364            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
365            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
366    
367            * R/lsparseMatrix.R: bug fix in "all" method
368            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
369    
370            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
371            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
372                    + matrix |-> nMatrix coercion
373            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
374            * man/pMatrix-class.Rd: ditto
375    
376            * R/Matrix.R (Summary): method for non-dMatrix
377    
378            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
379            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
380                    test all Summary methods.
381    
382    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
385    
386    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
389    
390            * R/pMatrix.R (t?crossprod): methods for pMatrix
391    
392    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
393    
394            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
395    
396    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
397    
398            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
399              trying to fix a subtle bug - which has been somewhere else.
400    
401    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
402    
403            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
404              solve the bug
405    
406    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * src/dgCMatrix.c (compressed_to_TMatrix):
409    
410    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * src/Csparse.c (Rsparse_validate): new, to have some validity
413            checking for RsparseMatrix
414            * src/dgCMatrix.c (xRMatrix_validate): ditto
415            * src/dtCMatrix.c (tRMatrix_validate): ditto
416    
417    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
418    
419            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
420              lgRMatrix
421            * [r4568] DESCRIPTION: Prepare for bug-fix release
422            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
423              for declaration of cholmod_symmetry
424    
425    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
428            release.
429    
430    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
431    
432            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
433              functions - no longer used
434            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
435              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
436              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
437              Alloca
438    
439    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
440    
441            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
442              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
443              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
444              src/t_gCMatrix_colSums.c: more R_CheckStack()s
445    
446    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
447    
448            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
449              the required amount of memory then call M_numeric_as_chm_dense.
450            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
451              (like Calloc but calling alloca)
452    
453    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
456            and extended with more sophisticated 'col.names' option.
457            * NAMESPACE: export  printSparseMatrix()
458            * man/printSpMatrix.Rd: document, incl. examples
459    
460    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
461    
462            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
463              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
464              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
465    
466    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * DESCRIPTION (Version): 0.99875-4
469    
470            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
471            some dimnames perservation.
472    
473            * R/dsTMatrix.R (t-method): keep dimnames
474            * R/dtTMatrix.R:  ditto
475    
476            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
477            and ncol(.) < 10
478    
479            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
480            from Mutils.h
481    
482            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
483            e.g. in as(<ngCMatrix>, "matrix")
484    
485    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
486    
487            * [r4529] .: Create a branch for the API changes from the 0.99875
488              series to the 0.999375 series
489            * [r4530] DESCRIPTION, inst/include/Matrix.h,
490              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
491              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
492              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
493              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
494              as_cholmod_x functions
495    
496    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
497    
498            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
499              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
500              to Comparisons
501    
502    >>>>>>> .merge-right.r4561
503    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * DESCRIPTION (Version): 0.99875-3 ready to be released.
506    
507            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
508    
509            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
510            that should also work in a future version of R.
511    
512    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
515    
516            * R/sparseVector.R: more *sparseVector coercions, notably for
517            non - double ones.
518    
519    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
520    
521            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
522              notably the new ones building on the new .Call(.)s:
523    
524            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
525            all 4 of [dlin]gCMatrix_colSums().
526    
527    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
528    
529            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
530            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
531              result
532    
533    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
534    
535            * R/kronecker.R: fix typo (could lead to inf.recursion)
536            * test/simple.R: testing that
537    
538            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
539            method as well (which can have arguments, show() can't).
540    
541    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
542    
543            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
544              added dgCMatrix_colSums for [col,row][Sums,Means]
545    
546    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
547    
548            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
549              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
550              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
551            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
552              class
553            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
554              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
555              row names to store the levels - duh!  Added an example.
556    
557    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * src/Csparse.c (Csparse_validate): check for *repeated* entries
560            thanks to example from Christian Buchta; with a test here:
561            * tests/simple.R:
562    
563    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
564    
565            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
566            of colSums(*, sparseResult = TRUE)
567    
568    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
569    
570            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
571            'na.rm = FALSE' as "everywhere" else in R.
572    
573    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
574    
575            * [r4421] src/CSparse_install.sh: Modify for new organization of
576              CSparse package
577            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
578              SuiteSparse
579            * [r4426] src/Makefile: add ./UFconfig to the include path for
580              compilation
581            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
582            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
583              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
584    
585    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
588            * R/sparseMatrix.R (prSpMatrix): now gives a message about
589            suppressed column names.
590    
591    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
592    
593            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
594              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
595              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
596              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
597              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
598              Remove warnings after change to const char* CHAR
599    
600    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
601    
602            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
603              type of M_cholmod_ssmult
604    
605    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
606    
607            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
608              src/init.c: Yet another cholmod export - cholmod_ssmult
609    
610    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * NAMESPACE: exported drop0(), since
613            * man/drop0.Rd: I have seen several cases, I really wanted to use
614            it, so our users may want too.
615    
616    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * man/colSums.Rd: separately document colSums() etc, since these
619            have the extra argument 'sparseResult'.
620    
621    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
622    
623            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
624            * man/spMatrix.Rd: docu., including examples
625    
626            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
627            in order to make colMeans() etc fast *and* correct.
628            * R/sparseVector.R (replSPvec): "[<-" functionality for
629            sparseVectors; tested in
630            * tests/simple.R:
631    
632    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
633    
634            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
635            (very) sparse Matrices; output similar to Matlab's print().
636    
637    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
638    
639            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
640            0-based, indices (Jose Quesada <quesada@gmail.com>).
641    
642    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
643    
644            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
645    
646    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Auxiliaries.R (sparsapply): new utility, much faster than
649            tapply1() for large sparse matrices.
650    
651    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653            * R/Matrix.R (dim<-): reshape now via sparseVector.
654    
655            * R/sparseVector.R: methods and function for
656            * R/AllClass.R: new "sparseVector" class and daughters.
657            * NAMESPACE: export new classes
658    
659    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
660    
661            * DESCRIPTION (Version): 0.99875-1
662            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
663    
664    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
665    
666            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
667            indexing
668            * tests/indexing.R: test set for that.
669    
670    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
671    
672            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
673            entries.
674            * tests/indexing.R(out): add regression test for it
675    
676    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
679            name for "!" method definitions.
680    
681    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
682    
683            * R/Tsparse.R (intI): new utility, used for "[" :
684                    Cleanup up there, and fixes for duplicated indices - more TODO!
685    
686            * tests/indexing.R(out): more tests
687    
688    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
689    
690            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
691            code that is now part of the R Lapack library.
692    
693            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
694            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
695    
696    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
699    
700    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
701    
702            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
703            up with extraneous names '0'...'<n-1>'
704    
705    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/dgTMatrix.R (mat2dgT): care about NAs
708    
709    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/kronecker.R: triangularity preserving methods
712    
713    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
714    
715            * R/kronecker.R: new file collecting kronecker() methods in one
716                    place.  Goal: become much faster!
717    
718    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
719    
720            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
721            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
722            can be much faster.
723    
724            * tests/matprod.R: add regression tests for these (upper & lower).
725    
726    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * R/Matrix.R (diff): method for our Matrices.
729    
730            * R/sparseMatrix.R (isDiagonal): check dim()!
731    
732    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
733    
734            * R/Matrix.R (dim<-): new method for "reshape()" built on a
735            proposal from Tamas Papp.
736    
737    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
738    
739            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
740    
741            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
742            rather define and export  cBind() and rBind() only.
743            --> useRs *must* change code that used to have cbind()/rbind() !!
744    
745            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
746            * R/bind.Rout.save: ditto
747    
748    2007-02-16  Douglas Bates  <bates@r-project.org>
749    
750            * DESCRIPTION (Date, Version): 0.9975-11 with new date
751            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
752            const modifier on declaration of the array 'valid'
753    
754    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
755    
756            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
757    
758    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
761    
762            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
763            * tests/simple.R: test the above and some of these coercions:
764    
765            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
766                    be careful to avoid infinite recursion, using new coercions in
767            * R/ngCMatrix.R and nsC... and ntC...
768            * R/lsparseMatrix.R: ditto
769    
770            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
771    
772            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
773            * R/Rsparse.R: reactivate .Call()s
774    
775            * tests/Class+Meth.R: a bit more on actual classes
776    
777    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
778    
779            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
780    
781    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
782    
783            * DESCRIPTION (Version): 0.9975-10 to upload
784    
785            * tests/Class+Meth.R (tstMatrixClass): require coercions to
786            specific classes less unconditionally.
787    
788            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
789    
790            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
791    
792            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
793            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
794            R_to_CMatrix segfaults on one platform.
795            Eliminate most coercion method to *specific* classes, and replace
796            with virtual classes coercions.
797    
798    
799    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
800    
801            * src/init.c: export the CHM...._validate() placeholders, since
802            they *are* called.
803    
804            * tests/Class+Meth.R (classCanCoerce): and starting to test
805            all as(<from>, <to>)
806    
807    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
808    
809            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
810            * tests/indexing.R: tested now
811            * tests/indexing.Rout.save: updated
812    
813            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
814            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
815            appropriate.
816    
817            * NAMESPACE: export a trivial
818            * R/Matrix.R: drop() Matrix-method
819    
820            * R/AllClass.R: moved all prototypes to virtual super classes.
821    
822            * R/Rsparse.R: many more coercions to have less exceptions in
823            * tests/Class+Meth.R:
824    
825            * R/Ops.R (Compare): tweak for case with NA
826            * tests/simpl.R: hence another 'FIXME' eliminated
827    
828    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
829    
830            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
831            objects.
832    
833            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
834              and more of "!", "&", "|", all, any; coercions
835    
836            * R/Rsparse.R: many coercions (which enable quite a few other
837            methods), thanks to enhancements in
838            * src/dgCMatrix.c (R_to_CMatrix): new, and
839            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
840            symmetric & triangular and ..RMatrix objects.
841    
842            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
843            renamed file from src/dsTMatrix.c;
844            now dealing with symmetric and triangular Tsparse coercions, both
845            to dense and general.
846    
847    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
848    
849            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
850    
851            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
852            where sensible when the <numeric> is of length > 1.
853    
854    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/Matrix.R ([<-): for M[] <- value: fix length
857    
858    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
859    
860            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
861            * R/ndenseMatrix.R: new coercions n* -> l*
862    
863    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
864    
865            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
866    
867            * R/Ops.R ("Logic"): and other "Ops", many updates
868    
869    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
870    
871            * src/Mutils.h (SET_DimNames): new utility
872    
873            * R/Auxiliaries.R (nnzero): improved and now exported via
874    
875            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
876    
877    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * R/diagMatrix.R (!): fix typo.
880    
881    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
882    
883            * R/Auxiliaries.R (as_Csparse): and quite a few others:
884                    allow to pass class definition --> speedup
885            * R/sparseMatrix.R: apply the above
886    
887            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
888    
889            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
890            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
891            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
892    
893            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
894    
895            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
896            and use it for "sparse*" as well, since it's faster than the
897            as_Csparse(.) way.
898    
899    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
902    
903    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
906            as method for   M[ ij ] <- v
907            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
908    
909            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
910            FALSE answer
911    
912            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
913            * tests/indexing.R: test it, and some of the above
914    
915    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/Auxiliaries.R (is_duplicatedT): new utility
918    
919    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
920    
921            * src/init.c (R_init_Matrix): export cholmod_scale
922    
923    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
924    
925            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
926            base::as.matrix to (x, ...)
927    
928    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
929    
930            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
931            file; start using "Logic", hence
932    
933            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
934            * NAMESPACE: import and export "Logic"
935    
936    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
937    
938            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
939            only needed previously to R version 2.5.0.
940    
941    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
942    
943            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
944    
945            * R/Tsparse.R (replTmat): fix subassignment of triangular
946            * R/Csparse.R (replCmat): ditto
947            * tests/indexing.R: more tests, incl the above fix
948    
949    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
950    
951            * R/Auxiliaries.R (drop0): extend for non CSparse
952            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
953    
954            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
955                    use uplo correctly (!); other places: use uplo_P() macro
956    
957            * R/Csparse.R (replCmat): call diagU2N() when needed
958            * R/Tsparse.R (replTmat): ditto
959    
960            * src/dtCMatrix.c (tCMatrix_validate): new
961            * src/dtTMatrix.c (tTMatrix_validate): new, used in
962            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
963    
964            * R/diagMatrix.R (replDiag): to use in [<-
965    
966    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
969                    also more general diagU2N().
970    
971    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
972    
973            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
974            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
975    
976    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
977    
978            * tests/bind.R: a few more cases
979            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
980    
981            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
982            * R/ddenseMatrix.R (cbind2/rbind2)
983            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
984            * tests/indexing.R
985            * tests/indexing.Rout.save: updated
986    
987    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
988    
989            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
990            * tests/indexing.R
991    
992    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
993    
994            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
995            align with proper position of "0", i.e., right for integers.
996            argument 'align' by default is "fancy".
997    
998    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
1001            * R/Csparse.R: and fix "Compare" for more cases.
1002            * tests/Class+Meth.R: test some of these (m == m, m != m)
1003    
1004    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
1005    
1006            * R/lsparseMatrix.R: all() and any() methods
1007            * R/ldenseMatrix.R:      ditto
1008            * NAMESPACE, R/Matrix.R: ditto
1009    
1010            * man/all-methods.Rd: document them minimally
1011    
1012            * tests/simple.R: add a few examples for these
1013    
1014    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1015    
1016            * R/Tsparse.R ([): fix long standing typo in symmetric case
1017            * man/dsCMatrix-class.Rd: add example exhibiting the above case
1018    
1019    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
1020    
1021            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
1022            to LL before converting to a sparse matrix. (The LDL form can be
1023            converted to a sparse matrix but it is implicitly a unit
1024            triangular matrix and a diagonal matrix overwritten on the diagonal.)
1025    
1026    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
1027    
1028            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
1029    
1030    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
1031    
1032            * DESCRIPTION (Version): updated -> release 0.9975-7
1033            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
1034    
1035    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
1038    
1039    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
1040    
1041            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
1042            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
1043            is exactly singular.
1044    
1045    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
1046    
1047            * DESCRIPTION (Date): updated -> release 0.9975-6
1048    
1049    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1050    
1051            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
1052            now returns symmetric.
1053    
1054            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
1055    
1056            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
1057            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
1058    
1059            * R/Auxiliaries.R (.type.kind): added
1060    
1061    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
1062    
1063            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
1064            running src/CSparse_install.sh
1065    
1066            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
1067    
1068    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
1069    
1070            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
1071            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
1072    
1073            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
1074    
1075            * tests/Class+Meth.R (tstMatrixClass): now assure
1076            the (important in method programming) property :
1077    
1078                    ###>>  Every "Matrix" is either
1079                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
1080    
1081                    (where "*" stands for "Matrix")
1082    
1083            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
1084    
1085            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
1086            * tests/validObj.R: checks for "comparison"
1087    
1088            * R/sparseMatrix.R ([): improved indexing for sparse;
1089                    trying to keep <symmetric>[ n, n] symmmetric
1090    
1091            * tests/indexing.R: indexing for logical sparse now ok
1092    
1093    
1094    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1095    
1096            * src/Tsparse.c: use xTsparse_validate() , and hence remove
1097    
1098            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
1099    
1100    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1101    
1102            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
1103    
1104            * tests/simple.R: validObject() checking the above.
1105    
1106            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
1107            replacing both dgCMatrix_validate and lgCM*.
1108    
1109            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
1110            fix dimnames setting in other places.
1111            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
1112    
1113    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1114    
1115            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
1116    
1117            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
1118            symmetry test, via
1119            * R/Auxiliaries.R (.as.dgC.0.factors):
1120    
1121    2006-11-01  Douglas Bates  <bates@r-project.org>
1122    
1123            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
1124            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
1125            <CsparseMatrix>) added
1126    
1127    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1128    
1129            * tests/matprod.R: add a variation of Harri's example
1130    
1131            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
1132            recursive infinitely.
1133    
1134            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
1135    
1136            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
1137    
1138    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1139    
1140            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
1141            matrix if possible; test m+m == 2*m; now test dgRMatrix.
1142            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
1143            satisfy the above test.
1144    
1145    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1146    
1147            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
1148    
1149            * R/dgCMatrix.R: solve(a, b="missing") based on
1150            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
1151            RHS = NULL.
1152    
1153            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
1154            add more (needed) [t]crossprod() methods.
1155    
1156            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
1157    
1158            * R/Auxiliaries.R (as_CspClass): cleanup
1159            (drop0): internal utility for "Csparse_drop(*, 0)"
1160            (.bail.out.2): encourage active feedback
1161    
1162    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
1163    
1164            * R/dMatrix.R(Compare): new(), then slots [no validity check]
1165    
1166            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
1167            non-valid or 'sorted' case).
1168    
1169            * R/dsparseMatrix.R: add "chol" method.
1170            * R/ddenseMatrix.R: ditto
1171    
1172            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
1173            * NAMESPACE (Ops)
1174            * R/diagMatrix.R (diag2T): simple utility used "higher level"
1175            coercion; deprecating direct lower level coercions.
1176    
1177            * R/*.R (seq): use seq_len() and seq_along() where possible.
1178    
1179    
1180    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
1181    
1182            * DESCRIPTION (Version): 0.9975-5 ready for release
1183    
1184    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
1185    
1186            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
1187    
1188    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
1189    
1190            * R/AllClass.R (corMatrix): add 'validity' check;
1191                    comment out unused "LDL" class definition
1192            * NAMESPACE: mention, but do not export "LDL" class
1193            * R/corMatrix.R: new (simple), needed for R-devel with
1194            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
1195              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
1196    
1197    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
1198    
1199            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
1200            use Rprintf and R's error handling.
1201    
1202    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
1203    
1204            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
1205            * tests/matprod.R: add tests for the bug fixed.
1206    
1207    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
1208    
1209            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
1210            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
1211    
1212    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
1213    
1214            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
1215    
1216    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
1217    
1218            * DESCRIPTION (Version): 0.9975-3
1219    
1220            * R/diagMatrix.R (bdiag): new function constructing block diagonal
1221            (sparse) matrices.
1222            * man/bdiag.Rd: docu + examples
1223    
1224            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
1225    
1226            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
1227            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
1228    
1229            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
1230            that result is sparse or diagonal (and not dense).
1231    
1232            * man/Subassign-methods.Rd: fix examples
1233    
1234            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
1235            should always return a sparse (and not sometimes a diagonal) matrix.
1236    
1237    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
1238    
1239            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
1240    
1241    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
1242    
1243            * DESCRIPTION (Version): 0.9975-2
1244    
1245            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
1246    
1247    2006-10-02  Douglas Bates  <bates@R-project.org>
1248    
1249            * tests/dg_Matrix.R: Simplify test taking into account new code.
1250    
1251  2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
1252    
1253            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
1254    
1255          * R/lsTMatrix.R: new files w/ missing methods          * R/lsTMatrix.R: new files w/ missing methods
1256          * R/nsTMatrix.R:  "  'for completeness'          * R/nsTMatrix.R:  "  'for completeness'
1257    

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