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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1893, Thu Jun 14 10:46:10 2007 UTC
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1    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/Csparse.c (Csparse_validate): check for *repeated* entries
4            thanks to example from Christian Buchta; with a test here:
5            * tests/simple.R:
6    
7    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
10            of colSums(*, sparseResult = TRUE)
11    
12    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
13    
14            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
15            'na.rm = FALSE' as "everywhere" else in R.
16    
17    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
18    
19            * [r4421] src/CSparse_install.sh: Modify for new organization of
20              CSparse package
21            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
22              SuiteSparse
23            * [r4426] src/Makefile: add ./UFconfig to the include path for
24              compilation
25            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
26            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
27              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
28    
29    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
30    
31            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
32            * R/sparseMatrix.R (prSpMatrix): now gives a message about
33            suppressed column names.
34    
35    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
36    
37            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
38              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
39              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
40              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
41              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
42              Remove warnings after change to const char* CHAR
43    
44    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
45    
46            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
47              type of M_cholmod_ssmult
48    
49    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
50    
51            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
52              src/init.c: Yet another cholmod export - cholmod_ssmult
53    
54    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
55    
56            * NAMESPACE: exported drop0(), since
57            * man/drop0.Rd: I have seen several cases, I really wanted to use
58            it, so our users may want too.
59    
60    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * man/colSums.Rd: separately document colSums() etc, since these
63            have the extra argument 'sparseResult'.
64    
65    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
66    
67            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
68            * man/spMatrix.Rd: docu., including examples
69    
70            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
71            in order to make colMeans() etc fast *and* correct.
72            * R/sparseVector.R (replSPvec): "[<-" functionality for
73            sparseVectors; tested in
74            * tests/simple.R:
75    
76    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
77    
78            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
79            (very) sparse Matrices; output similar to Matlab's print().
80    
81    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
82    
83            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
84            0-based, indices (Jose Quesada <quesada@gmail.com>).
85    
86    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
87    
88            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
89    
90    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
91    
92            * R/Auxiliaries.R (sparsapply): new utility, much faster than
93            tapply1() for large sparse matrices.
94    
95    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
96    
97            * R/Matrix.R (dim<-): reshape now via sparseVector.
98    
99            * R/sparseVector.R: methods and function for
100            * R/AllClass.R: new "sparseVector" class and daughters.
101            * NAMESPACE: export new classes
102    
103    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * DESCRIPTION (Version): 0.99875-1
106            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
107    
108    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
109    
110            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
111            indexing
112            * tests/indexing.R: test set for that.
113    
114    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
117            entries.
118            * tests/indexing.R(out): add regression test for it
119    
120    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
121    
122            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
123            name for "!" method definitions.
124    
125    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
126    
127            * R/Tsparse.R (intI): new utility, used for "[" :
128                    Cleanup up there, and fixes for duplicated indices - more TODO!
129    
130            * tests/indexing.R(out): more tests
131    
132    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
133    
134            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
135            code that is now part of the R Lapack library.
136    
137            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
138            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
139    
140    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
141    
142            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
143    
144    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
147            up with extraneous names '0'...'<n-1>'
148    
149    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/dgTMatrix.R (mat2dgT): care about NAs
152    
153    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
154    
155            * R/kronecker.R: triangularity preserving methods
156    
157    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/kronecker.R: new file collecting kronecker() methods in one
160                    place.  Goal: become much faster!
161    
162    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
163    
164            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
165            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
166            can be much faster.
167    
168            * tests/matprod.R: add regression tests for these (upper & lower).
169    
170    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * R/Matrix.R (diff): method for our Matrices.
173    
174            * R/sparseMatrix.R (isDiagonal): check dim()!
175    
176    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
177    
178            * R/Matrix.R (dim<-): new method for "reshape()" built on a
179            proposal from Tamas Papp.
180    
181    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
184    
185            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
186            rather define and export  cBind() and rBind() only.
187            --> useRs *must* change code that used to have cbind()/rbind() !!
188    
189            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
190            * R/bind.Rout.save: ditto
191    
192    2007-02-16  Douglas Bates  <bates@r-project.org>
193    
194            * DESCRIPTION (Date, Version): 0.9975-11 with new date
195            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
196            const modifier on declaration of the array 'valid'
197    
198    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
199    
200            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
201    
202    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
203    
204            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
205    
206            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
207            * tests/simple.R: test the above and some of these coercions:
208    
209            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
210                    be careful to avoid infinite recursion, using new coercions in
211            * R/ngCMatrix.R and nsC... and ntC...
212            * R/lsparseMatrix.R: ditto
213    
214            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
215    
216            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
217            * R/Rsparse.R: reactivate .Call()s
218    
219            * tests/Class+Meth.R: a bit more on actual classes
220    
221    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
222    
223            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
224    
225    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
226    
227            * DESCRIPTION (Version): 0.9975-10 to upload
228    
229            * tests/Class+Meth.R (tstMatrixClass): require coercions to
230            specific classes less unconditionally.
231    
232            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
233    
234            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
235    
236            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
237            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
238            R_to_CMatrix segfaults on one platform.
239            Eliminate most coercion method to *specific* classes, and replace
240            with virtual classes coercions.
241    
242    
243    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
244    
245            * src/init.c: export the CHM...._validate() placeholders, since
246            they *are* called.
247    
248            * tests/Class+Meth.R (classCanCoerce): and starting to test
249            all as(<from>, <to>)
250    
251    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
252    
253            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
254            * tests/indexing.R: tested now
255            * tests/indexing.Rout.save: updated
256    
257            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
258            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
259            appropriate.
260    
261            * NAMESPACE: export a trivial
262            * R/Matrix.R: drop() Matrix-method
263    
264            * R/AllClass.R: moved all prototypes to virtual super classes.
265    
266            * R/Rsparse.R: many more coercions to have less exceptions in
267            * tests/Class+Meth.R:
268    
269            * R/Ops.R (Compare): tweak for case with NA
270            * tests/simpl.R: hence another 'FIXME' eliminated
271    
272    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
273    
274            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
275            objects.
276    
277            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
278              and more of "!", "&", "|", all, any; coercions
279    
280            * R/Rsparse.R: many coercions (which enable quite a few other
281            methods), thanks to enhancements in
282            * src/dgCMatrix.c (R_to_CMatrix): new, and
283            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
284            symmetric & triangular and ..RMatrix objects.
285    
286            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
287            renamed file from src/dsTMatrix.c;
288            now dealing with symmetric and triangular Tsparse coercions, both
289            to dense and general.
290    
291    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
294    
295            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
296            where sensible when the <numeric> is of length > 1.
297    
298    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
299    
300            * R/Matrix.R ([<-): for M[] <- value: fix length
301    
302    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
303    
304            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
305            * R/ndenseMatrix.R: new coercions n* -> l*
306    
307    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
308    
309            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
310    
311            * R/Ops.R ("Logic"): and other "Ops", many updates
312    
313    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/Mutils.h (SET_DimNames): new utility
316    
317            * R/Auxiliaries.R (nnzero): improved and now exported via
318    
319            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
320    
321    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/diagMatrix.R (!): fix typo.
324    
325    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
326    
327            * R/Auxiliaries.R (as_Csparse): and quite a few others:
328                    allow to pass class definition --> speedup
329            * R/sparseMatrix.R: apply the above
330    
331            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
332    
333            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
334            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
335            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
336    
337            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
338    
339            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
340            and use it for "sparse*" as well, since it's faster than the
341            as_Csparse(.) way.
342    
343    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
346    
347    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
348    
349            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
350            as method for   M[ ij ] <- v
351            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
352    
353            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
354            FALSE answer
355    
356            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
357            * tests/indexing.R: test it, and some of the above
358    
359    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/Auxiliaries.R (is_duplicatedT): new utility
362    
363  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
364    
365          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
366    
367    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
370            base::as.matrix to (x, ...)
371    
372  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
373    
374          * 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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