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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 1870, Tue Jun 5 16:28:55 2007 UTC
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1    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
4            * R/sparseMatrix.R (prSpMatrix): now gives a message about
5            suppressed column names.
6    
7    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
8    
9            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
10              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
11              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
12              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
13              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
14              Remove warnings after change to const char* CHAR
15    
16    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
17    
18            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
19              type of M_cholmod_ssmult
20    
21    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
22    
23            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
24              src/init.c: Yet another cholmod export - cholmod_ssmult
25    
26    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
27    
28            * NAMESPACE: exported drop0(), since
29            * man/drop0.Rd: I have seen several cases, I really wanted to use
30            it, so our users may want too.
31    
32    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * man/colSums.Rd: separately document colSums() etc, since these
35            have the extra argument 'sparseResult'.
36    
37    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
40            * man/spMatrix.Rd: docu., including examples
41    
42            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
43            in order to make colMeans() etc fast *and* correct.
44            * R/sparseVector.R (replSPvec): "[<-" functionality for
45            sparseVectors; tested in
46            * tests/simple.R:
47    
48    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
51            (very) sparse Matrices; output similar to Matlab's print().
52    
53    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
54    
55            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
56            0-based, indices (Jose Quesada <quesada@gmail.com>).
57    
58    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
59    
60            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
61    
62    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * R/Auxiliaries.R (sparsapply): new utility, much faster than
65            tapply1() for large sparse matrices.
66    
67    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
68    
69            * R/Matrix.R (dim<-): reshape now via sparseVector.
70    
71            * R/sparseVector.R: methods and function for
72            * R/AllClass.R: new "sparseVector" class and daughters.
73            * NAMESPACE: export new classes
74    
75    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * DESCRIPTION (Version): 0.99875-1
78            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
79    
80    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
81    
82            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
83            indexing
84            * tests/indexing.R: test set for that.
85    
86    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
89            entries.
90            * tests/indexing.R(out): add regression test for it
91    
92    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
93    
94            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
95            name for "!" method definitions.
96    
97    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
98    
99            * R/Tsparse.R (intI): new utility, used for "[" :
100                    Cleanup up there, and fixes for duplicated indices - more TODO!
101    
102            * tests/indexing.R(out): more tests
103    
104    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
105    
106            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
107            code that is now part of the R Lapack library.
108    
109            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
110            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
111    
112    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
113    
114            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
115    
116    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
119            up with extraneous names '0'...'<n-1>'
120    
121    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
122    
123            * R/dgTMatrix.R (mat2dgT): care about NAs
124    
125    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/kronecker.R: triangularity preserving methods
128    
129    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
130    
131            * R/kronecker.R: new file collecting kronecker() methods in one
132                    place.  Goal: become much faster!
133    
134    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
135    
136            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
137            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
138            can be much faster.
139    
140            * tests/matprod.R: add regression tests for these (upper & lower).
141    
142    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
143    
144            * R/Matrix.R (diff): method for our Matrices.
145    
146            * R/sparseMatrix.R (isDiagonal): check dim()!
147    
148    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Matrix.R (dim<-): new method for "reshape()" built on a
151            proposal from Tamas Papp.
152    
153    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
156    
157            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
158            rather define and export  cBind() and rBind() only.
159            --> useRs *must* change code that used to have cbind()/rbind() !!
160    
161            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
162            * R/bind.Rout.save: ditto
163    
164    2007-02-16  Douglas Bates  <bates@r-project.org>
165    
166            * DESCRIPTION (Date, Version): 0.9975-11 with new date
167            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
168            const modifier on declaration of the array 'valid'
169    
170    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
171    
172            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
173    
174    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
175    
176            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
177    
178            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
179            * tests/simple.R: test the above and some of these coercions:
180    
181            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
182                    be careful to avoid infinite recursion, using new coercions in
183            * R/ngCMatrix.R and nsC... and ntC...
184            * R/lsparseMatrix.R: ditto
185    
186            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
187    
188            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
189            * R/Rsparse.R: reactivate .Call()s
190    
191            * tests/Class+Meth.R: a bit more on actual classes
192    
193    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
194    
195            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
196    
197    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
198    
199            * DESCRIPTION (Version): 0.9975-10 to upload
200    
201            * tests/Class+Meth.R (tstMatrixClass): require coercions to
202            specific classes less unconditionally.
203    
204            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
205    
206            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
207    
208            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
209            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
210            R_to_CMatrix segfaults on one platform.
211            Eliminate most coercion method to *specific* classes, and replace
212            with virtual classes coercions.
213    
214    
215    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
216    
217            * src/init.c: export the CHM...._validate() placeholders, since
218            they *are* called.
219    
220            * tests/Class+Meth.R (classCanCoerce): and starting to test
221            all as(<from>, <to>)
222    
223    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
224    
225            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
226            * tests/indexing.R: tested now
227            * tests/indexing.Rout.save: updated
228    
229            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
230            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
231            appropriate.
232    
233            * NAMESPACE: export a trivial
234            * R/Matrix.R: drop() Matrix-method
235    
236            * R/AllClass.R: moved all prototypes to virtual super classes.
237    
238            * R/Rsparse.R: many more coercions to have less exceptions in
239            * tests/Class+Meth.R:
240    
241            * R/Ops.R (Compare): tweak for case with NA
242            * tests/simpl.R: hence another 'FIXME' eliminated
243    
244    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
245    
246            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
247            objects.
248    
249            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
250              and more of "!", "&", "|", all, any; coercions
251    
252            * R/Rsparse.R: many coercions (which enable quite a few other
253            methods), thanks to enhancements in
254            * src/dgCMatrix.c (R_to_CMatrix): new, and
255            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
256            symmetric & triangular and ..RMatrix objects.
257    
258            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
259            renamed file from src/dsTMatrix.c;
260            now dealing with symmetric and triangular Tsparse coercions, both
261            to dense and general.
262    
263    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
266    
267            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
268            where sensible when the <numeric> is of length > 1.
269    
270    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
271    
272            * R/Matrix.R ([<-): for M[] <- value: fix length
273    
274    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
277            * R/ndenseMatrix.R: new coercions n* -> l*
278    
279    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
282    
283            * R/Ops.R ("Logic"): and other "Ops", many updates
284    
285    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
286    
287            * src/Mutils.h (SET_DimNames): new utility
288    
289            * R/Auxiliaries.R (nnzero): improved and now exported via
290    
291            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
292    
293    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
294    
295            * R/diagMatrix.R (!): fix typo.
296    
297    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
298    
299            * R/Auxiliaries.R (as_Csparse): and quite a few others:
300                    allow to pass class definition --> speedup
301            * R/sparseMatrix.R: apply the above
302    
303            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
304    
305            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
306            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
307            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
308    
309            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
310    
311            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
312            and use it for "sparse*" as well, since it's faster than the
313            as_Csparse(.) way.
314    
315    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
318    
319    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
322            as method for   M[ ij ] <- v
323            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
324    
325            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
326            FALSE answer
327    
328            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
329            * tests/indexing.R: test it, and some of the above
330    
331    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/Auxiliaries.R (is_duplicatedT): new utility
334    
335    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
336    
337            * src/init.c (R_init_Matrix): export cholmod_scale
338    
339    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
342            base::as.matrix to (x, ...)
343    
344    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
345    
346            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
347            file; start using "Logic", hence
348    
349            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
350            * NAMESPACE: import and export "Logic"
351    
352    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
353    
354            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
355            only needed previously to R version 2.5.0.
356    
357    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
358    
359            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
360    
361            * R/Tsparse.R (replTmat): fix subassignment of triangular
362            * R/Csparse.R (replCmat): ditto
363            * tests/indexing.R: more tests, incl the above fix
364    
365    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
366    
367            * R/Auxiliaries.R (drop0): extend for non CSparse
368            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
369    
370            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
371                    use uplo correctly (!); other places: use uplo_P() macro
372    
373            * R/Csparse.R (replCmat): call diagU2N() when needed
374            * R/Tsparse.R (replTmat): ditto
375    
376            * src/dtCMatrix.c (tCMatrix_validate): new
377            * src/dtTMatrix.c (tTMatrix_validate): new, used in
378            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
379    
380            * R/diagMatrix.R (replDiag): to use in [<-
381    
382    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
383    
384            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
385                    also more general diagU2N().
386    
387    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
388    
389            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
390            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
391    
392    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
393    
394            * tests/bind.R: a few more cases
395            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
396    
397            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
398            * R/ddenseMatrix.R (cbind2/rbind2)
399            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
400            * tests/indexing.R
401            * tests/indexing.Rout.save: updated
402    
403    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
406            * tests/indexing.R
407    
408    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
411            align with proper position of "0", i.e., right for integers.
412            argument 'align' by default is "fancy".
413    
414    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
415    
416            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
417            * R/Csparse.R: and fix "Compare" for more cases.
418            * tests/Class+Meth.R: test some of these (m == m, m != m)
419    
420    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
421    
422            * R/lsparseMatrix.R: all() and any() methods
423            * R/ldenseMatrix.R:      ditto
424            * NAMESPACE, R/Matrix.R: ditto
425    
426            * man/all-methods.Rd: document them minimally
427    
428            * tests/simple.R: add a few examples for these
429    
430    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
431    
432            * R/Tsparse.R ([): fix long standing typo in symmetric case
433            * man/dsCMatrix-class.Rd: add example exhibiting the above case
434    
435    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
436    
437            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
438            to LL before converting to a sparse matrix. (The LDL form can be
439            converted to a sparse matrix but it is implicitly a unit
440            triangular matrix and a diagonal matrix overwritten on the diagonal.)
441    
442    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
443    
444            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
445    
446    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
447    
448            * DESCRIPTION (Version): updated -> release 0.9975-7
449            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
450    
451  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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