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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1903, Sat Jun 16 18:31:51 2007 UTC
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1    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
4            method (which can have arguments, show() can't).
5    
6    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
7    
8            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
9              added dgCMatrix_colSums for [col,row][Sums,Means]
10    
11    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
12    
13            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
14              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
15              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
16            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
17              class
18            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
19              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
20              row names to store the levels - duh!  Added an example.
21    
22    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
23    
24            * src/Csparse.c (Csparse_validate): check for *repeated* entries
25            thanks to example from Christian Buchta; with a test here:
26            * tests/simple.R:
27    
28    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
29    
30            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
31            of colSums(*, sparseResult = TRUE)
32    
33    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
34    
35            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
36            'na.rm = FALSE' as "everywhere" else in R.
37    
38    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
39    
40            * [r4421] src/CSparse_install.sh: Modify for new organization of
41              CSparse package
42            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
43              SuiteSparse
44            * [r4426] src/Makefile: add ./UFconfig to the include path for
45              compilation
46            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
47            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
48              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
49    
50    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
53            * R/sparseMatrix.R (prSpMatrix): now gives a message about
54            suppressed column names.
55    
56    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
57    
58            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
59              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
60              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
61              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
62              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
63              Remove warnings after change to const char* CHAR
64    
65    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
66    
67            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
68              type of M_cholmod_ssmult
69    
70    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
71    
72            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
73              src/init.c: Yet another cholmod export - cholmod_ssmult
74    
75    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * NAMESPACE: exported drop0(), since
78            * man/drop0.Rd: I have seen several cases, I really wanted to use
79            it, so our users may want too.
80    
81    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
82    
83            * man/colSums.Rd: separately document colSums() etc, since these
84            have the extra argument 'sparseResult'.
85    
86    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
89            * man/spMatrix.Rd: docu., including examples
90    
91            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
92            in order to make colMeans() etc fast *and* correct.
93            * R/sparseVector.R (replSPvec): "[<-" functionality for
94            sparseVectors; tested in
95            * tests/simple.R:
96    
97    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
100            (very) sparse Matrices; output similar to Matlab's print().
101    
102    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
103    
104            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
105            0-based, indices (Jose Quesada <quesada@gmail.com>).
106    
107    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
108    
109            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
110    
111    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/Auxiliaries.R (sparsapply): new utility, much faster than
114            tapply1() for large sparse matrices.
115    
116    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Matrix.R (dim<-): reshape now via sparseVector.
119    
120            * R/sparseVector.R: methods and function for
121            * R/AllClass.R: new "sparseVector" class and daughters.
122            * NAMESPACE: export new classes
123    
124    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.99875-1
127            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
128    
129    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
132            indexing
133            * tests/indexing.R: test set for that.
134    
135    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
136    
137            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
138            entries.
139            * tests/indexing.R(out): add regression test for it
140    
141    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
144            name for "!" method definitions.
145    
146    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Tsparse.R (intI): new utility, used for "[" :
149                    Cleanup up there, and fixes for duplicated indices - more TODO!
150    
151            * tests/indexing.R(out): more tests
152    
153    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
154    
155            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
156            code that is now part of the R Lapack library.
157    
158            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
159            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
160    
161    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
164    
165    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
168            up with extraneous names '0'...'<n-1>'
169    
170    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/dgTMatrix.R (mat2dgT): care about NAs
173    
174    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * R/kronecker.R: triangularity preserving methods
177    
178    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/kronecker.R: new file collecting kronecker() methods in one
181                    place.  Goal: become much faster!
182    
183    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
184    
185            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
186            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
187            can be much faster.
188    
189            * tests/matprod.R: add regression tests for these (upper & lower).
190    
191    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/Matrix.R (diff): method for our Matrices.
194    
195            * R/sparseMatrix.R (isDiagonal): check dim()!
196    
197    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * R/Matrix.R (dim<-): new method for "reshape()" built on a
200            proposal from Tamas Papp.
201    
202    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
205    
206            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
207            rather define and export  cBind() and rBind() only.
208            --> useRs *must* change code that used to have cbind()/rbind() !!
209    
210            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
211            * R/bind.Rout.save: ditto
212    
213    2007-02-16  Douglas Bates  <bates@r-project.org>
214    
215            * DESCRIPTION (Date, Version): 0.9975-11 with new date
216            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
217            const modifier on declaration of the array 'valid'
218    
219    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
220    
221            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
222    
223    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
226    
227            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
228            * tests/simple.R: test the above and some of these coercions:
229    
230            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
231                    be careful to avoid infinite recursion, using new coercions in
232            * R/ngCMatrix.R and nsC... and ntC...
233            * R/lsparseMatrix.R: ditto
234    
235            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
236    
237            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
238            * R/Rsparse.R: reactivate .Call()s
239    
240            * tests/Class+Meth.R: a bit more on actual classes
241    
242    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
243    
244            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
245    
246    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * DESCRIPTION (Version): 0.9975-10 to upload
249    
250            * tests/Class+Meth.R (tstMatrixClass): require coercions to
251            specific classes less unconditionally.
252    
253            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
254    
255            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
256    
257            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
258            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
259            R_to_CMatrix segfaults on one platform.
260            Eliminate most coercion method to *specific* classes, and replace
261            with virtual classes coercions.
262    
263    
264    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
265    
266            * src/init.c: export the CHM...._validate() placeholders, since
267            they *are* called.
268    
269            * tests/Class+Meth.R (classCanCoerce): and starting to test
270            all as(<from>, <to>)
271    
272    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
275            * tests/indexing.R: tested now
276            * tests/indexing.Rout.save: updated
277    
278            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
279            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
280            appropriate.
281    
282            * NAMESPACE: export a trivial
283            * R/Matrix.R: drop() Matrix-method
284    
285            * R/AllClass.R: moved all prototypes to virtual super classes.
286    
287            * R/Rsparse.R: many more coercions to have less exceptions in
288            * tests/Class+Meth.R:
289    
290            * R/Ops.R (Compare): tweak for case with NA
291            * tests/simpl.R: hence another 'FIXME' eliminated
292    
293    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
296            objects.
297    
298            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
299              and more of "!", "&", "|", all, any; coercions
300    
301            * R/Rsparse.R: many coercions (which enable quite a few other
302            methods), thanks to enhancements in
303            * src/dgCMatrix.c (R_to_CMatrix): new, and
304            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
305            symmetric & triangular and ..RMatrix objects.
306    
307            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
308            renamed file from src/dsTMatrix.c;
309            now dealing with symmetric and triangular Tsparse coercions, both
310            to dense and general.
311    
312    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
315    
316            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
317            where sensible when the <numeric> is of length > 1.
318    
319    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Matrix.R ([<-): for M[] <- value: fix length
322    
323    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
324    
325            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
326            * R/ndenseMatrix.R: new coercions n* -> l*
327    
328    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
331    
332            * R/Ops.R ("Logic"): and other "Ops", many updates
333    
334    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * src/Mutils.h (SET_DimNames): new utility
337    
338            * R/Auxiliaries.R (nnzero): improved and now exported via
339    
340            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
341    
342    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
343    
344            * R/diagMatrix.R (!): fix typo.
345    
346    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Auxiliaries.R (as_Csparse): and quite a few others:
349                    allow to pass class definition --> speedup
350            * R/sparseMatrix.R: apply the above
351    
352            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
353    
354            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
355            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
356            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
357    
358            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
359    
360            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
361            and use it for "sparse*" as well, since it's faster than the
362            as_Csparse(.) way.
363    
364    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
365    
366            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
367    
368    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
369    
370            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
371            as method for   M[ ij ] <- v
372            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
373    
374            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
375            FALSE answer
376    
377            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
378            * tests/indexing.R: test it, and some of the above
379    
380    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Auxiliaries.R (is_duplicatedT): new utility
383    
384  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
385    
386          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
387    
388    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
391            base::as.matrix to (x, ...)
392    
393  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395          * 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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