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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1868, Mon Jun 4 17:15:09 2007 UTC
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1    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
4              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
5              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
6              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
7              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
8              Remove warnings after change to const char* CHAR
9    
10    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
11    
12            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
13              type of M_cholmod_ssmult
14    
15    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
16    
17            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
18              src/init.c: Yet another cholmod export - cholmod_ssmult
19    
20    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * NAMESPACE: exported drop0(), since
23            * man/drop0.Rd: I have seen several cases, I really wanted to use
24            it, so our users may want too.
25    
26    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * man/colSums.Rd: separately document colSums() etc, since these
29            have the extra argument 'sparseResult'.
30    
31    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
34            * man/spMatrix.Rd: docu., including examples
35    
36            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
37            in order to make colMeans() etc fast *and* correct.
38            * R/sparseVector.R (replSPvec): "[<-" functionality for
39            sparseVectors; tested in
40            * tests/simple.R:
41    
42    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
43    
44            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
45            (very) sparse Matrices; output similar to Matlab's print().
46    
47    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
48    
49            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
50            0-based, indices (Jose Quesada <quesada@gmail.com>).
51    
52    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
53    
54            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
55    
56    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/Auxiliaries.R (sparsapply): new utility, much faster than
59            tapply1() for large sparse matrices.
60    
61    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Matrix.R (dim<-): reshape now via sparseVector.
64    
65            * R/sparseVector.R: methods and function for
66            * R/AllClass.R: new "sparseVector" class and daughters.
67            * NAMESPACE: export new classes
68    
69    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
70    
71            * DESCRIPTION (Version): 0.99875-1
72            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
73    
74    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
75    
76            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
77            indexing
78            * tests/indexing.R: test set for that.
79    
80    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
83            entries.
84            * tests/indexing.R(out): add regression test for it
85    
86    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
89            name for "!" method definitions.
90    
91    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
92    
93            * R/Tsparse.R (intI): new utility, used for "[" :
94                    Cleanup up there, and fixes for duplicated indices - more TODO!
95    
96            * tests/indexing.R(out): more tests
97    
98    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
99    
100            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
101            code that is now part of the R Lapack library.
102    
103            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
104            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
105    
106    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
109    
110    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
111    
112            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
113            up with extraneous names '0'...'<n-1>'
114    
115    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/dgTMatrix.R (mat2dgT): care about NAs
118    
119    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/kronecker.R: triangularity preserving methods
122    
123    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
124    
125            * R/kronecker.R: new file collecting kronecker() methods in one
126                    place.  Goal: become much faster!
127    
128    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
131            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
132            can be much faster.
133    
134            * tests/matprod.R: add regression tests for these (upper & lower).
135    
136    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/Matrix.R (diff): method for our Matrices.
139    
140            * R/sparseMatrix.R (isDiagonal): check dim()!
141    
142    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R (dim<-): new method for "reshape()" built on a
145            proposal from Tamas Papp.
146    
147    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
148    
149            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
150    
151            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
152            rather define and export  cBind() and rBind() only.
153            --> useRs *must* change code that used to have cbind()/rbind() !!
154    
155            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
156            * R/bind.Rout.save: ditto
157    
158    2007-02-16  Douglas Bates  <bates@r-project.org>
159    
160            * DESCRIPTION (Date, Version): 0.9975-11 with new date
161            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
162            const modifier on declaration of the array 'valid'
163    
164    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
165    
166            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
167    
168    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
171    
172            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
173            * tests/simple.R: test the above and some of these coercions:
174    
175            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
176                    be careful to avoid infinite recursion, using new coercions in
177            * R/ngCMatrix.R and nsC... and ntC...
178            * R/lsparseMatrix.R: ditto
179    
180            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
181    
182            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
183            * R/Rsparse.R: reactivate .Call()s
184    
185            * tests/Class+Meth.R: a bit more on actual classes
186    
187    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
188    
189            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
190    
191    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * DESCRIPTION (Version): 0.9975-10 to upload
194    
195            * tests/Class+Meth.R (tstMatrixClass): require coercions to
196            specific classes less unconditionally.
197    
198            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
199    
200            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
201    
202            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
203            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
204            R_to_CMatrix segfaults on one platform.
205            Eliminate most coercion method to *specific* classes, and replace
206            with virtual classes coercions.
207    
208    
209    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
210    
211            * src/init.c: export the CHM...._validate() placeholders, since
212            they *are* called.
213    
214            * tests/Class+Meth.R (classCanCoerce): and starting to test
215            all as(<from>, <to>)
216    
217    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
218    
219            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
220            * tests/indexing.R: tested now
221            * tests/indexing.Rout.save: updated
222    
223            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
224            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
225            appropriate.
226    
227            * NAMESPACE: export a trivial
228            * R/Matrix.R: drop() Matrix-method
229    
230            * R/AllClass.R: moved all prototypes to virtual super classes.
231    
232            * R/Rsparse.R: many more coercions to have less exceptions in
233            * tests/Class+Meth.R:
234    
235            * R/Ops.R (Compare): tweak for case with NA
236            * tests/simpl.R: hence another 'FIXME' eliminated
237    
238    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
241            objects.
242    
243            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
244              and more of "!", "&", "|", all, any; coercions
245    
246            * R/Rsparse.R: many coercions (which enable quite a few other
247            methods), thanks to enhancements in
248            * src/dgCMatrix.c (R_to_CMatrix): new, and
249            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
250            symmetric & triangular and ..RMatrix objects.
251    
252            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
253            renamed file from src/dsTMatrix.c;
254            now dealing with symmetric and triangular Tsparse coercions, both
255            to dense and general.
256    
257    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
260    
261            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
262            where sensible when the <numeric> is of length > 1.
263    
264    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
265    
266            * R/Matrix.R ([<-): for M[] <- value: fix length
267    
268    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
271            * R/ndenseMatrix.R: new coercions n* -> l*
272    
273    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
274    
275            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
276    
277            * R/Ops.R ("Logic"): and other "Ops", many updates
278    
279    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * src/Mutils.h (SET_DimNames): new utility
282    
283            * R/Auxiliaries.R (nnzero): improved and now exported via
284    
285            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
286    
287    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/diagMatrix.R (!): fix typo.
290    
291    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Auxiliaries.R (as_Csparse): and quite a few others:
294                    allow to pass class definition --> speedup
295            * R/sparseMatrix.R: apply the above
296    
297            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
298    
299            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
300            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
301            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
302    
303            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
304    
305            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
306            and use it for "sparse*" as well, since it's faster than the
307            as_Csparse(.) way.
308    
309    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
312    
313    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
316            as method for   M[ ij ] <- v
317            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
318    
319            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
320            FALSE answer
321    
322            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
323            * tests/indexing.R: test it, and some of the above
324    
325    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Auxiliaries.R (is_duplicatedT): new utility
328    
329  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
330    
331          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
332    
333    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
336            base::as.matrix to (x, ...)
337    
338  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
339    
340          * 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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