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revision 1682, Fri Dec 1 18:42:40 2006 UTC revision 1897, Fri Jun 15 18:22:25 2007 UTC
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1    2007-06-15 18:20  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    
9    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
10    
11            * src/Csparse.c (Csparse_validate): check for *repeated* entries
12            thanks to example from Christian Buchta; with a test here:
13            * tests/simple.R:
14    
15    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
16    
17            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
18            of colSums(*, sparseResult = TRUE)
19    
20    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
23            'na.rm = FALSE' as "everywhere" else in R.
24    
25    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
26    
27            * [r4421] src/CSparse_install.sh: Modify for new organization of
28              CSparse package
29            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
30              SuiteSparse
31            * [r4426] src/Makefile: add ./UFconfig to the include path for
32              compilation
33            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
34            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
35              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
36    
37    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
38    
39            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
40            * R/sparseMatrix.R (prSpMatrix): now gives a message about
41            suppressed column names.
42    
43    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
44    
45            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
46              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
47              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
48              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
49              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
50              Remove warnings after change to const char* CHAR
51    
52    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
53    
54            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
55              type of M_cholmod_ssmult
56    
57    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
58    
59            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
60              src/init.c: Yet another cholmod export - cholmod_ssmult
61    
62    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
63    
64            * NAMESPACE: exported drop0(), since
65            * man/drop0.Rd: I have seen several cases, I really wanted to use
66            it, so our users may want too.
67    
68    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * man/colSums.Rd: separately document colSums() etc, since these
71            have the extra argument 'sparseResult'.
72    
73    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
74    
75            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
76            * man/spMatrix.Rd: docu., including examples
77    
78            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
79            in order to make colMeans() etc fast *and* correct.
80            * R/sparseVector.R (replSPvec): "[<-" functionality for
81            sparseVectors; tested in
82            * tests/simple.R:
83    
84    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
85    
86            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
87            (very) sparse Matrices; output similar to Matlab's print().
88    
89    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
90    
91            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
92            0-based, indices (Jose Quesada <quesada@gmail.com>).
93    
94    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
95    
96            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
97    
98    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * R/Auxiliaries.R (sparsapply): new utility, much faster than
101            tapply1() for large sparse matrices.
102    
103    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
104    
105            * R/Matrix.R (dim<-): reshape now via sparseVector.
106    
107            * R/sparseVector.R: methods and function for
108            * R/AllClass.R: new "sparseVector" class and daughters.
109            * NAMESPACE: export new classes
110    
111    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * DESCRIPTION (Version): 0.99875-1
114            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
115    
116    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
117    
118            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
119            indexing
120            * tests/indexing.R: test set for that.
121    
122    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
123    
124            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
125            entries.
126            * tests/indexing.R(out): add regression test for it
127    
128    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
131            name for "!" method definitions.
132    
133    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * R/Tsparse.R (intI): new utility, used for "[" :
136                    Cleanup up there, and fixes for duplicated indices - more TODO!
137    
138            * tests/indexing.R(out): more tests
139    
140    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
141    
142            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
143            code that is now part of the R Lapack library.
144    
145            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
146            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
147    
148    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
149    
150            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
151    
152    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
155            up with extraneous names '0'...'<n-1>'
156    
157    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
158    
159            * R/dgTMatrix.R (mat2dgT): care about NAs
160    
161    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * R/kronecker.R: triangularity preserving methods
164    
165    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
166    
167            * R/kronecker.R: new file collecting kronecker() methods in one
168                    place.  Goal: become much faster!
169    
170    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
173            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
174            can be much faster.
175    
176            * tests/matprod.R: add regression tests for these (upper & lower).
177    
178    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
179    
180            * R/Matrix.R (diff): method for our Matrices.
181    
182            * R/sparseMatrix.R (isDiagonal): check dim()!
183    
184    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
185    
186            * R/Matrix.R (dim<-): new method for "reshape()" built on a
187            proposal from Tamas Papp.
188    
189    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
190    
191            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
192    
193            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
194            rather define and export  cBind() and rBind() only.
195            --> useRs *must* change code that used to have cbind()/rbind() !!
196    
197            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
198            * R/bind.Rout.save: ditto
199    
200    2007-02-16  Douglas Bates  <bates@r-project.org>
201    
202            * DESCRIPTION (Date, Version): 0.9975-11 with new date
203            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
204            const modifier on declaration of the array 'valid'
205    
206    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
207    
208            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
209    
210    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
211    
212            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
213    
214            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
215            * tests/simple.R: test the above and some of these coercions:
216    
217            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
218                    be careful to avoid infinite recursion, using new coercions in
219            * R/ngCMatrix.R and nsC... and ntC...
220            * R/lsparseMatrix.R: ditto
221    
222            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
223    
224            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
225            * R/Rsparse.R: reactivate .Call()s
226    
227            * tests/Class+Meth.R: a bit more on actual classes
228    
229    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
230    
231            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
232    
233    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * DESCRIPTION (Version): 0.9975-10 to upload
236    
237            * tests/Class+Meth.R (tstMatrixClass): require coercions to
238            specific classes less unconditionally.
239    
240            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
241    
242            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
243    
244            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
245            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
246            R_to_CMatrix segfaults on one platform.
247            Eliminate most coercion method to *specific* classes, and replace
248            with virtual classes coercions.
249    
250    
251    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
252    
253            * src/init.c: export the CHM...._validate() placeholders, since
254            they *are* called.
255    
256            * tests/Class+Meth.R (classCanCoerce): and starting to test
257            all as(<from>, <to>)
258    
259    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
262            * tests/indexing.R: tested now
263            * tests/indexing.Rout.save: updated
264    
265            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
266            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
267            appropriate.
268    
269            * NAMESPACE: export a trivial
270            * R/Matrix.R: drop() Matrix-method
271    
272            * R/AllClass.R: moved all prototypes to virtual super classes.
273    
274            * R/Rsparse.R: many more coercions to have less exceptions in
275            * tests/Class+Meth.R:
276    
277            * R/Ops.R (Compare): tweak for case with NA
278            * tests/simpl.R: hence another 'FIXME' eliminated
279    
280    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
281    
282            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
283            objects.
284    
285            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
286              and more of "!", "&", "|", all, any; coercions
287    
288            * R/Rsparse.R: many coercions (which enable quite a few other
289            methods), thanks to enhancements in
290            * src/dgCMatrix.c (R_to_CMatrix): new, and
291            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
292            symmetric & triangular and ..RMatrix objects.
293    
294            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
295            renamed file from src/dsTMatrix.c;
296            now dealing with symmetric and triangular Tsparse coercions, both
297            to dense and general.
298    
299    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
300    
301            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
302    
303            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
304            where sensible when the <numeric> is of length > 1.
305    
306    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
307    
308            * R/Matrix.R ([<-): for M[] <- value: fix length
309    
310    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
311    
312            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
313            * R/ndenseMatrix.R: new coercions n* -> l*
314    
315    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
316    
317            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
318    
319            * R/Ops.R ("Logic"): and other "Ops", many updates
320    
321    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * src/Mutils.h (SET_DimNames): new utility
324    
325            * R/Auxiliaries.R (nnzero): improved and now exported via
326    
327            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
328    
329    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
330    
331            * R/diagMatrix.R (!): fix typo.
332    
333    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
334    
335            * R/Auxiliaries.R (as_Csparse): and quite a few others:
336                    allow to pass class definition --> speedup
337            * R/sparseMatrix.R: apply the above
338    
339            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
340    
341            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
342            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
343            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
344    
345            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
346    
347            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
348            and use it for "sparse*" as well, since it's faster than the
349            as_Csparse(.) way.
350    
351    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
352    
353            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
354    
355    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
356    
357            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
358            as method for   M[ ij ] <- v
359            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
360    
361            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
362            FALSE answer
363    
364            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
365            * tests/indexing.R: test it, and some of the above
366    
367    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/Auxiliaries.R (is_duplicatedT): new utility
370    
371    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
372    
373            * src/init.c (R_init_Matrix): export cholmod_scale
374    
375    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
376    
377            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
378            base::as.matrix to (x, ...)
379    
380    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
381    
382            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
383            file; start using "Logic", hence
384    
385            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
386            * NAMESPACE: import and export "Logic"
387    
388    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
389    
390            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
391            only needed previously to R version 2.5.0.
392    
393    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
394    
395            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
396    
397            * R/Tsparse.R (replTmat): fix subassignment of triangular
398            * R/Csparse.R (replCmat): ditto
399            * tests/indexing.R: more tests, incl the above fix
400    
401    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
402    
403            * R/Auxiliaries.R (drop0): extend for non CSparse
404            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
405    
406            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
407                    use uplo correctly (!); other places: use uplo_P() macro
408    
409            * R/Csparse.R (replCmat): call diagU2N() when needed
410            * R/Tsparse.R (replTmat): ditto
411    
412            * src/dtCMatrix.c (tCMatrix_validate): new
413            * src/dtTMatrix.c (tTMatrix_validate): new, used in
414            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
415    
416            * R/diagMatrix.R (replDiag): to use in [<-
417    
418    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
419    
420            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
421                    also more general diagU2N().
422    
423    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
426            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
427    
428    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
429    
430            * tests/bind.R: a few more cases
431            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
432    
433            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
434            * R/ddenseMatrix.R (cbind2/rbind2)
435            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
436            * tests/indexing.R
437            * tests/indexing.Rout.save: updated
438    
439    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
442            * tests/indexing.R
443    
444    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
445    
446            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
447            align with proper position of "0", i.e., right for integers.
448            argument 'align' by default is "fancy".
449    
450    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
451    
452            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
453            * R/Csparse.R: and fix "Compare" for more cases.
454            * tests/Class+Meth.R: test some of these (m == m, m != m)
455    
456    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
457    
458            * R/lsparseMatrix.R: all() and any() methods
459            * R/ldenseMatrix.R:      ditto
460            * NAMESPACE, R/Matrix.R: ditto
461    
462            * man/all-methods.Rd: document them minimally
463    
464            * tests/simple.R: add a few examples for these
465    
466    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
467    
468            * R/Tsparse.R ([): fix long standing typo in symmetric case
469            * man/dsCMatrix-class.Rd: add example exhibiting the above case
470    
471    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
472    
473            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
474            to LL before converting to a sparse matrix. (The LDL form can be
475            converted to a sparse matrix but it is implicitly a unit
476            triangular matrix and a diagonal matrix overwritten on the diagonal.)
477    
478    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
479    
480            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
481    
482    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
483    
484            * DESCRIPTION (Version): updated -> release 0.9975-7
485            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
486    
487  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
488    
489          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method          * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method

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