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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 1833, Tue May 8 12:25:57 2007 UTC
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1    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
4            entries.
5            * tests/indexing.R(out): add regression test for it
6    
7    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
10            name for "!" method definitions.
11    
12    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/Tsparse.R (intI): new utility, used for "[" :
15                    Cleanup up there, and fixes for duplicated indices - more TODO!
16    
17            * tests/indexing.R(out): more tests
18    
19    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
20    
21            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
22            code that is now part of the R Lapack library.
23    
24            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
25            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
26    
27    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
30    
31    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
34            up with extraneous names '0'...'<n-1>'
35    
36    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/dgTMatrix.R (mat2dgT): care about NAs
39    
40    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/kronecker.R: triangularity preserving methods
43    
44    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/kronecker.R: new file collecting kronecker() methods in one
47                    place.  Goal: become much faster!
48    
49    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
50    
51            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
52            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
53            can be much faster.
54    
55            * tests/matprod.R: add regression tests for these (upper & lower).
56    
57    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
58    
59            * R/Matrix.R (diff): method for our Matrices.
60    
61            * R/sparseMatrix.R (isDiagonal): check dim()!
62    
63    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
64    
65            * R/Matrix.R (dim<-): new method for "reshape()" built on a
66            proposal from Tamas Papp.
67    
68    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
71    
72            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
73            rather define and export  cBind() and rBind() only.
74            --> useRs *must* change code that used to have cbind()/rbind() !!
75    
76            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
77            * R/bind.Rout.save: ditto
78    
79    2007-02-16  Douglas Bates  <bates@r-project.org>
80    
81            * DESCRIPTION (Date, Version): 0.9975-11 with new date
82            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
83            const modifier on declaration of the array 'valid'
84    
85    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
86    
87            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
88    
89    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
92    
93            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
94            * tests/simple.R: test the above and some of these coercions:
95    
96            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
97                    be careful to avoid infinite recursion, using new coercions in
98            * R/ngCMatrix.R and nsC... and ntC...
99            * R/lsparseMatrix.R: ditto
100    
101            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
102    
103            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
104            * R/Rsparse.R: reactivate .Call()s
105    
106            * tests/Class+Meth.R: a bit more on actual classes
107    
108    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
109    
110            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
111    
112    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * DESCRIPTION (Version): 0.9975-10 to upload
115    
116            * tests/Class+Meth.R (tstMatrixClass): require coercions to
117            specific classes less unconditionally.
118    
119            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
120    
121            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
122    
123            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
124            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
125            R_to_CMatrix segfaults on one platform.
126            Eliminate most coercion method to *specific* classes, and replace
127            with virtual classes coercions.
128    
129    
130    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
131    
132            * src/init.c: export the CHM...._validate() placeholders, since
133            they *are* called.
134    
135            * tests/Class+Meth.R (classCanCoerce): and starting to test
136            all as(<from>, <to>)
137    
138    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
141            * tests/indexing.R: tested now
142            * tests/indexing.Rout.save: updated
143    
144            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
145            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
146            appropriate.
147    
148            * NAMESPACE: export a trivial
149            * R/Matrix.R: drop() Matrix-method
150    
151            * R/AllClass.R: moved all prototypes to virtual super classes.
152    
153            * R/Rsparse.R: many more coercions to have less exceptions in
154            * tests/Class+Meth.R:
155    
156            * R/Ops.R (Compare): tweak for case with NA
157            * tests/simpl.R: hence another 'FIXME' eliminated
158    
159    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
160    
161            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
162            objects.
163    
164            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
165              and more of "!", "&", "|", all, any; coercions
166    
167            * R/Rsparse.R: many coercions (which enable quite a few other
168            methods), thanks to enhancements in
169            * src/dgCMatrix.c (R_to_CMatrix): new, and
170            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
171            symmetric & triangular and ..RMatrix objects.
172    
173            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
174            renamed file from src/dsTMatrix.c;
175            now dealing with symmetric and triangular Tsparse coercions, both
176            to dense and general.
177    
178    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
181    
182            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
183            where sensible when the <numeric> is of length > 1.
184    
185    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
186    
187            * R/Matrix.R ([<-): for M[] <- value: fix length
188    
189    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
192            * R/ndenseMatrix.R: new coercions n* -> l*
193    
194    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
197    
198            * R/Ops.R ("Logic"): and other "Ops", many updates
199    
200    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * src/Mutils.h (SET_DimNames): new utility
203    
204            * R/Auxiliaries.R (nnzero): improved and now exported via
205    
206            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
207    
208    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/diagMatrix.R (!): fix typo.
211    
212    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
213    
214            * R/Auxiliaries.R (as_Csparse): and quite a few others:
215                    allow to pass class definition --> speedup
216            * R/sparseMatrix.R: apply the above
217    
218            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
219    
220            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
221            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
222            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
223    
224            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
225    
226            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
227            and use it for "sparse*" as well, since it's faster than the
228            as_Csparse(.) way.
229    
230    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
233    
234    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
237            as method for   M[ ij ] <- v
238            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
239    
240            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
241            FALSE answer
242    
243            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
244            * tests/indexing.R: test it, and some of the above
245    
246    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Auxiliaries.R (is_duplicatedT): new utility
249    
250    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
251    
252            * src/init.c (R_init_Matrix): export cholmod_scale
253    
254    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
257            base::as.matrix to (x, ...)
258    
259    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
262            file; start using "Logic", hence
263    
264            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
265            * NAMESPACE: import and export "Logic"
266    
267    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
268    
269            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
270            only needed previously to R version 2.5.0.
271    
272    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
275    
276            * R/Tsparse.R (replTmat): fix subassignment of triangular
277            * R/Csparse.R (replCmat): ditto
278            * tests/indexing.R: more tests, incl the above fix
279    
280    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/Auxiliaries.R (drop0): extend for non CSparse
283            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
284    
285            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
286                    use uplo correctly (!); other places: use uplo_P() macro
287    
288            * R/Csparse.R (replCmat): call diagU2N() when needed
289            * R/Tsparse.R (replTmat): ditto
290    
291            * src/dtCMatrix.c (tCMatrix_validate): new
292            * src/dtTMatrix.c (tTMatrix_validate): new, used in
293            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
294    
295            * R/diagMatrix.R (replDiag): to use in [<-
296    
297    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
300                    also more general diagU2N().
301    
302    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
305            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
306    
307    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * tests/bind.R: a few more cases
310            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
311    
312            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
313            * R/ddenseMatrix.R (cbind2/rbind2)
314            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
315            * tests/indexing.R
316            * tests/indexing.Rout.save: updated
317    
318    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
321            * tests/indexing.R
322    
323    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
326            align with proper position of "0", i.e., right for integers.
327            argument 'align' by default is "fancy".
328    
329    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
332            * R/Csparse.R: and fix "Compare" for more cases.
333            * tests/Class+Meth.R: test some of these (m == m, m != m)
334    
335    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
336    
337            * R/lsparseMatrix.R: all() and any() methods
338            * R/ldenseMatrix.R:      ditto
339            * NAMESPACE, R/Matrix.R: ditto
340    
341            * man/all-methods.Rd: document them minimally
342    
343            * tests/simple.R: add a few examples for these
344    
345    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/Tsparse.R ([): fix long standing typo in symmetric case
348            * man/dsCMatrix-class.Rd: add example exhibiting the above case
349    
350    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
351    
352            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
353            to LL before converting to a sparse matrix. (The LDL form can be
354            converted to a sparse matrix but it is implicitly a unit
355            triangular matrix and a diagonal matrix overwritten on the diagonal.)
356    
357    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
358    
359            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
360    
361    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
362    
363            * DESCRIPTION (Version): updated -> release 0.9975-7
364            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
365    
366  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
367    
368          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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