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revision 1716, Sat Jan 6 02:01:24 2007 UTC revision 1904, Sat Jun 16 18:34:05 2007 UTC
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1    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * R/kronecker.R: fix typo (could lead to inf.recursion)
4            * test/simple.R: testing that
5    
6            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
7            method (which can have arguments, show() can't).
8    
9    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
10    
11            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
12              added dgCMatrix_colSums for [col,row][Sums,Means]
13    
14    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
15    
16            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
17              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
18              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
19            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
20              class
21            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
22              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
23              row names to store the levels - duh!  Added an example.
24    
25    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
26    
27            * src/Csparse.c (Csparse_validate): check for *repeated* entries
28            thanks to example from Christian Buchta; with a test here:
29            * tests/simple.R:
30    
31    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
32    
33            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
34            of colSums(*, sparseResult = TRUE)
35    
36    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
37    
38            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
39            'na.rm = FALSE' as "everywhere" else in R.
40    
41    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
42    
43            * [r4421] src/CSparse_install.sh: Modify for new organization of
44              CSparse package
45            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
46              SuiteSparse
47            * [r4426] src/Makefile: add ./UFconfig to the include path for
48              compilation
49            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
50            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
51              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
52    
53    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
54    
55            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
56            * R/sparseMatrix.R (prSpMatrix): now gives a message about
57            suppressed column names.
58    
59    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
60    
61            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
62              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
63              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
64              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
65              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
66              Remove warnings after change to const char* CHAR
67    
68    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
69    
70            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
71              type of M_cholmod_ssmult
72    
73    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
74    
75            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
76              src/init.c: Yet another cholmod export - cholmod_ssmult
77    
78    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
79    
80            * NAMESPACE: exported drop0(), since
81            * man/drop0.Rd: I have seen several cases, I really wanted to use
82            it, so our users may want too.
83    
84    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * man/colSums.Rd: separately document colSums() etc, since these
87            have the extra argument 'sparseResult'.
88    
89    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
90    
91            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
92            * man/spMatrix.Rd: docu., including examples
93    
94            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
95            in order to make colMeans() etc fast *and* correct.
96            * R/sparseVector.R (replSPvec): "[<-" functionality for
97            sparseVectors; tested in
98            * tests/simple.R:
99    
100    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
101    
102            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
103            (very) sparse Matrices; output similar to Matlab's print().
104    
105    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
106    
107            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
108            0-based, indices (Jose Quesada <quesada@gmail.com>).
109    
110    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
111    
112            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
113    
114    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/Auxiliaries.R (sparsapply): new utility, much faster than
117            tapply1() for large sparse matrices.
118    
119    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
120    
121            * R/Matrix.R (dim<-): reshape now via sparseVector.
122    
123            * R/sparseVector.R: methods and function for
124            * R/AllClass.R: new "sparseVector" class and daughters.
125            * NAMESPACE: export new classes
126    
127    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
128    
129            * DESCRIPTION (Version): 0.99875-1
130            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
131    
132    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
133    
134            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
135            indexing
136            * tests/indexing.R: test set for that.
137    
138    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
139    
140            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
141            entries.
142            * tests/indexing.R(out): add regression test for it
143    
144    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
145    
146            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
147            name for "!" method definitions.
148    
149    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
150    
151            * R/Tsparse.R (intI): new utility, used for "[" :
152                    Cleanup up there, and fixes for duplicated indices - more TODO!
153    
154            * tests/indexing.R(out): more tests
155    
156    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
157    
158            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
159            code that is now part of the R Lapack library.
160    
161            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
162            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
163    
164    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
165    
166            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
167    
168    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
169    
170            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
171            up with extraneous names '0'...'<n-1>'
172    
173    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
174    
175            * R/dgTMatrix.R (mat2dgT): care about NAs
176    
177    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/kronecker.R: triangularity preserving methods
180    
181    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
182    
183            * R/kronecker.R: new file collecting kronecker() methods in one
184                    place.  Goal: become much faster!
185    
186    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
187    
188            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
189            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
190            can be much faster.
191    
192            * tests/matprod.R: add regression tests for these (upper & lower).
193    
194    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
195    
196            * R/Matrix.R (diff): method for our Matrices.
197    
198            * R/sparseMatrix.R (isDiagonal): check dim()!
199    
200    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
201    
202            * R/Matrix.R (dim<-): new method for "reshape()" built on a
203            proposal from Tamas Papp.
204    
205    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
208    
209            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
210            rather define and export  cBind() and rBind() only.
211            --> useRs *must* change code that used to have cbind()/rbind() !!
212    
213            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
214            * R/bind.Rout.save: ditto
215    
216    2007-02-16  Douglas Bates  <bates@r-project.org>
217    
218            * DESCRIPTION (Date, Version): 0.9975-11 with new date
219            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
220            const modifier on declaration of the array 'valid'
221    
222    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
223    
224            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
225    
226    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
229    
230            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
231            * tests/simple.R: test the above and some of these coercions:
232    
233            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
234                    be careful to avoid infinite recursion, using new coercions in
235            * R/ngCMatrix.R and nsC... and ntC...
236            * R/lsparseMatrix.R: ditto
237    
238            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
239    
240            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
241            * R/Rsparse.R: reactivate .Call()s
242    
243            * tests/Class+Meth.R: a bit more on actual classes
244    
245    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
246    
247            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
248    
249    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
250    
251            * DESCRIPTION (Version): 0.9975-10 to upload
252    
253            * tests/Class+Meth.R (tstMatrixClass): require coercions to
254            specific classes less unconditionally.
255    
256            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
257    
258            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
259    
260            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
261            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
262            R_to_CMatrix segfaults on one platform.
263            Eliminate most coercion method to *specific* classes, and replace
264            with virtual classes coercions.
265    
266    
267    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
268    
269            * src/init.c: export the CHM...._validate() placeholders, since
270            they *are* called.
271    
272            * tests/Class+Meth.R (classCanCoerce): and starting to test
273            all as(<from>, <to>)
274    
275    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
276    
277            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
278            * tests/indexing.R: tested now
279            * tests/indexing.Rout.save: updated
280    
281            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
282            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
283            appropriate.
284    
285            * NAMESPACE: export a trivial
286            * R/Matrix.R: drop() Matrix-method
287    
288            * R/AllClass.R: moved all prototypes to virtual super classes.
289    
290            * R/Rsparse.R: many more coercions to have less exceptions in
291            * tests/Class+Meth.R:
292    
293            * R/Ops.R (Compare): tweak for case with NA
294            * tests/simpl.R: hence another 'FIXME' eliminated
295    
296    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
297    
298            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
299            objects.
300    
301            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
302              and more of "!", "&", "|", all, any; coercions
303    
304            * R/Rsparse.R: many coercions (which enable quite a few other
305            methods), thanks to enhancements in
306            * src/dgCMatrix.c (R_to_CMatrix): new, and
307            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
308            symmetric & triangular and ..RMatrix objects.
309    
310            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
311            renamed file from src/dsTMatrix.c;
312            now dealing with symmetric and triangular Tsparse coercions, both
313            to dense and general.
314    
315    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
318    
319            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
320            where sensible when the <numeric> is of length > 1.
321    
322    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Matrix.R ([<-): for M[] <- value: fix length
325    
326    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
327    
328            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
329            * R/ndenseMatrix.R: new coercions n* -> l*
330    
331    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
332    
333            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
334    
335            * R/Ops.R ("Logic"): and other "Ops", many updates
336    
337    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * src/Mutils.h (SET_DimNames): new utility
340    
341            * R/Auxiliaries.R (nnzero): improved and now exported via
342    
343            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
344    
345    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
346    
347            * R/diagMatrix.R (!): fix typo.
348    
349    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
350    
351            * R/Auxiliaries.R (as_Csparse): and quite a few others:
352                    allow to pass class definition --> speedup
353            * R/sparseMatrix.R: apply the above
354    
355            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
356    
357            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
358            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
359            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
360    
361            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
362    
363            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
364            and use it for "sparse*" as well, since it's faster than the
365            as_Csparse(.) way.
366    
367    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
370    
371    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
374            as method for   M[ ij ] <- v
375            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
376    
377            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
378            FALSE answer
379    
380            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
381            * tests/indexing.R: test it, and some of the above
382    
383    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
384    
385            * R/Auxiliaries.R (is_duplicatedT): new utility
386    
387  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>  2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
388    
389          * src/init.c (R_init_Matrix): export cholmod_scale          * src/init.c (R_init_Matrix): export cholmod_scale
390    
391    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
394            base::as.matrix to (x, ...)
395    
396  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
397    
398          * 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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