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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1911, Tue Jun 19 16:16:58 2007 UTC
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1    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
4              notably the new ones building on the new .Call(.)s:
5    
6            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
7            all 4 of [dlin]gCMatrix_colSums().
8    
9    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
10    
11            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
12            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
13              result
14    
15    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/kronecker.R: fix typo (could lead to inf.recursion)
18            * test/simple.R: testing that
19    
20            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
21            method (which can have arguments, show() can't).
22    
23    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
24    
25            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
26              added dgCMatrix_colSums for [col,row][Sums,Means]
27    
28    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
29    
30            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
31              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
32              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
33            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
34              class
35            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
36              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
37              row names to store the levels - duh!  Added an example.
38    
39    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * src/Csparse.c (Csparse_validate): check for *repeated* entries
42            thanks to example from Christian Buchta; with a test here:
43            * tests/simple.R:
44    
45    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
46    
47            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
48            of colSums(*, sparseResult = TRUE)
49    
50    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
53            'na.rm = FALSE' as "everywhere" else in R.
54    
55    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4421] src/CSparse_install.sh: Modify for new organization of
58              CSparse package
59            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
60              SuiteSparse
61            * [r4426] src/Makefile: add ./UFconfig to the include path for
62              compilation
63            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
64            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
65              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
66    
67    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
70            * R/sparseMatrix.R (prSpMatrix): now gives a message about
71            suppressed column names.
72    
73    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
76              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
77              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
78              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
79              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
80              Remove warnings after change to const char* CHAR
81    
82    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
83    
84            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
85              type of M_cholmod_ssmult
86    
87    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
88    
89            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
90              src/init.c: Yet another cholmod export - cholmod_ssmult
91    
92    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * NAMESPACE: exported drop0(), since
95            * man/drop0.Rd: I have seen several cases, I really wanted to use
96            it, so our users may want too.
97    
98    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * man/colSums.Rd: separately document colSums() etc, since these
101            have the extra argument 'sparseResult'.
102    
103    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
106            * man/spMatrix.Rd: docu., including examples
107    
108            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
109            in order to make colMeans() etc fast *and* correct.
110            * R/sparseVector.R (replSPvec): "[<-" functionality for
111            sparseVectors; tested in
112            * tests/simple.R:
113    
114    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
117            (very) sparse Matrices; output similar to Matlab's print().
118    
119    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
122            0-based, indices (Jose Quesada <quesada@gmail.com>).
123    
124    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
125    
126            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
127    
128    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/Auxiliaries.R (sparsapply): new utility, much faster than
131            tapply1() for large sparse matrices.
132    
133    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Matrix.R (dim<-): reshape now via sparseVector.
136    
137            * R/sparseVector.R: methods and function for
138            * R/AllClass.R: new "sparseVector" class and daughters.
139            * NAMESPACE: export new classes
140    
141    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
142    
143            * DESCRIPTION (Version): 0.99875-1
144            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
145    
146    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
147    
148            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
149            indexing
150            * tests/indexing.R: test set for that.
151    
152    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
155            entries.
156            * tests/indexing.R(out): add regression test for it
157    
158    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
161            name for "!" method definitions.
162    
163    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/Tsparse.R (intI): new utility, used for "[" :
166                    Cleanup up there, and fixes for duplicated indices - more TODO!
167    
168            * tests/indexing.R(out): more tests
169    
170    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
171    
172            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
173            code that is now part of the R Lapack library.
174    
175            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
176            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
177    
178    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
181    
182    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
183    
184            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
185            up with extraneous names '0'...'<n-1>'
186    
187    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/dgTMatrix.R (mat2dgT): care about NAs
190    
191    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/kronecker.R: triangularity preserving methods
194    
195    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
196    
197            * R/kronecker.R: new file collecting kronecker() methods in one
198                    place.  Goal: become much faster!
199    
200    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
203            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
204            can be much faster.
205    
206            * tests/matprod.R: add regression tests for these (upper & lower).
207    
208    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/Matrix.R (diff): method for our Matrices.
211    
212            * R/sparseMatrix.R (isDiagonal): check dim()!
213    
214    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/Matrix.R (dim<-): new method for "reshape()" built on a
217            proposal from Tamas Papp.
218    
219    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
220    
221            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
222    
223            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
224            rather define and export  cBind() and rBind() only.
225            --> useRs *must* change code that used to have cbind()/rbind() !!
226    
227            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
228            * R/bind.Rout.save: ditto
229    
230    2007-02-16  Douglas Bates  <bates@r-project.org>
231    
232            * DESCRIPTION (Date, Version): 0.9975-11 with new date
233            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
234            const modifier on declaration of the array 'valid'
235    
236    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
237    
238            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
239    
240    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
241    
242            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
243    
244            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
245            * tests/simple.R: test the above and some of these coercions:
246    
247            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
248                    be careful to avoid infinite recursion, using new coercions in
249            * R/ngCMatrix.R and nsC... and ntC...
250            * R/lsparseMatrix.R: ditto
251    
252            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
253    
254            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
255            * R/Rsparse.R: reactivate .Call()s
256    
257            * tests/Class+Meth.R: a bit more on actual classes
258    
259    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
260    
261            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
262    
263    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * DESCRIPTION (Version): 0.9975-10 to upload
266    
267            * tests/Class+Meth.R (tstMatrixClass): require coercions to
268            specific classes less unconditionally.
269    
270            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
271    
272            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
273    
274            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
275            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
276            R_to_CMatrix segfaults on one platform.
277            Eliminate most coercion method to *specific* classes, and replace
278            with virtual classes coercions.
279    
280    
281    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
282    
283            * src/init.c: export the CHM...._validate() placeholders, since
284            they *are* called.
285    
286            * tests/Class+Meth.R (classCanCoerce): and starting to test
287            all as(<from>, <to>)
288    
289    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
290    
291            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
292            * tests/indexing.R: tested now
293            * tests/indexing.Rout.save: updated
294    
295            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
296            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
297            appropriate.
298    
299            * NAMESPACE: export a trivial
300            * R/Matrix.R: drop() Matrix-method
301    
302            * R/AllClass.R: moved all prototypes to virtual super classes.
303    
304            * R/Rsparse.R: many more coercions to have less exceptions in
305            * tests/Class+Meth.R:
306    
307            * R/Ops.R (Compare): tweak for case with NA
308            * tests/simpl.R: hence another 'FIXME' eliminated
309    
310    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
313            objects.
314    
315            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
316              and more of "!", "&", "|", all, any; coercions
317    
318            * R/Rsparse.R: many coercions (which enable quite a few other
319            methods), thanks to enhancements in
320            * src/dgCMatrix.c (R_to_CMatrix): new, and
321            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
322            symmetric & triangular and ..RMatrix objects.
323    
324            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
325            renamed file from src/dsTMatrix.c;
326            now dealing with symmetric and triangular Tsparse coercions, both
327            to dense and general.
328    
329    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
332    
333            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
334            where sensible when the <numeric> is of length > 1.
335    
336    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/Matrix.R ([<-): for M[] <- value: fix length
339    
340    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
343            * R/ndenseMatrix.R: new coercions n* -> l*
344    
345    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
348    
349            * R/Ops.R ("Logic"): and other "Ops", many updates
350    
351    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * src/Mutils.h (SET_DimNames): new utility
354    
355            * R/Auxiliaries.R (nnzero): improved and now exported via
356    
357            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
358    
359    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/diagMatrix.R (!): fix typo.
362    
363    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/Auxiliaries.R (as_Csparse): and quite a few others:
366                    allow to pass class definition --> speedup
367            * R/sparseMatrix.R: apply the above
368    
369            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
370    
371            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
372            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
373            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
374    
375            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
376    
377            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
378            and use it for "sparse*" as well, since it's faster than the
379            as_Csparse(.) way.
380    
381    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
382    
383            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
384    
385    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
386    
387            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
388            as method for   M[ ij ] <- v
389            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
390    
391            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
392            FALSE answer
393    
394            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
395            * tests/indexing.R: test it, and some of the above
396    
397    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Auxiliaries.R (is_duplicatedT): new utility
400    
401  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
402    
403          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
404    
405    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
406    
407            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
408            base::as.matrix to (x, ...)
409    
410  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412          * 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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