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revision 1665, Fri Nov 3 23:18:07 2006 UTC revision 1852, Mon May 21 16:42:35 2007 UTC
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1    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
4            * man/spMatrix.Rd: docu., including examples
5    
6            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
7            in order to make colMeans() etc fast *and* correct.
8            * R/sparseVector.R (replSPvec): "[<-" functionality for
9            sparseVectors; tested in
10            * tests/simple.R:
11    
12    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
15            (very) sparse Matrices; output similar to Matlab's print().
16    
17    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
18    
19            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
20            0-based, indices (Jose Quesada <quesada@gmail.com>).
21    
22    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
23    
24            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
25    
26    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * R/Auxiliaries.R (sparsapply): new utility, much faster than
29            tapply1() for large sparse matrices.
30    
31    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Matrix.R (dim<-): reshape now via sparseVector.
34    
35            * R/sparseVector.R: methods and function for
36            * R/AllClass.R: new "sparseVector" class and daughters.
37            * NAMESPACE: export new classes
38    
39    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
40    
41            * DESCRIPTION (Version): 0.99875-1
42            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
43    
44    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
47            indexing
48            * tests/indexing.R: test set for that.
49    
50    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
51    
52            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
53            entries.
54            * tests/indexing.R(out): add regression test for it
55    
56    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
57    
58            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
59            name for "!" method definitions.
60    
61    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * R/Tsparse.R (intI): new utility, used for "[" :
64                    Cleanup up there, and fixes for duplicated indices - more TODO!
65    
66            * tests/indexing.R(out): more tests
67    
68    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
69    
70            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
71            code that is now part of the R Lapack library.
72    
73            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
74            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
75    
76    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
79    
80    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
83            up with extraneous names '0'...'<n-1>'
84    
85    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * R/dgTMatrix.R (mat2dgT): care about NAs
88    
89    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/kronecker.R: triangularity preserving methods
92    
93    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
94    
95            * R/kronecker.R: new file collecting kronecker() methods in one
96                    place.  Goal: become much faster!
97    
98    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
101            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
102            can be much faster.
103    
104            * tests/matprod.R: add regression tests for these (upper & lower).
105    
106    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Matrix.R (diff): method for our Matrices.
109    
110            * R/sparseMatrix.R (isDiagonal): check dim()!
111    
112    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/Matrix.R (dim<-): new method for "reshape()" built on a
115            proposal from Tamas Papp.
116    
117    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
118    
119            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
120    
121            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
122            rather define and export  cBind() and rBind() only.
123            --> useRs *must* change code that used to have cbind()/rbind() !!
124    
125            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
126            * R/bind.Rout.save: ditto
127    
128    2007-02-16  Douglas Bates  <bates@r-project.org>
129    
130            * DESCRIPTION (Date, Version): 0.9975-11 with new date
131            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
132            const modifier on declaration of the array 'valid'
133    
134    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
135    
136            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
137    
138    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
141    
142            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
143            * tests/simple.R: test the above and some of these coercions:
144    
145            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
146                    be careful to avoid infinite recursion, using new coercions in
147            * R/ngCMatrix.R and nsC... and ntC...
148            * R/lsparseMatrix.R: ditto
149    
150            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
151    
152            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
153            * R/Rsparse.R: reactivate .Call()s
154    
155            * tests/Class+Meth.R: a bit more on actual classes
156    
157    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
158    
159            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
160    
161    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * DESCRIPTION (Version): 0.9975-10 to upload
164    
165            * tests/Class+Meth.R (tstMatrixClass): require coercions to
166            specific classes less unconditionally.
167    
168            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
169    
170            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
171    
172            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
173            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
174            R_to_CMatrix segfaults on one platform.
175            Eliminate most coercion method to *specific* classes, and replace
176            with virtual classes coercions.
177    
178    
179    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
180    
181            * src/init.c: export the CHM...._validate() placeholders, since
182            they *are* called.
183    
184            * tests/Class+Meth.R (classCanCoerce): and starting to test
185            all as(<from>, <to>)
186    
187    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
190            * tests/indexing.R: tested now
191            * tests/indexing.Rout.save: updated
192    
193            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
194            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
195            appropriate.
196    
197            * NAMESPACE: export a trivial
198            * R/Matrix.R: drop() Matrix-method
199    
200            * R/AllClass.R: moved all prototypes to virtual super classes.
201    
202            * R/Rsparse.R: many more coercions to have less exceptions in
203            * tests/Class+Meth.R:
204    
205            * R/Ops.R (Compare): tweak for case with NA
206            * tests/simpl.R: hence another 'FIXME' eliminated
207    
208    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
209    
210            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
211            objects.
212    
213            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
214              and more of "!", "&", "|", all, any; coercions
215    
216            * R/Rsparse.R: many coercions (which enable quite a few other
217            methods), thanks to enhancements in
218            * src/dgCMatrix.c (R_to_CMatrix): new, and
219            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
220            symmetric & triangular and ..RMatrix objects.
221    
222            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
223            renamed file from src/dsTMatrix.c;
224            now dealing with symmetric and triangular Tsparse coercions, both
225            to dense and general.
226    
227    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
230    
231            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
232            where sensible when the <numeric> is of length > 1.
233    
234    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
235    
236            * R/Matrix.R ([<-): for M[] <- value: fix length
237    
238    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
239    
240            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
241            * R/ndenseMatrix.R: new coercions n* -> l*
242    
243    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
246    
247            * R/Ops.R ("Logic"): and other "Ops", many updates
248    
249    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * src/Mutils.h (SET_DimNames): new utility
252    
253            * R/Auxiliaries.R (nnzero): improved and now exported via
254    
255            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
256    
257    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
258    
259            * R/diagMatrix.R (!): fix typo.
260    
261    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
262    
263            * R/Auxiliaries.R (as_Csparse): and quite a few others:
264                    allow to pass class definition --> speedup
265            * R/sparseMatrix.R: apply the above
266    
267            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
268    
269            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
270            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
271            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
272    
273            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
274    
275            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
276            and use it for "sparse*" as well, since it's faster than the
277            as_Csparse(.) way.
278    
279    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
282    
283    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
286            as method for   M[ ij ] <- v
287            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
288    
289            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
290            FALSE answer
291    
292            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
293            * tests/indexing.R: test it, and some of the above
294    
295    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Auxiliaries.R (is_duplicatedT): new utility
298    
299    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
300    
301            * src/init.c (R_init_Matrix): export cholmod_scale
302    
303    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
304    
305            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
306            base::as.matrix to (x, ...)
307    
308    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
311            file; start using "Logic", hence
312    
313            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
314            * NAMESPACE: import and export "Logic"
315    
316    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
317    
318            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
319            only needed previously to R version 2.5.0.
320    
321    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
324    
325            * R/Tsparse.R (replTmat): fix subassignment of triangular
326            * R/Csparse.R (replCmat): ditto
327            * tests/indexing.R: more tests, incl the above fix
328    
329    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/Auxiliaries.R (drop0): extend for non CSparse
332            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
333    
334            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
335                    use uplo correctly (!); other places: use uplo_P() macro
336    
337            * R/Csparse.R (replCmat): call diagU2N() when needed
338            * R/Tsparse.R (replTmat): ditto
339    
340            * src/dtCMatrix.c (tCMatrix_validate): new
341            * src/dtTMatrix.c (tTMatrix_validate): new, used in
342            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
343    
344            * R/diagMatrix.R (replDiag): to use in [<-
345    
346    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
347    
348            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
349                    also more general diagU2N().
350    
351    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
354            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
355    
356    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
357    
358            * tests/bind.R: a few more cases
359            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
360    
361            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
362            * R/ddenseMatrix.R (cbind2/rbind2)
363            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
364            * tests/indexing.R
365            * tests/indexing.Rout.save: updated
366    
367    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
370            * tests/indexing.R
371    
372    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
375            align with proper position of "0", i.e., right for integers.
376            argument 'align' by default is "fancy".
377    
378    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
381            * R/Csparse.R: and fix "Compare" for more cases.
382            * tests/Class+Meth.R: test some of these (m == m, m != m)
383    
384    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/lsparseMatrix.R: all() and any() methods
387            * R/ldenseMatrix.R:      ditto
388            * NAMESPACE, R/Matrix.R: ditto
389    
390            * man/all-methods.Rd: document them minimally
391    
392            * tests/simple.R: add a few examples for these
393    
394    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
395    
396            * R/Tsparse.R ([): fix long standing typo in symmetric case
397            * man/dsCMatrix-class.Rd: add example exhibiting the above case
398    
399    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
400    
401            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
402            to LL before converting to a sparse matrix. (The LDL form can be
403            converted to a sparse matrix but it is implicitly a unit
404            triangular matrix and a diagonal matrix overwritten on the diagonal.)
405    
406    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
407    
408            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
409    
410    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
411    
412            * DESCRIPTION (Version): updated -> release 0.9975-7
413            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
414    
415    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
416    
417            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
418    
419    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
420    
421            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
422            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
423            is exactly singular.
424    
425    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
426    
427            * DESCRIPTION (Date): updated -> release 0.9975-6
428    
429    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
432            now returns symmetric.
433    
434            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
435    
436            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
437            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
438    
439            * R/Auxiliaries.R (.type.kind): added
440    
441    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
442    
443            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
444            running src/CSparse_install.sh
445    
446            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
447    
448  2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
449    
450          * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new          * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
# Line 24  Line 471 
471          * tests/indexing.R: indexing for logical sparse now ok          * tests/indexing.R: indexing for logical sparse now ok
472    
473    
   
474  2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
475    
476          * src/Tsparse.c: use xTsparse_validate() , and hence remove          * src/Tsparse.c: use xTsparse_validate() , and hence remove

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