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revision 1767, Mon Feb 5 16:53:17 2007 UTC revision 2128, Thu Mar 13 23:08:34 2008 UTC
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1    2008-03-13  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * DESCRIPTION (Version, Date): bug-fix release 0.999375-6
4    
5            * R/diagMatrix.R (diag2tT.u): utility to be smarter in
6              <diagonal> o <sparse_triangular>
7              setAs(., "nMatrix") added.
8    
9            * R/diagMatrix.R (Diagonal): Diagonal(4, x=3) now works too
10    
11            * R/Auxiliaries.R (.diagU2N): more careful coercion in 2 steps
12                    new argument 'checkDense = FALSE'.
13    
14    
15    2008-03-07  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * src/dgeMatrix.c (dgeMatrix_exp): fix the octave-origin bug in the
18            back-permutation of the matrix exponential.
19    
20            * tests/matr-exp.R: test the fix (for an example where expm() was wrong).
21    
22            * DESCRIPTION (Date,Version): ready to release 0.999375-5
23    
24            * tests/simple.R: testing diagN2U
25    
26    2008-03-06  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (diagN2U): interface to
29    
30            * src/Csparse.c (Csparse_diagN2U): .Call()able SEXP version of chm_diagN2U()
31    
32            * tests/matprod.R: test for triangularity preserving <dtC> %*% <dtC>
33    
34    2008-03-05  Martin Maechler  <maechler@stat.math.ethz.ch>
35    
36            * src/chm_common.c (chm_diagN2U): new utility.
37    
38            * src/Csparse.c (Csparse_Csparse_crossprod, Csparse_Csparse_prod):
39            make use of chm_diagN2U() and hence now preserve triangularity and
40            unit-triangularity.
41    
42            * DESCRIPTION (LicenseDetails): new; such that 'License:' becomes "canonical"
43    
44    2008-03-04  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/diagMatrix.R (subDiag): fix when x[..] became a vector
47    
48            * src/Tsparse.c (Tsparse_diagU2N): new utility, necessary for e.g.
49            * src/Csparse.c (Csparse_crossprod): use [CT]sparse_diagU2N() !!
50    
51            * R/Auxiliaries.R (.diagU2N): make use of new Tsparse_diagU2N
52    
53            * R/Ops.R ("-" (<sparseMatrix>)): use diagU2N()
54    
55            * src/chm_common.c (AS_CHM_FINISH): add note about problem
56            for triangular (diag = "U").
57    
58    2008-02-21  Martin Maechler  <maechler@stat.math.ethz.ch>
59    
60            * R/Auxiliaries.R (as_Csparse2): drop this, replacing by
61            * R/bind.R:  .Call(dense_to_Csparse, *)
62    
63    2008-02-20  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (Matrix): no longer use coercions to specific classes
66                    (since we are discouraging them in user code).
67    
68            * tests/*.R: also replaces coercions to specific classes by
69            coercions to super classes.
70    
71            * R/denseMatrix.R (.dense2C): simplified by using forceSymmetric()
72    
73    
74    2008-02-19  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * man/CAex.Rd: example: coerce to symmetric*, not dsC*
77    
78            * src/dense.c (dense_band): generalized from ddense_band
79    
80            * R/ddenseMatrix.R (.trilDense,.triuDense, .bandDense):
81              now for "denseMatrix" (instead of just "ddense*"); much
82              simplified setMethod()s for these.
83    
84            * src/dense.c (dense_to_symmetric): generalized from ddense_*
85    
86    2008-02-18  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/AllGeneric.R: forceSymmetric() generic: fast no-checking
89            version of as(*, "symmetricMatric").
90    
91            * src/dense.c (ddense_to_symmetric): add 'symm_test' argument, and
92            * R/symmetricMatrix.R: set it TRUE in coercion to "symmetricMatrix"
93    
94    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * R/Matrix.R (subset.ij): utility, as first step to faster
97               M [ <ij-matrix> ] indexing.
98    
99            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
100    
101            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
102            for more efficient symmpart() and skewpart() methods.
103    
104            * src/Mutils.c (equal_string_vectors): utility
105    
106            * src/dense.c (ddense_to_symmetric): new function used in
107    
108            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
109    
110            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
111            order to match the generic (and evade .local(..)).
112    
113            * R/dsCMatrix.R: dgC -> dsC: use C code!
114    
115            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
116            as per TODO
117    
118            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
119    
120            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
121    
122    
123    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
126    
127            * R/Auxiliaries.R (non0.i): take out of non0ind
128    
129            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
130            make tril(), triu(), band() work for "matrix" and all "dense*"
131    
132            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
133            * tests/simple.R: test the fix above
134    
135            * R/sparseMatrix.R ([): simplification: no coerce to <general>
136                    before we use as(., <Tsparse>)[...] anyway
137    
138            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
139    
140            * R/triangularMatrix.R (isTriangular): methods for all subclasses
141            instead of "triangularMatrix" -- just to disambiguate
142    
143    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
144    
145            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
146            * tests/indexing.R: example that fails above
147    
148    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
151            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
152                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
153    
154            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
155            * src/Tsparse.h, init.c: ditto
156            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
157                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
158            * R/sparseMatrix.R (isTriangular): hence simplified
159    
160    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/Ops.R (.Arith.Csparse): new utility factored out of former
163              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
164    
165    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
168    
169            * inst/test-tools.R (isOrthogonal): new function; also file restructured
170    
171    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
172    
173            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
174            coercion to "nMatrix" and "pMatrix"
175    
176            * R/AllClass.R: "Schur" class;  "number" class union
177            * man/number-class.Rd:
178            * man/Schur-class.Rd:
179    
180            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
181            (.simpleSchur): Schur() method for diagonal matrices
182            (.triSchur):    Schur() method for triangular matrices
183            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
184    
185    
186    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
189    
190    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
191    
192            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
193                    in order to ensure 'system = *' is not lost;
194                    formals()$system instead of cut&paste.
195            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
196    
197    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Date): make ready for release --> 0.999375-4
200    
201            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
202    
203    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
206                    and hence does as.vector(.).
207            * man/pMatrix-class.Rd: docs
208            * R/sparseMatrix.R: fix for printing "integer sparse"
209    
210            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
211    
212            * R/Matrix.R and others: use "exact" function argument list for
213                    both "["   : (x, i,j, ..., drop)
214                    and  "[<-" : (x, i,j, ..., value)
215    
216            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
217            * R/Tsparse.R (replTmat):    ditto
218            * R/diagMatrix.R (replDiag): ditto
219            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
220            * tests/indexing.R: testing the above
221    
222    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/sparseMatrix.R (cov2cor): method for sparse matrices
225    
226            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
227    
228            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
229    
230            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
231    
232    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
233    
234            * R/Matrix.R: "generic" cov2cor() method
235    
236            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
237                    speed up Q %*% D %*% t(Q)
238            * tests/dpoMatrix.R: test nearPD()
239    
240    2007-12-05  Doug Bates and Martin Maechler
241    
242            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
243            stats::xtabs() allowing to create sparse matrices.
244    
245    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
246    
247            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
248    
249    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
252    
253    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
254    
255            * R/LU.R: solve() method for "denseLU"
256    
257    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * DESCRIPTION (Version): 0.999375-3 preparing for release
260    
261            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
262    
263            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
264    
265    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
268              thanks to Kasper Kristensen.
269            * tests/matprod.R: regression test for that.
270    
271    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
272    
273            * [r4778] R/AllGeneric.R: Check R version before defining generics for
274              primitives
275    
276    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/denseMatrix.R (rcond): method
279            * R/sparseQR.R (rcond): method, use x or t(x)
280    
281    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
282    
283            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
284            matrices.
285            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
286    
287            * man/rcond.Rd: mention the more general definition, and add
288            example for non-square matrices.
289    
290            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
291    
292    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
293    
294            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
295    
296    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
299            * tests/indexing.R: add new regression for the above cases.
300    
301    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
302    
303            * src/Mutils.h (__sun): clause for alloca.h on Solaris
304    
305    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * DESCRIPTION (Date, Version): 0.999375-2
308    
309    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/HBMM.R (readMM): make work for pattern matrices as well
312    
313    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
314    
315            * [r4730] src/Mutils.h: declare alloca
316            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
317              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
318              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
319              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
320              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
321              methods; switch writeMM to use CHOLMOD code; repair readMM
322    
323    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
326            Oehlschlaegel's ... result type still to be discussed!
327    
328    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * man/image-methods.Rd: new, combining all image() methods
331    
332    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
335            to work via dgC...
336    
337            * R/Matrix.R (Matrix): special treatment for "table" (S3)
338    
339    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/dgTMatrix.R (image): change defaults to
342                    aspect = "iso", colorkey = FALSE
343    
344    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
347            must copy its *expanded* x slot before LAPACK call.
348    
349            * tests/matprod.R: test the last days' changes.
350    
351    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
352    
353            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
354              as well as in sources
355            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
356              Lapack call
357    
358    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
361                    ("Matrix", "matrix") which is needed in some cases.
362            Ditto for solve().
363    
364            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
365            infinite recursion in dispatch for some cases.
366    
367    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
368    
369            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
370              so pointers match
371    
372    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * DESCRIPTION (Date): set ready for release -- 0.999375-1
375    
376    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
377    
378            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
379              src/chm_common.c, src/chm_common.h: Change API for
380              numeric_as_chm_dense and N_AS_CHM_DN
381    
382    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
385            * tests/matprod.R: regr.test for it
386    
387    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
390            * tests/group-methods.R: and regression-test it
391    
392    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
393    
394            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
395              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
396              triplet_to_sparse, documentation, use typedefs
397    
398    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
399    
400            * man/dpoMatrix-class.Rd: added 'corMatrix' example
401    
402            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
403            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
404            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
405    
406            * R/lsparseMatrix.R: bug fix in "all" method
407            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
408    
409            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
410            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
411                    + matrix |-> nMatrix coercion
412            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
413            * man/pMatrix-class.Rd: ditto
414    
415            * R/Matrix.R (Summary): method for non-dMatrix
416    
417            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
418            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
419                    test all Summary methods.
420    
421    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
422    
423            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
424    
425    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
428    
429            * R/pMatrix.R (t?crossprod): methods for pMatrix
430    
431    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
432    
433            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
434    
435    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
436    
437            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
438              trying to fix a subtle bug - which has been somewhere else.
439    
440    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
441    
442            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
443              solve the bug
444    
445    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * src/dgCMatrix.c (compressed_to_TMatrix):
448    
449    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * src/Csparse.c (Rsparse_validate): new, to have some validity
452            checking for RsparseMatrix
453            * src/dgCMatrix.c (xRMatrix_validate): ditto
454            * src/dtCMatrix.c (tRMatrix_validate): ditto
455    
456    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
457    
458            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
459              lgRMatrix
460            * [r4568] DESCRIPTION: Prepare for bug-fix release
461            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
462              for declaration of cholmod_symmetry
463    
464    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
467            release.
468    
469    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
470    
471            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
472              functions - no longer used
473            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
474              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
475              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
476              Alloca
477    
478    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
479    
480            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
481              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
482              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
483              src/t_gCMatrix_colSums.c: more R_CheckStack()s
484    
485    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
486    
487            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
488              the required amount of memory then call M_numeric_as_chm_dense.
489            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
490              (like Calloc but calling alloca)
491    
492    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
493    
494            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
495            and extended with more sophisticated 'col.names' option.
496            * NAMESPACE: export  printSparseMatrix()
497            * man/printSpMatrix.Rd: document, incl. examples
498    
499    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
500    
501            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
502              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
503              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
504    
505    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * DESCRIPTION (Version): 0.99875-4
508    
509            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
510            some dimnames perservation.
511    
512            * R/dsTMatrix.R (t-method): keep dimnames
513            * R/dtTMatrix.R:  ditto
514    
515            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
516            and ncol(.) < 10
517    
518            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
519            from Mutils.h
520    
521            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
522            e.g. in as(<ngCMatrix>, "matrix")
523    
524    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
525    
526            * [r4529] .: Create a branch for the API changes from the 0.99875
527              series to the 0.999375 series
528            * [r4530] DESCRIPTION, inst/include/Matrix.h,
529              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
530              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
531              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
532              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
533              as_cholmod_x functions
534    
535    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
536    
537            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
538              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
539              to Comparisons
540    
541    >>>>>>> .merge-right.r4561
542    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
543    
544            * DESCRIPTION (Version): 0.99875-3 ready to be released.
545    
546            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
547    
548            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
549            that should also work in a future version of R.
550    
551    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
552    
553            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
554    
555            * R/sparseVector.R: more *sparseVector coercions, notably for
556            non - double ones.
557    
558    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
561              notably the new ones building on the new .Call(.)s:
562    
563            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
564            all 4 of [dlin]gCMatrix_colSums().
565    
566    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
567    
568            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
569            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
570              result
571    
572    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
573    
574            * R/kronecker.R: fix typo (could lead to inf.recursion)
575            * test/simple.R: testing that
576    
577            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
578            method as well (which can have arguments, show() can't).
579    
580    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
581    
582            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
583              added dgCMatrix_colSums for [col,row][Sums,Means]
584    
585    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
586    
587            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
588              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
589              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
590            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
591              class
592            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
593              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
594              row names to store the levels - duh!  Added an example.
595    
596    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * src/Csparse.c (Csparse_validate): check for *repeated* entries
599            thanks to example from Christian Buchta; with a test here:
600            * tests/simple.R:
601    
602    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
603    
604            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
605            of colSums(*, sparseResult = TRUE)
606    
607    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
610            'na.rm = FALSE' as "everywhere" else in R.
611    
612    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
613    
614            * [r4421] src/CSparse_install.sh: Modify for new organization of
615              CSparse package
616            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
617              SuiteSparse
618            * [r4426] src/Makefile: add ./UFconfig to the include path for
619              compilation
620            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
621            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
622              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
623    
624    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
627            * R/sparseMatrix.R (prSpMatrix): now gives a message about
628            suppressed column names.
629    
630    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
631    
632            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
633              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
634              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
635              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
636              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
637              Remove warnings after change to const char* CHAR
638    
639    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
640    
641            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
642              type of M_cholmod_ssmult
643    
644    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
645    
646            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
647              src/init.c: Yet another cholmod export - cholmod_ssmult
648    
649    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
650    
651            * NAMESPACE: exported drop0(), since
652            * man/drop0.Rd: I have seen several cases, I really wanted to use
653            it, so our users may want too.
654    
655    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * man/colSums.Rd: separately document colSums() etc, since these
658            have the extra argument 'sparseResult'.
659    
660    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
661    
662            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
663            * man/spMatrix.Rd: docu., including examples
664    
665            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
666            in order to make colMeans() etc fast *and* correct.
667            * R/sparseVector.R (replSPvec): "[<-" functionality for
668            sparseVectors; tested in
669            * tests/simple.R:
670    
671    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
672    
673            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
674            (very) sparse Matrices; output similar to Matlab's print().
675    
676    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
677    
678            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
679            0-based, indices (Jose Quesada <quesada@gmail.com>).
680    
681    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
682    
683            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
684    
685    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
686    
687            * R/Auxiliaries.R (sparsapply): new utility, much faster than
688            tapply1() for large sparse matrices.
689    
690    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
691    
692            * R/Matrix.R (dim<-): reshape now via sparseVector.
693    
694            * R/sparseVector.R: methods and function for
695            * R/AllClass.R: new "sparseVector" class and daughters.
696            * NAMESPACE: export new classes
697    
698    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * DESCRIPTION (Version): 0.99875-1
701            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
702    
703    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
706            indexing
707            * tests/indexing.R: test set for that.
708    
709    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
712            entries.
713            * tests/indexing.R(out): add regression test for it
714    
715    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
716    
717            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
718            name for "!" method definitions.
719    
720    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * R/Tsparse.R (intI): new utility, used for "[" :
723                    Cleanup up there, and fixes for duplicated indices - more TODO!
724    
725            * tests/indexing.R(out): more tests
726    
727    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
728    
729            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
730            code that is now part of the R Lapack library.
731    
732            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
733            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
734    
735    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
736    
737            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
738    
739    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
740    
741            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
742            up with extraneous names '0'...'<n-1>'
743    
744    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/dgTMatrix.R (mat2dgT): care about NAs
747    
748    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
749    
750            * R/kronecker.R: triangularity preserving methods
751    
752    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * R/kronecker.R: new file collecting kronecker() methods in one
755                    place.  Goal: become much faster!
756    
757    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
760            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
761            can be much faster.
762    
763            * tests/matprod.R: add regression tests for these (upper & lower).
764    
765    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
766    
767            * R/Matrix.R (diff): method for our Matrices.
768    
769            * R/sparseMatrix.R (isDiagonal): check dim()!
770    
771    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/Matrix.R (dim<-): new method for "reshape()" built on a
774            proposal from Tamas Papp.
775    
776    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
779    
780            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
781            rather define and export  cBind() and rBind() only.
782            --> useRs *must* change code that used to have cbind()/rbind() !!
783    
784            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
785            * R/bind.Rout.save: ditto
786    
787    2007-02-16  Douglas Bates  <bates@r-project.org>
788    
789            * DESCRIPTION (Date, Version): 0.9975-11 with new date
790            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
791            const modifier on declaration of the array 'valid'
792    
793    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
794    
795            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
796    
797  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
800    
801          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix          * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
802          * tests/simple.R: test the above and some of these coercions:          * tests/simple.R: test the above and some of these coercions:
803    

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