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revision 1827, Wed Apr 25 22:22:41 2007 UTC revision 2113, Mon Feb 18 08:27:41 2008 UTC
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1    2008-02-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Matrix.R (subset.ij): utility, as first step to faster
4               M [ <ij-matrix> ] indexing.
5    
6            * R/Matrix.R (.M.sub.i.logical): M[ <logical> ] : try better.
7    
8            * src/dense.c (ddense_symmpart, ddense_skewpart): new functions
9            for more efficient symmpart() and skewpart() methods.
10    
11            * src/Mutils.c (equal_string_vectors): utility
12    
13            * src/dense.c (ddense_to_symmetric): new function used in
14    
15            * R/symmetricMatrix.R: setAs(., "symmetricMatrix")
16    
17            * R/sparseMatrix.R, et_al (isSymmetric): add '...' to formals, in
18            order to match the generic (and evade .local(..)).
19    
20            * R/dsCMatrix.R: dgC -> dsC: use C code!
21    
22            * NAMESPACE, R/AllGeneric.R (symmpart, skewpart): new functions
23            as per TODO
24    
25            * R/Auxiliaries.R (setZero, all0Matrix): new utilities
26    
27            * R/symmetricMatrix.R: obvious symmpart(), skewpart() methods
28    
29    
30    2008-02-15  Martin Maechler  <maechler@stat.math.ethz.ch>
31    
32            * R/Ops.R (.Arith.Csparse): use diagU2N when needed in triangular
33    
34            * R/Auxiliaries.R (non0.i): take out of non0ind
35    
36            * R/ddenseMatrix.R (.trilDense, .triuDense, .bandDense):
37            make tril(), triu(), band() work for "matrix" and all "dense*"
38    
39            * R/triangularMatrix.R (.tri[lu].tr): need .diagU2N(*)
40            * tests/simple.R: test the fix above
41    
42            * R/sparseMatrix.R ([): simplification: no coerce to <general>
43                    before we use as(., <Tsparse>)[...] anyway
44    
45            * R/Rsparse.R (.viaC.to.R): mostly instead of .viaC.to.dgR()
46    
47            * R/triangularMatrix.R (isTriangular): methods for all subclasses
48            instead of "triangularMatrix" -- just to disambiguate
49    
50    2008-02-14  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * tests/Class+Meth.R (dotestMat): add m[FALSE, FALSE] { <-> TODO}
53            * tests/indexing.R: example that fails above
54    
55    2008-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (.M.sub.i.2col): fix for logical matrix indexing
58            * R/Tsparse.R (.TM.sub.i.2col, .TM.repl.i.2col): ditto;
59                    now, M[lower.tri(M)] and  M[lower.tri(M)] <- v  work better
60    
61            * src/Tsparse.c (Tsparse_to_tCsparse): new fast utility.
62            * src/Tsparse.h, init.c: ditto
63            * R/Auxiliaries.R (isTriT): new; faster than going via Csparse
64                 both isTriC() and isTriT() now return TRUE with "kind" or FALSE.
65            * R/sparseMatrix.R (isTriangular): hence simplified
66    
67    2008-01-24  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Ops.R (.Arith.Csparse): new utility factored out of former
70              <dgC> o <dgC>, extended for triangular and also used in  <dtC> o <dtC>.
71    
72    2008-01-23  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * tests/factorizing.R (checkSchur): and more tests for checking Schur()
75    
76            * inst/test-tools.R (isOrthogonal): new function; also file restructured
77    
78    2008-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * R/ngTMatrix.R: allow as(<numeric matrix>, "ngTMatrix") and hence
81            coercion to "nMatrix" and "pMatrix"
82    
83            * R/AllClass.R: "Schur" class;  "number" class union
84            * man/number-class.Rd:
85            * man/Schur-class.Rd:
86    
87            * R/eigen.R (.dgeSchur): utility, and return "Schur" class
88            (.simpleSchur): Schur() method for diagonal matrices
89            (.triSchur):    Schur() method for triangular matrices
90            (Schur.sym):    Schur() for symmetric matrices {building on eigen()}.
91    
92    
93    2008-01-21  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * src/dgCMatrix.c (dgCMatrix_QR): set @Dim slot (as per doc)
96    
97    2008-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/CHMfactor.R (solve): method for b="numeric", but also b="ANY"
100                    in order to ensure 'system = *' is not lost;
101                    formals()$system instead of cut&paste.
102            * tests/factorizing.R: test solve(<CHM..>, <numeric>)
103    
104    2008-01-11  Martin Maechler  <maechler@stat.math.ethz.ch>
105    
106            * DESCRIPTION (Date): make ready for release --> 0.999375-4
107    
108            * R/dgeMatrix.R: fix rcond() method for "dgeMatrix".
109    
110    2007-12-08  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/pMatrix.R: as(*, "matrix") now returns 0/1 *integer* matrix,
113                    and hence does as.vector(.).
114            * man/pMatrix-class.Rd: docs
115            * R/sparseMatrix.R: fix for printing "integer sparse"
116    
117            * tests/Class+Meth.R (tstMatrixClass): test M[FALSE], M[2] etc
118    
119            * R/Matrix.R and others: use "exact" function argument list for
120                    both "["   : (x, i,j, ..., drop)
121                    and  "[<-" : (x, i,j, ..., value)
122    
123            * R/denseMatrix.R: M[i] and M[i] <- v  (i vector) now work
124            * R/Tsparse.R (replTmat):    ditto
125            * R/diagMatrix.R (replDiag): ditto
126            * R/Csparse.R (replCmat):    ditto {was it worth the pain?}
127            * tests/indexing.R: testing the above
128    
129    2007-12-07  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/sparseMatrix.R (cov2cor): method for sparse matrices
132    
133            * R/diagMatrix.R ([<-): fix   D[ cbind(i,j) ] <- v
134    
135            * R/bind2.R: fix for Rsparse* and rbind2(dense,dense)
136    
137            * tests/Class+Meth.R: test cbind2, rbind2  and  diag<-
138    
139    2007-12-06  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * R/Matrix.R: "generic" cov2cor() method
142    
143            * R/nearPD.R: new 'only.values', 'keepDiag' arguments;
144                    speed up Q %*% D %*% t(Q)
145            * tests/dpoMatrix.R: test nearPD()
146    
147    2007-12-05  Doug Bates and Martin Maechler
148    
149            * R/sparseMatrix.R: xtabs(*, sparse=.) function; an extention of
150            stats::xtabs() allowing to create sparse matrices.
151    
152    2007-10-08  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * DESCRIPTION (Version): *-4 (released *-3 two days ago)
155    
156    2007-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
157    
158            * R/pMatrix.R: solve(<Matrix>, <pMatrix>)
159    
160    2007-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/LU.R: solve() method for "denseLU"
163    
164    2007-10-01  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * DESCRIPTION (Version): 0.999375-3 preparing for release
167    
168            * R/AllGeneric.R: simplify  if(.) .. else .. for R <= 2.5.1
169    
170            * R/Matrix.R (Matrix): .Internal(matrix(..)) different for R >= 2.7.0
171    
172    2007-09-26  Martin Maechler  <maechler@stat.math.ethz.ch>
173    
174            * R/pMatrix.R (.m.mult.pMat): fix <matrix> %*% <pMatrix>,
175              thanks to Kasper Kristensen.
176            * tests/matprod.R: regression test for that.
177    
178    2007-09-23 17:32  Douglas Bates <bates@stat.wisc.edu>
179    
180            * [r4778] R/AllGeneric.R: Check R version before defining generics for
181              primitives
182    
183    2007-09-13  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * R/denseMatrix.R (rcond): method
186            * R/sparseQR.R (rcond): method, use x or t(x)
187    
188    2007-09-12  Martin Maechler  <maechler@stat.math.ethz.ch>
189    
190            * R/dgeMatrix.R (rcond): method: work via qr.R() for non-square
191            matrices.
192            * R/sparseMatrix.R: Ditto for all other rcond() method definitions.
193    
194            * man/rcond.Rd: mention the more general definition, and add
195            example for non-square matrices.
196    
197            * man/chol.Rd: new file, for the S4 chol() generic and all methods.
198    
199    2007-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
200    
201            * R/sparseQR.R: add qr.R() method [to be used for rcond()]
202    
203    2007-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/Matrix.R ([<-): add (Matrix,missing,ANY,Matrix) etc
206            * tests/indexing.R: add new regression for the above cases.
207    
208    2007-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * src/Mutils.h (__sun): clause for alloca.h on Solaris
211    
212    2007-08-16  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * DESCRIPTION (Date, Version): 0.999375-2
215    
216    2007-08-15  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/HBMM.R (readMM): make work for pattern matrices as well
219    
220    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
221    
222            * [r4730] src/Mutils.h: declare alloca
223            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
224              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
225              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
226              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
227              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
228              methods; switch writeMM to use CHOLMOD code; repair readMM
229    
230    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
233            Oehlschlaegel's ... result type still to be discussed!
234    
235    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
236    
237            * man/image-methods.Rd: new, combining all image() methods
238    
239    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
242            to work via dgC...
243    
244            * R/Matrix.R (Matrix): special treatment for "table" (S3)
245    
246    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/dgTMatrix.R (image): change defaults to
249                    aspect = "iso", colorkey = FALSE
250    
251    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
254            must copy its *expanded* x slot before LAPACK call.
255    
256            * tests/matprod.R: test the last days' changes.
257    
258    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
259    
260            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
261              as well as in sources
262            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
263              Lapack call
264    
265    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
268                    ("Matrix", "matrix") which is needed in some cases.
269            Ditto for solve().
270    
271            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
272            infinite recursion in dispatch for some cases.
273    
274    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
275    
276            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
277              so pointers match
278    
279    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * DESCRIPTION (Date): set ready for release -- 0.999375-1
282    
283    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
284    
285            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
286              src/chm_common.c, src/chm_common.h: Change API for
287              numeric_as_chm_dense and N_AS_CHM_DN
288    
289    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
292            * tests/matprod.R: regr.test for it
293    
294    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
295    
296            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
297            * tests/group-methods.R: and regression-test it
298    
299    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
300    
301            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
302              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
303              triplet_to_sparse, documentation, use typedefs
304    
305    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
306    
307            * man/dpoMatrix-class.Rd: added 'corMatrix' example
308    
309            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
310            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
311            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
312    
313            * R/lsparseMatrix.R: bug fix in "all" method
314            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
315    
316            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
317            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
318                    + matrix |-> nMatrix coercion
319            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
320            * man/pMatrix-class.Rd: ditto
321    
322            * R/Matrix.R (Summary): method for non-dMatrix
323    
324            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
325            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
326                    test all Summary methods.
327    
328    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
331    
332    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
335    
336            * R/pMatrix.R (t?crossprod): methods for pMatrix
337    
338    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
339    
340            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
341    
342    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
343    
344            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
345              trying to fix a subtle bug - which has been somewhere else.
346    
347    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
348    
349            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
350              solve the bug
351    
352    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * src/dgCMatrix.c (compressed_to_TMatrix):
355    
356    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * src/Csparse.c (Rsparse_validate): new, to have some validity
359            checking for RsparseMatrix
360            * src/dgCMatrix.c (xRMatrix_validate): ditto
361            * src/dtCMatrix.c (tRMatrix_validate): ditto
362    
363    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
364    
365            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
366              lgRMatrix
367            * [r4568] DESCRIPTION: Prepare for bug-fix release
368            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
369              for declaration of cholmod_symmetry
370    
371    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
374            release.
375    
376    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
377    
378            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
379              functions - no longer used
380            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
381              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
382              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
383              Alloca
384    
385    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
386    
387            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
388              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
389              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
390              src/t_gCMatrix_colSums.c: more R_CheckStack()s
391    
392    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
393    
394            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
395              the required amount of memory then call M_numeric_as_chm_dense.
396            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
397              (like Calloc but calling alloca)
398    
399    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
400    
401            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
402            and extended with more sophisticated 'col.names' option.
403            * NAMESPACE: export  printSparseMatrix()
404            * man/printSpMatrix.Rd: document, incl. examples
405    
406    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
407    
408            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
409              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
410              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
411    
412    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
413    
414            * DESCRIPTION (Version): 0.99875-4
415    
416            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
417            some dimnames perservation.
418    
419            * R/dsTMatrix.R (t-method): keep dimnames
420            * R/dtTMatrix.R:  ditto
421    
422            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
423            and ncol(.) < 10
424    
425            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
426            from Mutils.h
427    
428            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
429            e.g. in as(<ngCMatrix>, "matrix")
430    
431    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
432    
433            * [r4529] .: Create a branch for the API changes from the 0.99875
434              series to the 0.999375 series
435            * [r4530] DESCRIPTION, inst/include/Matrix.h,
436              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
437              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
438              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
439              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
440              as_cholmod_x functions
441    
442    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
443    
444            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
445              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
446              to Comparisons
447    
448    >>>>>>> .merge-right.r4561
449    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * DESCRIPTION (Version): 0.99875-3 ready to be released.
452    
453            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
454    
455            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
456            that should also work in a future version of R.
457    
458    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
461    
462            * R/sparseVector.R: more *sparseVector coercions, notably for
463            non - double ones.
464    
465    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
468              notably the new ones building on the new .Call(.)s:
469    
470            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
471            all 4 of [dlin]gCMatrix_colSums().
472    
473    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
474    
475            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
476            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
477              result
478    
479    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
480    
481            * R/kronecker.R: fix typo (could lead to inf.recursion)
482            * test/simple.R: testing that
483    
484            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
485            method as well (which can have arguments, show() can't).
486    
487    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
488    
489            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
490              added dgCMatrix_colSums for [col,row][Sums,Means]
491    
492    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
493    
494            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
495              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
496              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
497            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
498              class
499            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
500              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
501              row names to store the levels - duh!  Added an example.
502    
503    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
504    
505            * src/Csparse.c (Csparse_validate): check for *repeated* entries
506            thanks to example from Christian Buchta; with a test here:
507            * tests/simple.R:
508    
509    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
510    
511            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
512            of colSums(*, sparseResult = TRUE)
513    
514    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
515    
516            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
517            'na.rm = FALSE' as "everywhere" else in R.
518    
519    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
520    
521            * [r4421] src/CSparse_install.sh: Modify for new organization of
522              CSparse package
523            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
524              SuiteSparse
525            * [r4426] src/Makefile: add ./UFconfig to the include path for
526              compilation
527            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
528            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
529              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
530    
531    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
534            * R/sparseMatrix.R (prSpMatrix): now gives a message about
535            suppressed column names.
536    
537    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
538    
539            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
540              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
541              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
542              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
543              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
544              Remove warnings after change to const char* CHAR
545    
546    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
547    
548            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
549              type of M_cholmod_ssmult
550    
551    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
552    
553            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
554              src/init.c: Yet another cholmod export - cholmod_ssmult
555    
556    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
557    
558            * NAMESPACE: exported drop0(), since
559            * man/drop0.Rd: I have seen several cases, I really wanted to use
560            it, so our users may want too.
561    
562    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
563    
564            * man/colSums.Rd: separately document colSums() etc, since these
565            have the extra argument 'sparseResult'.
566    
567    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
568    
569            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
570            * man/spMatrix.Rd: docu., including examples
571    
572            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
573            in order to make colMeans() etc fast *and* correct.
574            * R/sparseVector.R (replSPvec): "[<-" functionality for
575            sparseVectors; tested in
576            * tests/simple.R:
577    
578    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
579    
580            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
581            (very) sparse Matrices; output similar to Matlab's print().
582    
583    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
584    
585            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
586            0-based, indices (Jose Quesada <quesada@gmail.com>).
587    
588    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
589    
590            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
591    
592    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
593    
594            * R/Auxiliaries.R (sparsapply): new utility, much faster than
595            tapply1() for large sparse matrices.
596    
597    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
598    
599            * R/Matrix.R (dim<-): reshape now via sparseVector.
600    
601            * R/sparseVector.R: methods and function for
602            * R/AllClass.R: new "sparseVector" class and daughters.
603            * NAMESPACE: export new classes
604    
605    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
606    
607            * DESCRIPTION (Version): 0.99875-1
608            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
609    
610    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
611    
612            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
613            indexing
614            * tests/indexing.R: test set for that.
615    
616    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
617    
618            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
619            entries.
620            * tests/indexing.R(out): add regression test for it
621    
622    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
623    
624            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
625            name for "!" method definitions.
626    
627    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * R/Tsparse.R (intI): new utility, used for "[" :
630                    Cleanup up there, and fixes for duplicated indices - more TODO!
631    
632            * tests/indexing.R(out): more tests
633    
634  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>  2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
635    
636          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack          * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
# Line 6  Line 639 
639          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export          * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
640          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).          cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
641    
642    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
645    
646    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
647    
648            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
649            up with extraneous names '0'...'<n-1>'
650    
651  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>  2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
652    
653          * R/dgTMatrix.R (mat2dgT): care about NAs          * R/dgTMatrix.R (mat2dgT): care about NAs

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