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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1845, Wed May 16 21:24:41 2007 UTC
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1    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
2    
3            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
4    
5    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * R/Auxiliaries.R (sparsapply): new utility, much faster than
8            tapply1() for large sparse matrices.
9    
10    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
11    
12            * R/Matrix.R (dim<-): reshape now via sparseVector.
13    
14            * R/sparseVector.R: methods and function for
15            * R/AllClass.R: new "sparseVector" class and daughters.
16            * NAMESPACE: export new classes
17    
18    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * DESCRIPTION (Version): 0.99875-1
21            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
22    
23    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
26            indexing
27            * tests/indexing.R: test set for that.
28    
29    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
32            entries.
33            * tests/indexing.R(out): add regression test for it
34    
35    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
38            name for "!" method definitions.
39    
40    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Tsparse.R (intI): new utility, used for "[" :
43                    Cleanup up there, and fixes for duplicated indices - more TODO!
44    
45            * tests/indexing.R(out): more tests
46    
47    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
50            code that is now part of the R Lapack library.
51    
52            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
53            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
54    
55    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
56    
57            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
58    
59    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
60    
61            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
62            up with extraneous names '0'...'<n-1>'
63    
64    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * R/dgTMatrix.R (mat2dgT): care about NAs
67    
68    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * R/kronecker.R: triangularity preserving methods
71    
72    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
73    
74            * R/kronecker.R: new file collecting kronecker() methods in one
75                    place.  Goal: become much faster!
76    
77    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
78    
79            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
80            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
81            can be much faster.
82    
83            * tests/matprod.R: add regression tests for these (upper & lower).
84    
85    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/Matrix.R (diff): method for our Matrices.
88    
89            * R/sparseMatrix.R (isDiagonal): check dim()!
90    
91    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Matrix.R (dim<-): new method for "reshape()" built on a
94            proposal from Tamas Papp.
95    
96    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
97    
98            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
99    
100            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
101            rather define and export  cBind() and rBind() only.
102            --> useRs *must* change code that used to have cbind()/rbind() !!
103    
104            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
105            * R/bind.Rout.save: ditto
106    
107    2007-02-16  Douglas Bates  <bates@r-project.org>
108    
109            * DESCRIPTION (Date, Version): 0.9975-11 with new date
110            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
111            const modifier on declaration of the array 'valid'
112    
113    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
114    
115            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
116    
117    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
120    
121            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
122            * tests/simple.R: test the above and some of these coercions:
123    
124            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
125                    be careful to avoid infinite recursion, using new coercions in
126            * R/ngCMatrix.R and nsC... and ntC...
127            * R/lsparseMatrix.R: ditto
128    
129            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
130    
131            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
132            * R/Rsparse.R: reactivate .Call()s
133    
134            * tests/Class+Meth.R: a bit more on actual classes
135    
136    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
137    
138            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
139    
140    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * DESCRIPTION (Version): 0.9975-10 to upload
143    
144            * tests/Class+Meth.R (tstMatrixClass): require coercions to
145            specific classes less unconditionally.
146    
147            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
148    
149            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
150    
151            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
152            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
153            R_to_CMatrix segfaults on one platform.
154            Eliminate most coercion method to *specific* classes, and replace
155            with virtual classes coercions.
156    
157    
158    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
159    
160            * src/init.c: export the CHM...._validate() placeholders, since
161            they *are* called.
162    
163            * tests/Class+Meth.R (classCanCoerce): and starting to test
164            all as(<from>, <to>)
165    
166    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
167    
168            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
169            * tests/indexing.R: tested now
170            * tests/indexing.Rout.save: updated
171    
172            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
173            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
174            appropriate.
175    
176            * NAMESPACE: export a trivial
177            * R/Matrix.R: drop() Matrix-method
178    
179            * R/AllClass.R: moved all prototypes to virtual super classes.
180    
181            * R/Rsparse.R: many more coercions to have less exceptions in
182            * tests/Class+Meth.R:
183    
184            * R/Ops.R (Compare): tweak for case with NA
185            * tests/simpl.R: hence another 'FIXME' eliminated
186    
187    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
190            objects.
191    
192            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
193              and more of "!", "&", "|", all, any; coercions
194    
195            * R/Rsparse.R: many coercions (which enable quite a few other
196            methods), thanks to enhancements in
197            * src/dgCMatrix.c (R_to_CMatrix): new, and
198            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
199            symmetric & triangular and ..RMatrix objects.
200    
201            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
202            renamed file from src/dsTMatrix.c;
203            now dealing with symmetric and triangular Tsparse coercions, both
204            to dense and general.
205    
206    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
207    
208            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
209    
210            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
211            where sensible when the <numeric> is of length > 1.
212    
213    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * R/Matrix.R ([<-): for M[] <- value: fix length
216    
217    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
220            * R/ndenseMatrix.R: new coercions n* -> l*
221    
222    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
223    
224            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
225    
226            * R/Ops.R ("Logic"): and other "Ops", many updates
227    
228    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * src/Mutils.h (SET_DimNames): new utility
231    
232            * R/Auxiliaries.R (nnzero): improved and now exported via
233    
234            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
235    
236    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * R/diagMatrix.R (!): fix typo.
239    
240    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * R/Auxiliaries.R (as_Csparse): and quite a few others:
243                    allow to pass class definition --> speedup
244            * R/sparseMatrix.R: apply the above
245    
246            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
247    
248            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
249            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
250            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
251    
252            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
253    
254            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
255            and use it for "sparse*" as well, since it's faster than the
256            as_Csparse(.) way.
257    
258    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
261    
262    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
265            as method for   M[ ij ] <- v
266            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
267    
268            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
269            FALSE answer
270    
271            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
272            * tests/indexing.R: test it, and some of the above
273    
274    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Auxiliaries.R (is_duplicatedT): new utility
277    
278  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
279    
280          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
281    
282    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
285            base::as.matrix to (x, ...)
286    
287  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289          * 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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