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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1899, Fri Jun 15 23:17:45 2007 UTC
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1    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
4              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
5              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
6            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
7              class
8            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
9              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
10              row names to store the levels - duh!  Added an example.
11    
12    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * src/Csparse.c (Csparse_validate): check for *repeated* entries
15            thanks to example from Christian Buchta; with a test here:
16            * tests/simple.R:
17    
18    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
19    
20            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
21            of colSums(*, sparseResult = TRUE)
22    
23    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
24    
25            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
26            'na.rm = FALSE' as "everywhere" else in R.
27    
28    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
29    
30            * [r4421] src/CSparse_install.sh: Modify for new organization of
31              CSparse package
32            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
33              SuiteSparse
34            * [r4426] src/Makefile: add ./UFconfig to the include path for
35              compilation
36            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
37            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
38              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
39    
40    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
43            * R/sparseMatrix.R (prSpMatrix): now gives a message about
44            suppressed column names.
45    
46    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
47    
48            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
49              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
50              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
51              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
52              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
53              Remove warnings after change to const char* CHAR
54    
55    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
58              type of M_cholmod_ssmult
59    
60    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
61    
62            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
63              src/init.c: Yet another cholmod export - cholmod_ssmult
64    
65    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * NAMESPACE: exported drop0(), since
68            * man/drop0.Rd: I have seen several cases, I really wanted to use
69            it, so our users may want too.
70    
71    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
72    
73            * man/colSums.Rd: separately document colSums() etc, since these
74            have the extra argument 'sparseResult'.
75    
76    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
79            * man/spMatrix.Rd: docu., including examples
80    
81            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
82            in order to make colMeans() etc fast *and* correct.
83            * R/sparseVector.R (replSPvec): "[<-" functionality for
84            sparseVectors; tested in
85            * tests/simple.R:
86    
87    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
88    
89            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
90            (very) sparse Matrices; output similar to Matlab's print().
91    
92    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
93    
94            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
95            0-based, indices (Jose Quesada <quesada@gmail.com>).
96    
97    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
98    
99            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
100    
101    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/Auxiliaries.R (sparsapply): new utility, much faster than
104            tapply1() for large sparse matrices.
105    
106    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
107    
108            * R/Matrix.R (dim<-): reshape now via sparseVector.
109    
110            * R/sparseVector.R: methods and function for
111            * R/AllClass.R: new "sparseVector" class and daughters.
112            * NAMESPACE: export new classes
113    
114    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * DESCRIPTION (Version): 0.99875-1
117            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
118    
119    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
122            indexing
123            * tests/indexing.R: test set for that.
124    
125    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
128            entries.
129            * tests/indexing.R(out): add regression test for it
130    
131    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
132    
133            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
134            name for "!" method definitions.
135    
136    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
137    
138            * R/Tsparse.R (intI): new utility, used for "[" :
139                    Cleanup up there, and fixes for duplicated indices - more TODO!
140    
141            * tests/indexing.R(out): more tests
142    
143    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
144    
145            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
146            code that is now part of the R Lapack library.
147    
148            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
149            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
150    
151    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
152    
153            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
154    
155    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
156    
157            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
158            up with extraneous names '0'...'<n-1>'
159    
160    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
161    
162            * R/dgTMatrix.R (mat2dgT): care about NAs
163    
164    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/kronecker.R: triangularity preserving methods
167    
168    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/kronecker.R: new file collecting kronecker() methods in one
171                    place.  Goal: become much faster!
172    
173    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
176            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
177            can be much faster.
178    
179            * tests/matprod.R: add regression tests for these (upper & lower).
180    
181    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/Matrix.R (diff): method for our Matrices.
184    
185            * R/sparseMatrix.R (isDiagonal): check dim()!
186    
187    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
188    
189            * R/Matrix.R (dim<-): new method for "reshape()" built on a
190            proposal from Tamas Papp.
191    
192    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
195    
196            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
197            rather define and export  cBind() and rBind() only.
198            --> useRs *must* change code that used to have cbind()/rbind() !!
199    
200            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
201            * R/bind.Rout.save: ditto
202    
203    2007-02-16  Douglas Bates  <bates@r-project.org>
204    
205            * DESCRIPTION (Date, Version): 0.9975-11 with new date
206            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
207            const modifier on declaration of the array 'valid'
208    
209    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
210    
211            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
212    
213    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
214    
215            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
216    
217            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
218            * tests/simple.R: test the above and some of these coercions:
219    
220            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
221                    be careful to avoid infinite recursion, using new coercions in
222            * R/ngCMatrix.R and nsC... and ntC...
223            * R/lsparseMatrix.R: ditto
224    
225            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
226    
227            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
228            * R/Rsparse.R: reactivate .Call()s
229    
230            * tests/Class+Meth.R: a bit more on actual classes
231    
232    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
235    
236    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
237    
238            * DESCRIPTION (Version): 0.9975-10 to upload
239    
240            * tests/Class+Meth.R (tstMatrixClass): require coercions to
241            specific classes less unconditionally.
242    
243            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
244    
245            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
246    
247            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
248            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
249            R_to_CMatrix segfaults on one platform.
250            Eliminate most coercion method to *specific* classes, and replace
251            with virtual classes coercions.
252    
253    
254    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
255    
256            * src/init.c: export the CHM...._validate() placeholders, since
257            they *are* called.
258    
259            * tests/Class+Meth.R (classCanCoerce): and starting to test
260            all as(<from>, <to>)
261    
262    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
263    
264            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
265            * tests/indexing.R: tested now
266            * tests/indexing.Rout.save: updated
267    
268            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
269            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
270            appropriate.
271    
272            * NAMESPACE: export a trivial
273            * R/Matrix.R: drop() Matrix-method
274    
275            * R/AllClass.R: moved all prototypes to virtual super classes.
276    
277            * R/Rsparse.R: many more coercions to have less exceptions in
278            * tests/Class+Meth.R:
279    
280            * R/Ops.R (Compare): tweak for case with NA
281            * tests/simpl.R: hence another 'FIXME' eliminated
282    
283    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
284    
285            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
286            objects.
287    
288            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
289              and more of "!", "&", "|", all, any; coercions
290    
291            * R/Rsparse.R: many coercions (which enable quite a few other
292            methods), thanks to enhancements in
293            * src/dgCMatrix.c (R_to_CMatrix): new, and
294            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
295            symmetric & triangular and ..RMatrix objects.
296    
297            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
298            renamed file from src/dsTMatrix.c;
299            now dealing with symmetric and triangular Tsparse coercions, both
300            to dense and general.
301    
302    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
305    
306            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
307            where sensible when the <numeric> is of length > 1.
308    
309    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Matrix.R ([<-): for M[] <- value: fix length
312    
313    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
316            * R/ndenseMatrix.R: new coercions n* -> l*
317    
318    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
319    
320            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
321    
322            * R/Ops.R ("Logic"): and other "Ops", many updates
323    
324    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
325    
326            * src/Mutils.h (SET_DimNames): new utility
327    
328            * R/Auxiliaries.R (nnzero): improved and now exported via
329    
330            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
331    
332    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/diagMatrix.R (!): fix typo.
335    
336    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
337    
338            * R/Auxiliaries.R (as_Csparse): and quite a few others:
339                    allow to pass class definition --> speedup
340            * R/sparseMatrix.R: apply the above
341    
342            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
343    
344            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
345            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
346            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
347    
348            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
349    
350            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
351            and use it for "sparse*" as well, since it's faster than the
352            as_Csparse(.) way.
353    
354    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
357    
358    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
361            as method for   M[ ij ] <- v
362            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
363    
364            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
365            FALSE answer
366    
367            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
368            * tests/indexing.R: test it, and some of the above
369    
370    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
371    
372            * R/Auxiliaries.R (is_duplicatedT): new utility
373    
374  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
375    
376          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
377    
378    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
381            base::as.matrix to (x, ...)
382    
383  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385          * 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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