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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 2120, Tue Mar 4 21:44:41 2008 UTC
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1    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
4    
5            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
6            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
7    
8            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
9    
10            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
11    
12            * src/chm_common.c (AS_CHM_FINISH): add note about problem
13            for triangular (diag = "U").
14    
15    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
18            * R/bind.R:  .Call(dense_to_Csparse, *)
19    
20    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/Matrix.R (Matrix): no longer use coercions to specific classes
23                    (since we are discouraging them in user code).
24    
25            * tests/*.R: also replaces coercions to specific classes by
26            coercions to super classes.
27    
28            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
29    
30    
31    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
34    
35            * src/dense.c (dense_band): generalized from ddense_band
36    
37            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
38              now for "denseMatrix" (instead of just "ddense*"); much
39              simplified setMethod()s for these.
40    
41            * src/dense.c (dense_to_symmetric): generalized from ddense_*
42    
43    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
44    
45            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
46            version of as(*, "symmetricMatric").
47    
48            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
49            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
50    
51    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
52    
53            * R/Matrix.R (subset.ij): utility, as first step to faster
54               M [ <ij-matrix> ] indexing.
55    
56            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
57    
58            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
59            for more efficient symmpart() and skewpart() methods.
60    
61            * src/Mutils.c (equal_string_vectors): utility
62    
63            * src/dense.c (ddense_to_symmetric): new function used in
64    
65            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
66    
67            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
68            order to match the generic (and evade .local(..)).
69    
70            * R/dsCMatrix.R: dgC -> dsC: use C code!
71    
72            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
73            as per TODO
74    
75            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
76    
77            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
78    
79    
80    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
83    
84            * R/Auxiliaries.R (non0.i): take out of non0ind
85    
86            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
87            make tril(), triu(), band() work for "matrix" and all "dense*"
88    
89            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
90            * tests/simple.R: test the fix above
91    
92            * R/sparseMatrix.R ([): simplification: no coerce to <general>
93                    before we use as(., <Tsparse>)[...] anyway
94    
95            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
96    
97            * R/triangularMatrix.R (isTriangular): methods for all subclasses
98            instead of "triangularMatrix" -- just to disambiguate
99    
100    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
103            * tests/indexing.R: example that fails above
104    
105    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
106    
107            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
108            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
109                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
110    
111            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
112            * src/Tsparse.h, init.c: ditto
113            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
114                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
115            * R/sparseMatrix.R (isTriangular): hence simplified
116    
117    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/Ops.R (.Arith.Csparse): new utility factored out of former
120              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
121    
122    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
125    
126            * inst/test-tools.R (isOrthogonal): new function; also file restructured
127    
128    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
131            coercion to "nMatrix" and "pMatrix"
132    
133            * R/AllClass.R: "Schur" class;  "number" class union
134            * man/number-class.Rd:
135            * man/Schur-class.Rd:
136    
137            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
138            (.simpleSchur): Schur() method for diagonal matrices
139            (.triSchur):    Schur() method for triangular matrices
140            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
141    
142    
143    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
146    
147    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
150                    in order to ensure 'system = *' is not lost;
151                    formals()$system instead of cut&paste.
152            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
153    
154    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
155    
156            * DESCRIPTION (Date): make ready for release --> 0.999375-4
157    
158            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
159    
160    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
163                    and hence does as.vector(.).
164            * man/pMatrix-class.Rd: docs
165            * R/sparseMatrix.R: fix for printing "integer sparse"
166    
167            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
168    
169            * R/Matrix.R and others: use "exact" function argument list for
170                    both "["   : (x, i,j, ..., drop)
171                    and  "[<-" : (x, i,j, ..., value)
172    
173            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
174            * R/Tsparse.R (replTmat):    ditto
175            * R/diagMatrix.R (replDiag): ditto
176            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
177            * tests/indexing.R: testing the above
178    
179    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
180    
181            * R/sparseMatrix.R (cov2cor): method for sparse matrices
182    
183            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
184    
185            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
186    
187            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
188    
189    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Matrix.R: "generic" cov2cor() method
192    
193            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
194                    speed up Q %*% D %*% t(Q)
195            * tests/dpoMatrix.R: test nearPD()
196    
197    2007-12-05  Doug Bates and Martin Maechler
198    
199            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
200            stats::xtabs() allowing to create sparse matrices.
201    
202    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
205    
206    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
209    
210    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * R/LU.R: solve() method for "denseLU"
213    
214    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * DESCRIPTION (Version): 0.999375-3 preparing for release
217    
218            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
219    
220            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
221    
222    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
225              thanks to Kasper Kristensen.
226            * tests/matprod.R: regression test for that.
227    
228    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
229    
230            * [r4778] R/AllGeneric.R: Check R version before defining generics for
231              primitives
232    
233    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/denseMatrix.R (rcond): method
236            * R/sparseQR.R (rcond): method, use x or t(x)
237    
238    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
241            matrices.
242            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
243    
244            * man/rcond.Rd: mention the more general definition, and add
245            example for non-square matrices.
246    
247            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
248    
249    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
252    
253    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
256            * tests/indexing.R: add new regression for the above cases.
257    
258    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * src/Mutils.h (__sun): clause for alloca.h on Solaris
261    
262    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * DESCRIPTION (Date, Version): 0.999375-2
265    
266    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
267    
268            * R/HBMM.R (readMM): make work for pattern matrices as well
269    
270    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
271    
272            * [r4730] src/Mutils.h: declare alloca
273            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
274              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
275              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
276              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
277              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
278              methods; switch writeMM to use CHOLMOD code; repair readMM
279    
280    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
283            Oehlschlaegel's ... result type still to be discussed!
284    
285    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * man/image-methods.Rd: new, combining all image() methods
288    
289    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
292            to work via dgC...
293    
294            * R/Matrix.R (Matrix): special treatment for "table" (S3)
295    
296    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/dgTMatrix.R (image): change defaults to
299                    aspect = "iso", colorkey = FALSE
300    
301    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
304            must copy its *expanded* x slot before LAPACK call.
305    
306            * tests/matprod.R: test the last days' changes.
307    
308    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
309    
310            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
311              as well as in sources
312            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
313              Lapack call
314    
315    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
318                    ("Matrix", "matrix") which is needed in some cases.
319            Ditto for solve().
320    
321            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
322            infinite recursion in dispatch for some cases.
323    
324    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
325    
326            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
327              so pointers match
328    
329    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * DESCRIPTION (Date): set ready for release -- 0.999375-1
332    
333    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
334    
335            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
336              src/chm_common.c, src/chm_common.h: Change API for
337              numeric_as_chm_dense and N_AS_CHM_DN
338    
339    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
342            * tests/matprod.R: regr.test for it
343    
344    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
347            * tests/group-methods.R: and regression-test it
348    
349    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
350    
351            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
352              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
353              triplet_to_sparse, documentation, use typedefs
354    
355    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * man/dpoMatrix-class.Rd: added 'corMatrix' example
358    
359            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
360            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
361            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
362    
363            * R/lsparseMatrix.R: bug fix in "all" method
364            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
365    
366            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
367            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
368                    + matrix |-> nMatrix coercion
369            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
370            * man/pMatrix-class.Rd: ditto
371    
372            * R/Matrix.R (Summary): method for non-dMatrix
373    
374            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
375            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
376                    test all Summary methods.
377    
378    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
381    
382    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
385    
386            * R/pMatrix.R (t?crossprod): methods for pMatrix
387    
388    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
389    
390            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
391    
392    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
393    
394            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
395              trying to fix a subtle bug - which has been somewhere else.
396    
397    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
398    
399            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
400              solve the bug
401    
402    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * src/dgCMatrix.c (compressed_to_TMatrix):
405    
406    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
407    
408            * src/Csparse.c (Rsparse_validate): new, to have some validity
409            checking for RsparseMatrix
410            * src/dgCMatrix.c (xRMatrix_validate): ditto
411            * src/dtCMatrix.c (tRMatrix_validate): ditto
412    
413    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
414    
415            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
416              lgRMatrix
417            * [r4568] DESCRIPTION: Prepare for bug-fix release
418            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
419              for declaration of cholmod_symmetry
420    
421    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
424            release.
425    
426    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
427    
428            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
429              functions - no longer used
430            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
431              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
432              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
433              Alloca
434    
435    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
436    
437            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
438              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
439              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
440              src/t_gCMatrix_colSums.c: more R_CheckStack()s
441    
442    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
443    
444            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
445              the required amount of memory then call M_numeric_as_chm_dense.
446            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
447              (like Calloc but calling alloca)
448    
449    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
452            and extended with more sophisticated 'col.names' option.
453            * NAMESPACE: export  printSparseMatrix()
454            * man/printSpMatrix.Rd: document, incl. examples
455    
456    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
457    
458            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
459              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
460              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
461    
462    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
463    
464            * DESCRIPTION (Version): 0.99875-4
465    
466            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
467            some dimnames perservation.
468    
469            * R/dsTMatrix.R (t-method): keep dimnames
470            * R/dtTMatrix.R:  ditto
471    
472            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
473            and ncol(.) < 10
474    
475            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
476            from Mutils.h
477    
478            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
479            e.g. in as(<ngCMatrix>, "matrix")
480    
481    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
482    
483            * [r4529] .: Create a branch for the API changes from the 0.99875
484              series to the 0.999375 series
485            * [r4530] DESCRIPTION, inst/include/Matrix.h,
486              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
487              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
488              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
489              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
490              as_cholmod_x functions
491    
492    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
493    
494            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
495              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
496              to Comparisons
497    
498    >>>>>>> .merge-right.r4561
499    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
500    
501            * DESCRIPTION (Version): 0.99875-3 ready to be released.
502    
503            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
504    
505            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
506            that should also work in a future version of R.
507    
508    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
511    
512            * R/sparseVector.R: more *sparseVector coercions, notably for
513            non - double ones.
514    
515    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
516    
517            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
518              notably the new ones building on the new .Call(.)s:
519    
520            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
521            all 4 of [dlin]gCMatrix_colSums().
522    
523    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
524    
525            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
526            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
527              result
528    
529    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
530    
531            * R/kronecker.R: fix typo (could lead to inf.recursion)
532            * test/simple.R: testing that
533    
534            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
535            method as well (which can have arguments, show() can't).
536    
537    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
538    
539            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
540              added dgCMatrix_colSums for [col,row][Sums,Means]
541    
542    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
543    
544            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
545              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
546              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
547            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
548              class
549            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
550              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
551              row names to store the levels - duh!  Added an example.
552    
553    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * src/Csparse.c (Csparse_validate): check for *repeated* entries
556            thanks to example from Christian Buchta; with a test here:
557            * tests/simple.R:
558    
559    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
560    
561            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
562            of colSums(*, sparseResult = TRUE)
563    
564    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
565    
566            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
567            'na.rm = FALSE' as "everywhere" else in R.
568    
569    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
570    
571            * [r4421] src/CSparse_install.sh: Modify for new organization of
572              CSparse package
573            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
574              SuiteSparse
575            * [r4426] src/Makefile: add ./UFconfig to the include path for
576              compilation
577            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
578            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
579              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
580    
581    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
584            * R/sparseMatrix.R (prSpMatrix): now gives a message about
585            suppressed column names.
586    
587    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
588    
589            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
590              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
591              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
592              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
593              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
594              Remove warnings after change to const char* CHAR
595    
596    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
597    
598            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
599              type of M_cholmod_ssmult
600    
601    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
602    
603            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
604              src/init.c: Yet another cholmod export - cholmod_ssmult
605    
606    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
607    
608            * NAMESPACE: exported drop0(), since
609            * man/drop0.Rd: I have seen several cases, I really wanted to use
610            it, so our users may want too.
611    
612    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
613    
614            * man/colSums.Rd: separately document colSums() etc, since these
615            have the extra argument 'sparseResult'.
616    
617    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
620            * man/spMatrix.Rd: docu., including examples
621    
622            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
623            in order to make colMeans() etc fast *and* correct.
624            * R/sparseVector.R (replSPvec): "[<-" functionality for
625            sparseVectors; tested in
626            * tests/simple.R:
627    
628    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
629    
630            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
631            (very) sparse Matrices; output similar to Matlab's print().
632    
633    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
634    
635            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
636            0-based, indices (Jose Quesada <quesada@gmail.com>).
637    
638    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
639    
640            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
641    
642    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/Auxiliaries.R (sparsapply): new utility, much faster than
645            tapply1() for large sparse matrices.
646    
647    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
648    
649            * R/Matrix.R (dim<-): reshape now via sparseVector.
650    
651            * R/sparseVector.R: methods and function for
652            * R/AllClass.R: new "sparseVector" class and daughters.
653            * NAMESPACE: export new classes
654    
655    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * DESCRIPTION (Version): 0.99875-1
658            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
659    
660    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
663            indexing
664            * tests/indexing.R: test set for that.
665    
666    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
667    
668            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
669            entries.
670            * tests/indexing.R(out): add regression test for it
671    
672    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
675            name for "!" method definitions.
676    
677    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
678    
679            * R/Tsparse.R (intI): new utility, used for "[" :
680                    Cleanup up there, and fixes for duplicated indices - more TODO!
681    
682            * tests/indexing.R(out): more tests
683    
684    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
685    
686            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
687            code that is now part of the R Lapack library.
688    
689            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
690            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
691    
692    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
693    
694            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
695    
696    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
697    
698            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
699            up with extraneous names '0'...'<n-1>'
700    
701    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
702    
703            * R/dgTMatrix.R (mat2dgT): care about NAs
704    
705    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
706    
707            * R/kronecker.R: triangularity preserving methods
708    
709    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/kronecker.R: new file collecting kronecker() methods in one
712                    place.  Goal: become much faster!
713    
714    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
717            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
718            can be much faster.
719    
720            * tests/matprod.R: add regression tests for these (upper & lower).
721    
722    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * R/Matrix.R (diff): method for our Matrices.
725    
726            * R/sparseMatrix.R (isDiagonal): check dim()!
727    
728    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
729    
730            * R/Matrix.R (dim<-): new method for "reshape()" built on a
731            proposal from Tamas Papp.
732    
733    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
736    
737            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
738            rather define and export  cBind() and rBind() only.
739            --> useRs *must* change code that used to have cbind()/rbind() !!
740    
741            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
742            * R/bind.Rout.save: ditto
743    
744    2007-02-16  Douglas Bates  <bates@r-project.org>
745    
746            * DESCRIPTION (Date, Version): 0.9975-11 with new date
747            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
748            const modifier on declaration of the array 'valid'
749    
750    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
751    
752            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
753    
754    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
755    
756            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
757    
758            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
759            * tests/simple.R: test the above and some of these coercions:
760    
761            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
762                    be careful to avoid infinite recursion, using new coercions in
763            * R/ngCMatrix.R and nsC... and ntC...
764            * R/lsparseMatrix.R: ditto
765    
766            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
767    
768            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
769            * R/Rsparse.R: reactivate .Call()s
770    
771            * tests/Class+Meth.R: a bit more on actual classes
772    
773    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
774    
775            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
776    
777    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
778    
779            * DESCRIPTION (Version): 0.9975-10 to upload
780    
781            * tests/Class+Meth.R (tstMatrixClass): require coercions to
782            specific classes less unconditionally.
783    
784            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
785    
786            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
787    
788            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
789            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
790            R_to_CMatrix segfaults on one platform.
791            Eliminate most coercion method to *specific* classes, and replace
792            with virtual classes coercions.
793    
794    
795    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
796    
797            * src/init.c: export the CHM...._validate() placeholders, since
798            they *are* called.
799    
800            * tests/Class+Meth.R (classCanCoerce): and starting to test
801            all as(<from>, <to>)
802    
803    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
806            * tests/indexing.R: tested now
807            * tests/indexing.Rout.save: updated
808    
809            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
810            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
811            appropriate.
812    
813            * NAMESPACE: export a trivial
814            * R/Matrix.R: drop() Matrix-method
815    
816            * R/AllClass.R: moved all prototypes to virtual super classes.
817    
818            * R/Rsparse.R: many more coercions to have less exceptions in
819            * tests/Class+Meth.R:
820    
821            * R/Ops.R (Compare): tweak for case with NA
822            * tests/simpl.R: hence another 'FIXME' eliminated
823    
824    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
825    
826            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
827            objects.
828    
829            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
830              and more of "!", "&", "|", all, any; coercions
831    
832            * R/Rsparse.R: many coercions (which enable quite a few other
833            methods), thanks to enhancements in
834            * src/dgCMatrix.c (R_to_CMatrix): new, and
835            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
836            symmetric & triangular and ..RMatrix objects.
837    
838            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
839            renamed file from src/dsTMatrix.c;
840            now dealing with symmetric and triangular Tsparse coercions, both
841            to dense and general.
842    
843    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
844    
845            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
846    
847            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
848            where sensible when the <numeric> is of length > 1.
849    
850    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
851    
852            * R/Matrix.R ([<-): for M[] <- value: fix length
853    
854    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
857            * R/ndenseMatrix.R: new coercions n* -> l*
858    
859    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
860    
861            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
862    
863            * R/Ops.R ("Logic"): and other "Ops", many updates
864    
865    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
866    
867            * src/Mutils.h (SET_DimNames): new utility
868    
869            * R/Auxiliaries.R (nnzero): improved and now exported via
870    
871            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
872    
873    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
874    
875            * R/diagMatrix.R (!): fix typo.
876    
877    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
878    
879            * R/Auxiliaries.R (as_Csparse): and quite a few others:
880                    allow to pass class definition --> speedup
881            * R/sparseMatrix.R: apply the above
882    
883            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
884    
885            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
886            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
887            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
888    
889            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
890    
891            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
892            and use it for "sparse*" as well, since it's faster than the
893            as_Csparse(.) way.
894    
895    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
898    
899    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
900    
901            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
902            as method for   M[ ij ] <- v
903            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
904    
905            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
906            FALSE answer
907    
908            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
909            * tests/indexing.R: test it, and some of the above
910    
911    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
912    
913            * R/Auxiliaries.R (is_duplicatedT): new utility
914    
915  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
916    
917          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
918    
919    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
922            base::as.matrix to (x, ...)
923    
924  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
925    
926          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R          * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R

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