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revision 1548, Mon Sep 11 22:13:07 2006 UTC revision 1964, Sat Jul 7 18:26:22 2007 UTC
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1    2007-07-07 18:23  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
4              lgRMatrix
5            * [r4568] DESCRIPTION: Prepare for bug-fix release
6    
7    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
8    
9            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
10            release.
11    
12    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
13    
14            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
15              functions - no longer used
16            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
17              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
18              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
19              Alloca
20    
21    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
22    
23            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
24              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
25              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
26              src/t_gCMatrix_colSums.c: more R_CheckStack()s
27    
28    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
29    
30            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
31              the required amount of memory then call M_numeric_as_chm_dense.
32            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
33              (like Calloc but calling alloca)
34    
35    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
36    
37            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
38            and extended with more sophisticated 'col.names' option.
39            * NAMESPACE: export  printSparseMatrix()
40            * man/printSpMatrix.Rd: document, incl. examples
41    
42    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
43    
44            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
45              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
46              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
47    
48    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * DESCRIPTION (Version): 0.99875-4
51    
52            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
53            some dimnames perservation.
54    
55            * R/dsTMatrix.R (t-method): keep dimnames
56            * R/dtTMatrix.R:  ditto
57    
58            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
59            and ncol(.) < 10
60    
61            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
62            from Mutils.h
63    
64            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
65            e.g. in as(<ngCMatrix>, "matrix")
66    
67    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
68    
69            * [r4529] .: Create a branch for the API changes from the 0.99875
70              series to the 0.999375 series
71            * [r4530] DESCRIPTION, inst/include/Matrix.h,
72              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
73              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
74              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
75              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
76              as_cholmod_x functions
77    
78    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
79    
80            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
81              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
82              to Comparisons
83    
84    >>>>>>> .merge-right.r4561
85    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
86    
87            * DESCRIPTION (Version): 0.99875-3 ready to be released.
88    
89            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
90    
91            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
92            that should also work in a future version of R.
93    
94    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
95    
96            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
97    
98            * R/sparseVector.R: more *sparseVector coercions, notably for
99            non - double ones.
100    
101    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
102    
103            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
104              notably the new ones building on the new .Call(.)s:
105    
106            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
107            all 4 of [dlin]gCMatrix_colSums().
108    
109    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
110    
111            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
112            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
113              result
114    
115    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
116    
117            * R/kronecker.R: fix typo (could lead to inf.recursion)
118            * test/simple.R: testing that
119    
120            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
121            method as well (which can have arguments, show() can't).
122    
123    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
124    
125            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
126              added dgCMatrix_colSums for [col,row][Sums,Means]
127    
128    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
129    
130            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
131              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
132              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
133            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
134              class
135            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
136              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
137              row names to store the levels - duh!  Added an example.
138    
139    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
140    
141            * src/Csparse.c (Csparse_validate): check for *repeated* entries
142            thanks to example from Christian Buchta; with a test here:
143            * tests/simple.R:
144    
145    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
146    
147            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
148            of colSums(*, sparseResult = TRUE)
149    
150    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
151    
152            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
153            'na.rm = FALSE' as "everywhere" else in R.
154    
155    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
156    
157            * [r4421] src/CSparse_install.sh: Modify for new organization of
158              CSparse package
159            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
160              SuiteSparse
161            * [r4426] src/Makefile: add ./UFconfig to the include path for
162              compilation
163            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
164            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
165              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
166    
167    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
168    
169            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
170            * R/sparseMatrix.R (prSpMatrix): now gives a message about
171            suppressed column names.
172    
173    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
174    
175            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
176              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
177              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
178              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
179              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
180              Remove warnings after change to const char* CHAR
181    
182    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
183    
184            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
185              type of M_cholmod_ssmult
186    
187    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
190              src/init.c: Yet another cholmod export - cholmod_ssmult
191    
192    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
193    
194            * NAMESPACE: exported drop0(), since
195            * man/drop0.Rd: I have seen several cases, I really wanted to use
196            it, so our users may want too.
197    
198    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
199    
200            * man/colSums.Rd: separately document colSums() etc, since these
201            have the extra argument 'sparseResult'.
202    
203    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
204    
205            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
206            * man/spMatrix.Rd: docu., including examples
207    
208            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
209            in order to make colMeans() etc fast *and* correct.
210            * R/sparseVector.R (replSPvec): "[<-" functionality for
211            sparseVectors; tested in
212            * tests/simple.R:
213    
214    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
215    
216            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
217            (very) sparse Matrices; output similar to Matlab's print().
218    
219    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
220    
221            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
222            0-based, indices (Jose Quesada <quesada@gmail.com>).
223    
224    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
225    
226            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
227    
228    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
229    
230            * R/Auxiliaries.R (sparsapply): new utility, much faster than
231            tapply1() for large sparse matrices.
232    
233    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
234    
235            * R/Matrix.R (dim<-): reshape now via sparseVector.
236    
237            * R/sparseVector.R: methods and function for
238            * R/AllClass.R: new "sparseVector" class and daughters.
239            * NAMESPACE: export new classes
240    
241    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * DESCRIPTION (Version): 0.99875-1
244            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
245    
246    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
249            indexing
250            * tests/indexing.R: test set for that.
251    
252    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
253    
254            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
255            entries.
256            * tests/indexing.R(out): add regression test for it
257    
258    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
259    
260            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
261            name for "!" method definitions.
262    
263    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
264    
265            * R/Tsparse.R (intI): new utility, used for "[" :
266                    Cleanup up there, and fixes for duplicated indices - more TODO!
267    
268            * tests/indexing.R(out): more tests
269    
270    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
271    
272            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
273            code that is now part of the R Lapack library.
274    
275            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
276            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
277    
278    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
279    
280            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
281    
282    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
283    
284            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
285            up with extraneous names '0'...'<n-1>'
286    
287    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
288    
289            * R/dgTMatrix.R (mat2dgT): care about NAs
290    
291    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/kronecker.R: triangularity preserving methods
294    
295    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/kronecker.R: new file collecting kronecker() methods in one
298                    place.  Goal: become much faster!
299    
300    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
303            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
304            can be much faster.
305    
306            * tests/matprod.R: add regression tests for these (upper & lower).
307    
308    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/Matrix.R (diff): method for our Matrices.
311    
312            * R/sparseMatrix.R (isDiagonal): check dim()!
313    
314    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
315    
316            * R/Matrix.R (dim<-): new method for "reshape()" built on a
317            proposal from Tamas Papp.
318    
319    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
320    
321            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
322    
323            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
324            rather define and export  cBind() and rBind() only.
325            --> useRs *must* change code that used to have cbind()/rbind() !!
326    
327            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
328            * R/bind.Rout.save: ditto
329    
330    2007-02-16  Douglas Bates  <bates@r-project.org>
331    
332            * DESCRIPTION (Date, Version): 0.9975-11 with new date
333            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
334            const modifier on declaration of the array 'valid'
335    
336    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
337    
338            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
339    
340    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
341    
342            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
343    
344            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
345            * tests/simple.R: test the above and some of these coercions:
346    
347            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
348                    be careful to avoid infinite recursion, using new coercions in
349            * R/ngCMatrix.R and nsC... and ntC...
350            * R/lsparseMatrix.R: ditto
351    
352            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
353    
354            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
355            * R/Rsparse.R: reactivate .Call()s
356    
357            * tests/Class+Meth.R: a bit more on actual classes
358    
359    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
360    
361            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
362    
363    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * DESCRIPTION (Version): 0.9975-10 to upload
366    
367            * tests/Class+Meth.R (tstMatrixClass): require coercions to
368            specific classes less unconditionally.
369    
370            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
371    
372            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
373    
374            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
375            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
376            R_to_CMatrix segfaults on one platform.
377            Eliminate most coercion method to *specific* classes, and replace
378            with virtual classes coercions.
379    
380    
381    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
382    
383            * src/init.c: export the CHM...._validate() placeholders, since
384            they *are* called.
385    
386            * tests/Class+Meth.R (classCanCoerce): and starting to test
387            all as(<from>, <to>)
388    
389    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
390    
391            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
392            * tests/indexing.R: tested now
393            * tests/indexing.Rout.save: updated
394    
395            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
396            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
397            appropriate.
398    
399            * NAMESPACE: export a trivial
400            * R/Matrix.R: drop() Matrix-method
401    
402            * R/AllClass.R: moved all prototypes to virtual super classes.
403    
404            * R/Rsparse.R: many more coercions to have less exceptions in
405            * tests/Class+Meth.R:
406    
407            * R/Ops.R (Compare): tweak for case with NA
408            * tests/simpl.R: hence another 'FIXME' eliminated
409    
410    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
411    
412            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
413            objects.
414    
415            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
416              and more of "!", "&", "|", all, any; coercions
417    
418            * R/Rsparse.R: many coercions (which enable quite a few other
419            methods), thanks to enhancements in
420            * src/dgCMatrix.c (R_to_CMatrix): new, and
421            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
422            symmetric & triangular and ..RMatrix objects.
423    
424            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
425            renamed file from src/dsTMatrix.c;
426            now dealing with symmetric and triangular Tsparse coercions, both
427            to dense and general.
428    
429    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
430    
431            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
432    
433            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
434            where sensible when the <numeric> is of length > 1.
435    
436    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/Matrix.R ([<-): for M[] <- value: fix length
439    
440    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
443            * R/ndenseMatrix.R: new coercions n* -> l*
444    
445    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
448    
449            * R/Ops.R ("Logic"): and other "Ops", many updates
450    
451    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
452    
453            * src/Mutils.h (SET_DimNames): new utility
454    
455            * R/Auxiliaries.R (nnzero): improved and now exported via
456    
457            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
458    
459    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/diagMatrix.R (!): fix typo.
462    
463    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
464    
465            * R/Auxiliaries.R (as_Csparse): and quite a few others:
466                    allow to pass class definition --> speedup
467            * R/sparseMatrix.R: apply the above
468    
469            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
470    
471            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
472            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
473            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
474    
475            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
476    
477            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
478            and use it for "sparse*" as well, since it's faster than the
479            as_Csparse(.) way.
480    
481    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
482    
483            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
484    
485    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
488            as method for   M[ ij ] <- v
489            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
490    
491            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
492            FALSE answer
493    
494            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
495            * tests/indexing.R: test it, and some of the above
496    
497    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
498    
499            * R/Auxiliaries.R (is_duplicatedT): new utility
500    
501    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
502    
503            * src/init.c (R_init_Matrix): export cholmod_scale
504    
505    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
508            base::as.matrix to (x, ...)
509    
510    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
513            file; start using "Logic", hence
514    
515            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
516            * NAMESPACE: import and export "Logic"
517    
518    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
521            only needed previously to R version 2.5.0.
522    
523    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
526    
527            * R/Tsparse.R (replTmat): fix subassignment of triangular
528            * R/Csparse.R (replCmat): ditto
529            * tests/indexing.R: more tests, incl the above fix
530    
531    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * R/Auxiliaries.R (drop0): extend for non CSparse
534            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
535    
536            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
537                    use uplo correctly (!); other places: use uplo_P() macro
538    
539            * R/Csparse.R (replCmat): call diagU2N() when needed
540            * R/Tsparse.R (replTmat): ditto
541    
542            * src/dtCMatrix.c (tCMatrix_validate): new
543            * src/dtTMatrix.c (tTMatrix_validate): new, used in
544            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
545    
546            * R/diagMatrix.R (replDiag): to use in [<-
547    
548    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
549    
550            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
551                    also more general diagU2N().
552    
553    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
554    
555            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
556            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
557    
558    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
559    
560            * tests/bind.R: a few more cases
561            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
562    
563            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
564            * R/ddenseMatrix.R (cbind2/rbind2)
565            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
566            * tests/indexing.R
567            * tests/indexing.Rout.save: updated
568    
569    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
570    
571            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
572            * tests/indexing.R
573    
574    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
577            align with proper position of "0", i.e., right for integers.
578            argument 'align' by default is "fancy".
579    
580    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
581    
582            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
583            * R/Csparse.R: and fix "Compare" for more cases.
584            * tests/Class+Meth.R: test some of these (m == m, m != m)
585    
586    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/lsparseMatrix.R: all() and any() methods
589            * R/ldenseMatrix.R:      ditto
590            * NAMESPACE, R/Matrix.R: ditto
591    
592            * man/all-methods.Rd: document them minimally
593    
594            * tests/simple.R: add a few examples for these
595    
596    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * R/Tsparse.R ([): fix long standing typo in symmetric case
599            * man/dsCMatrix-class.Rd: add example exhibiting the above case
600    
601    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
602    
603            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
604            to LL before converting to a sparse matrix. (The LDL form can be
605            converted to a sparse matrix but it is implicitly a unit
606            triangular matrix and a diagonal matrix overwritten on the diagonal.)
607    
608    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
609    
610            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
611    
612    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
613    
614            * DESCRIPTION (Version): updated -> release 0.9975-7
615            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
616    
617    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
618    
619            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
620    
621    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
622    
623            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
624            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
625            is exactly singular.
626    
627    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
628    
629            * DESCRIPTION (Date): updated -> release 0.9975-6
630    
631    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
632    
633            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
634            now returns symmetric.
635    
636            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
637    
638            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
639            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
640    
641            * R/Auxiliaries.R (.type.kind): added
642    
643    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
644    
645            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
646            running src/CSparse_install.sh
647    
648            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
649    
650    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
653            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
654    
655            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
656    
657            * tests/Class+Meth.R (tstMatrixClass): now assure
658            the (important in method programming) property :
659    
660                    ###>>  Every "Matrix" is either
661                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
662    
663                    (where "*" stands for "Matrix")
664    
665            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
666    
667            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
668            * tests/validObj.R: checks for "comparison"
669    
670            * R/sparseMatrix.R ([): improved indexing for sparse;
671                    trying to keep <symmetric>[ n, n] symmmetric
672    
673            * tests/indexing.R: indexing for logical sparse now ok
674    
675    
676    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * src/Tsparse.c: use xTsparse_validate() , and hence remove
679    
680            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
681    
682    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
683    
684            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
685    
686            * tests/simple.R: validObject() checking the above.
687    
688            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
689            replacing both dgCMatrix_validate and lgCM*.
690    
691            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
692            fix dimnames setting in other places.
693            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
694    
695    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
698    
699            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
700            symmetry test, via
701            * R/Auxiliaries.R (.as.dgC.0.factors):
702    
703    2006-11-01  Douglas Bates  <bates@r-project.org>
704    
705            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
706            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
707            <CsparseMatrix>) added
708    
709    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
710    
711            * tests/matprod.R: add a variation of Harri's example
712    
713            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
714            recursive infinitely.
715    
716            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
717    
718            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
719    
720    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
721    
722            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
723            matrix if possible; test m+m == 2*m; now test dgRMatrix.
724            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
725            satisfy the above test.
726    
727    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
728    
729            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
730    
731            * R/dgCMatrix.R: solve(a, b="missing") based on
732            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
733            RHS = NULL.
734    
735            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
736            add more (needed) [t]crossprod() methods.
737    
738            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
739    
740            * R/Auxiliaries.R (as_CspClass): cleanup
741            (drop0): internal utility for "Csparse_drop(*, 0)"
742            (.bail.out.2): encourage active feedback
743    
744    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
745    
746            * R/dMatrix.R(Compare): new(), then slots [no validity check]
747    
748            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
749            non-valid or 'sorted' case).
750    
751            * R/dsparseMatrix.R: add "chol" method.
752            * R/ddenseMatrix.R: ditto
753    
754            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
755            * NAMESPACE (Ops)
756            * R/diagMatrix.R (diag2T): simple utility used "higher level"
757            coercion; deprecating direct lower level coercions.
758    
759            * R/*.R (seq): use seq_len() and seq_along() where possible.
760    
761    
762    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * DESCRIPTION (Version): 0.9975-5 ready for release
765    
766    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
767    
768            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
769    
770    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
771    
772            * R/AllClass.R (corMatrix): add 'validity' check;
773                    comment out unused "LDL" class definition
774            * NAMESPACE: mention, but do not export "LDL" class
775            * R/corMatrix.R: new (simple), needed for R-devel with
776            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
777              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
778    
779    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
782            use Rprintf and R's error handling.
783    
784    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
785    
786            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
787            * tests/matprod.R: add tests for the bug fixed.
788    
789    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
790    
791            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
792            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
793    
794    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
795    
796            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
797    
798    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
799    
800            * DESCRIPTION (Version): 0.9975-3
801    
802            * R/diagMatrix.R (bdiag): new function constructing block diagonal
803            (sparse) matrices.
804            * man/bdiag.Rd: docu + examples
805    
806            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
807    
808            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
809            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
810    
811            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
812            that result is sparse or diagonal (and not dense).
813    
814            * man/Subassign-methods.Rd: fix examples
815    
816            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
817            should always return a sparse (and not sometimes a diagonal) matrix.
818    
819    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
820    
821            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
822    
823    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
824    
825            * DESCRIPTION (Version): 0.9975-2
826    
827            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
828    
829    2006-10-02  Douglas Bates  <bates@R-project.org>
830    
831            * tests/dg_Matrix.R: Simplify test taking into account new code.
832    
833    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
834    
835            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
836    
837            * R/lsTMatrix.R: new files w/ missing methods
838            * R/nsTMatrix.R:  "  'for completeness'
839    
840            * tests/Class+Meth.R: a bit less 'not.ok.classes'
841    
842            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
843    
844    
845    2006-09-28  Douglas Bates  <bates@R-project.org>
846    
847            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
848            included.
849    
850            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
851            Export C-callable functions used in Zt_create in lme4.
852    
853    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
854    
855            * DESCRIPTION (Version): 0.9975-1
856    
857            * tests/simple.R: less checks fail; using NA, found that our
858                    kronecker() is not base-compatible with NA's.
859    
860            * R/dMatrix.R: "Compare" method now implemented for all cases
861    
862            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
863    
864            * man/dtpMatrix-class.Rd: mention length of 'x' slot
865    
866            * src/dtpMatrix.c (dtpMatrix_validate): fix check
867            * src/dspMatrix.c (dspMatrix_validate): ditto
868    
869            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
870              including coercion to [nl]tTMatrix.
871    
872            * R/diagMatrix.R (show): print a header line as for other classes.
873    
874    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * src/Makefile.win (SUBDIRS): fix typo
877    
878    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
879    
880            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
881    
882    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
883    
884            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
885            symmetric and y missing in R code using %*% (cholmod_aat doesn't
886            accept a symmetric matrix).
887            * tests/group-methods.R: Uncomment test of crossprod applied to
888            lsCMatrix objects.
889    
890    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
891    
892            * R/AllClass.R (symmetricMatrix): add validity method (available
893            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
894    
895            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
896    
897            * tests/indexing.Rout.save:
898            * tests/indexing.R: additions, mainly for 'lsparse'
899    
900            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
901            case.
902    
903            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
904    
905    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
906    
907            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
908                    as 'N' (1-letter - Ok?)
909    
910            * tests/group-methods.R: add test for logical + NAs
911    
912            * R/dMatrix.R ("Compare"): fix to work with NA's
913    
914            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
915    
916            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
917                    which is implemented.
918    
919    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
920    
921            * src/chm_common.c: coerce logical <-> double instead of
922            typecasting;  needed for "l" matrix handling in cholmod.
923    
924            * tests/other-pkgs.R (graph): small extension in "graph" checks.
925    
926            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
927            (Tsp2grNEL): other fixes needed
928    
929  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"          * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
# Line 7  Line 935 
935          * tests/: adaptions          * tests/: adaptions
936          * src/chm_common.c (chm_dense_to_SEXP): and others:          * src/chm_common.c (chm_dense_to_SEXP): and others:
937                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL                  new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
938          * src/Csparse.c, etc: dito          * src/Csparse.c, etc: ditto
939    
940  2006-09-11  Douglas Bates  <bates@R-project.org>  2006-09-11  Douglas Bates  <bates@R-project.org>
941    
# Line 26  Line 954 
954          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()          * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
955    
956          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"          * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
957          * man/tcrossprod.Rd: dito          * man/tcrossprod.Rd: ditto
958    
959  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>  2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
960    
# Line 69  Line 997 
997    
998          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
999          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1000          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1001          * R/Csparse.R: dito          * R/Csparse.R: ditto
1002    
1003  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1004    
# Line 86  Line 1014 
1014    
1015          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's          * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1016          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1017          (.is.diagonal): dito          (.is.diagonal): ditto
1018    
1019          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1020    

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