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revision 1517, Wed Sep 6 13:34:03 2006 UTC revision 1968, Sat Jul 7 22:49:12 2007 UTC
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1    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dgCMatrix.c (compressed_to_TMatrix):
4    
5    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
6    
7            * src/Csparse.c (Rsparse_validate): new, to have some validity
8            checking for RsparseMatrix
9            * src/dgCMatrix.c (xRMatrix_validate): ditto
10            * src/dtCMatrix.c (tRMatrix_validate): ditto
11    
12    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
13    
14            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
15              lgRMatrix
16            * [r4568] DESCRIPTION: Prepare for bug-fix release
17            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
18              for declaration of cholmod_symmetry
19    
20    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
23            release.
24    
25    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
26    
27            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
28              functions - no longer used
29            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
30              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
31              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
32              Alloca
33    
34    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
35    
36            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
37              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
38              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
39              src/t_gCMatrix_colSums.c: more R_CheckStack()s
40    
41    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
42    
43            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
44              the required amount of memory then call M_numeric_as_chm_dense.
45            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
46              (like Calloc but calling alloca)
47    
48    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
49    
50            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
51            and extended with more sophisticated 'col.names' option.
52            * NAMESPACE: export  printSparseMatrix()
53            * man/printSpMatrix.Rd: document, incl. examples
54    
55    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
56    
57            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
58              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
59              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
60    
61    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
62    
63            * DESCRIPTION (Version): 0.99875-4
64    
65            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
66            some dimnames perservation.
67    
68            * R/dsTMatrix.R (t-method): keep dimnames
69            * R/dtTMatrix.R:  ditto
70    
71            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
72            and ncol(.) < 10
73    
74            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
75            from Mutils.h
76    
77            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
78            e.g. in as(<ngCMatrix>, "matrix")
79    
80    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
81    
82            * [r4529] .: Create a branch for the API changes from the 0.99875
83              series to the 0.999375 series
84            * [r4530] DESCRIPTION, inst/include/Matrix.h,
85              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
86              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
87              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
88              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
89              as_cholmod_x functions
90    
91    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
92    
93            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
94              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
95              to Comparisons
96    
97    >>>>>>> .merge-right.r4561
98    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
99    
100            * DESCRIPTION (Version): 0.99875-3 ready to be released.
101    
102            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
103    
104            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
105            that should also work in a future version of R.
106    
107    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
108    
109            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
110    
111            * R/sparseVector.R: more *sparseVector coercions, notably for
112            non - double ones.
113    
114    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
115    
116            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
117              notably the new ones building on the new .Call(.)s:
118    
119            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
120            all 4 of [dlin]gCMatrix_colSums().
121    
122    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
123    
124            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
125            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
126              result
127    
128    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
129    
130            * R/kronecker.R: fix typo (could lead to inf.recursion)
131            * test/simple.R: testing that
132    
133            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
134            method as well (which can have arguments, show() can't).
135    
136    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
137    
138            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
139              added dgCMatrix_colSums for [col,row][Sums,Means]
140    
141    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
142    
143            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
144              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
145              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
146            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
147              class
148            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
149              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
150              row names to store the levels - duh!  Added an example.
151    
152    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * src/Csparse.c (Csparse_validate): check for *repeated* entries
155            thanks to example from Christian Buchta; with a test here:
156            * tests/simple.R:
157    
158    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
159    
160            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
161            of colSums(*, sparseResult = TRUE)
162    
163    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
164    
165            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
166            'na.rm = FALSE' as "everywhere" else in R.
167    
168    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
169    
170            * [r4421] src/CSparse_install.sh: Modify for new organization of
171              CSparse package
172            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
173              SuiteSparse
174            * [r4426] src/Makefile: add ./UFconfig to the include path for
175              compilation
176            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
177            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
178              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
179    
180    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
183            * R/sparseMatrix.R (prSpMatrix): now gives a message about
184            suppressed column names.
185    
186    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
187    
188            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
189              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
190              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
191              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
192              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
193              Remove warnings after change to const char* CHAR
194    
195    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
196    
197            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
198              type of M_cholmod_ssmult
199    
200    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
201    
202            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
203              src/init.c: Yet another cholmod export - cholmod_ssmult
204    
205    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
206    
207            * NAMESPACE: exported drop0(), since
208            * man/drop0.Rd: I have seen several cases, I really wanted to use
209            it, so our users may want too.
210    
211    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
212    
213            * man/colSums.Rd: separately document colSums() etc, since these
214            have the extra argument 'sparseResult'.
215    
216    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
217    
218            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
219            * man/spMatrix.Rd: docu., including examples
220    
221            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
222            in order to make colMeans() etc fast *and* correct.
223            * R/sparseVector.R (replSPvec): "[<-" functionality for
224            sparseVectors; tested in
225            * tests/simple.R:
226    
227    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
228    
229            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
230            (very) sparse Matrices; output similar to Matlab's print().
231    
232    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
233    
234            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
235            0-based, indices (Jose Quesada <quesada@gmail.com>).
236    
237    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
238    
239            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
240    
241    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
242    
243            * R/Auxiliaries.R (sparsapply): new utility, much faster than
244            tapply1() for large sparse matrices.
245    
246    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/Matrix.R (dim<-): reshape now via sparseVector.
249    
250            * R/sparseVector.R: methods and function for
251            * R/AllClass.R: new "sparseVector" class and daughters.
252            * NAMESPACE: export new classes
253    
254    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
255    
256            * DESCRIPTION (Version): 0.99875-1
257            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
258    
259    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
260    
261            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
262            indexing
263            * tests/indexing.R: test set for that.
264    
265    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
266    
267            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
268            entries.
269            * tests/indexing.R(out): add regression test for it
270    
271    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
272    
273            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
274            name for "!" method definitions.
275    
276    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
277    
278            * R/Tsparse.R (intI): new utility, used for "[" :
279                    Cleanup up there, and fixes for duplicated indices - more TODO!
280    
281            * tests/indexing.R(out): more tests
282    
283    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
284    
285            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
286            code that is now part of the R Lapack library.
287    
288            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
289            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
290    
291    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
292    
293            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
294    
295    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
298            up with extraneous names '0'...'<n-1>'
299    
300    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
301    
302            * R/dgTMatrix.R (mat2dgT): care about NAs
303    
304    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/kronecker.R: triangularity preserving methods
307    
308    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
309    
310            * R/kronecker.R: new file collecting kronecker() methods in one
311                    place.  Goal: become much faster!
312    
313    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
314    
315            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
316            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
317            can be much faster.
318    
319            * tests/matprod.R: add regression tests for these (upper & lower).
320    
321    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
322    
323            * R/Matrix.R (diff): method for our Matrices.
324    
325            * R/sparseMatrix.R (isDiagonal): check dim()!
326    
327    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
328    
329            * R/Matrix.R (dim<-): new method for "reshape()" built on a
330            proposal from Tamas Papp.
331    
332    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
333    
334            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
335    
336            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
337            rather define and export  cBind() and rBind() only.
338            --> useRs *must* change code that used to have cbind()/rbind() !!
339    
340            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
341            * R/bind.Rout.save: ditto
342    
343    2007-02-16  Douglas Bates  <bates@r-project.org>
344    
345            * DESCRIPTION (Date, Version): 0.9975-11 with new date
346            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
347            const modifier on declaration of the array 'valid'
348    
349    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
350    
351            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
352    
353    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
354    
355            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
356    
357            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
358            * tests/simple.R: test the above and some of these coercions:
359    
360            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
361                    be careful to avoid infinite recursion, using new coercions in
362            * R/ngCMatrix.R and nsC... and ntC...
363            * R/lsparseMatrix.R: ditto
364    
365            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
366    
367            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
368            * R/Rsparse.R: reactivate .Call()s
369    
370            * tests/Class+Meth.R: a bit more on actual classes
371    
372    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
373    
374            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
375    
376    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * DESCRIPTION (Version): 0.9975-10 to upload
379    
380            * tests/Class+Meth.R (tstMatrixClass): require coercions to
381            specific classes less unconditionally.
382    
383            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
384    
385            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
386    
387            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
388            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
389            R_to_CMatrix segfaults on one platform.
390            Eliminate most coercion method to *specific* classes, and replace
391            with virtual classes coercions.
392    
393    
394    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
395    
396            * src/init.c: export the CHM...._validate() placeholders, since
397            they *are* called.
398    
399            * tests/Class+Meth.R (classCanCoerce): and starting to test
400            all as(<from>, <to>)
401    
402    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
403    
404            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
405            * tests/indexing.R: tested now
406            * tests/indexing.Rout.save: updated
407    
408            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
409            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
410            appropriate.
411    
412            * NAMESPACE: export a trivial
413            * R/Matrix.R: drop() Matrix-method
414    
415            * R/AllClass.R: moved all prototypes to virtual super classes.
416    
417            * R/Rsparse.R: many more coercions to have less exceptions in
418            * tests/Class+Meth.R:
419    
420            * R/Ops.R (Compare): tweak for case with NA
421            * tests/simpl.R: hence another 'FIXME' eliminated
422    
423    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
426            objects.
427    
428            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
429              and more of "!", "&", "|", all, any; coercions
430    
431            * R/Rsparse.R: many coercions (which enable quite a few other
432            methods), thanks to enhancements in
433            * src/dgCMatrix.c (R_to_CMatrix): new, and
434            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
435            symmetric & triangular and ..RMatrix objects.
436    
437            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
438            renamed file from src/dsTMatrix.c;
439            now dealing with symmetric and triangular Tsparse coercions, both
440            to dense and general.
441    
442    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
443    
444            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
445    
446            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
447            where sensible when the <numeric> is of length > 1.
448    
449    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
450    
451            * R/Matrix.R ([<-): for M[] <- value: fix length
452    
453    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
456            * R/ndenseMatrix.R: new coercions n* -> l*
457    
458    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
459    
460            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
461    
462            * R/Ops.R ("Logic"): and other "Ops", many updates
463    
464    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * src/Mutils.h (SET_DimNames): new utility
467    
468            * R/Auxiliaries.R (nnzero): improved and now exported via
469    
470            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
471    
472    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
473    
474            * R/diagMatrix.R (!): fix typo.
475    
476    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
477    
478            * R/Auxiliaries.R (as_Csparse): and quite a few others:
479                    allow to pass class definition --> speedup
480            * R/sparseMatrix.R: apply the above
481    
482            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
483    
484            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
485            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
486            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
487    
488            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
489    
490            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
491            and use it for "sparse*" as well, since it's faster than the
492            as_Csparse(.) way.
493    
494    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
495    
496            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
497    
498    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
499    
500            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
501            as method for   M[ ij ] <- v
502            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
503    
504            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
505            FALSE answer
506    
507            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
508            * tests/indexing.R: test it, and some of the above
509    
510    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
511    
512            * R/Auxiliaries.R (is_duplicatedT): new utility
513    
514    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
515    
516            * src/init.c (R_init_Matrix): export cholmod_scale
517    
518    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
519    
520            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
521            base::as.matrix to (x, ...)
522    
523    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
524    
525            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
526            file; start using "Logic", hence
527    
528            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
529            * NAMESPACE: import and export "Logic"
530    
531    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
532    
533            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
534            only needed previously to R version 2.5.0.
535    
536    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
537    
538            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
539    
540            * R/Tsparse.R (replTmat): fix subassignment of triangular
541            * R/Csparse.R (replCmat): ditto
542            * tests/indexing.R: more tests, incl the above fix
543    
544    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
545    
546            * R/Auxiliaries.R (drop0): extend for non CSparse
547            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
548    
549            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
550                    use uplo correctly (!); other places: use uplo_P() macro
551    
552            * R/Csparse.R (replCmat): call diagU2N() when needed
553            * R/Tsparse.R (replTmat): ditto
554    
555            * src/dtCMatrix.c (tCMatrix_validate): new
556            * src/dtTMatrix.c (tTMatrix_validate): new, used in
557            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
558    
559            * R/diagMatrix.R (replDiag): to use in [<-
560    
561    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
564                    also more general diagU2N().
565    
566    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
567    
568            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
569            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
570    
571    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
572    
573            * tests/bind.R: a few more cases
574            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
575    
576            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
577            * R/ddenseMatrix.R (cbind2/rbind2)
578            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
579            * tests/indexing.R
580            * tests/indexing.Rout.save: updated
581    
582    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
583    
584            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
585            * tests/indexing.R
586    
587    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
588    
589            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
590            align with proper position of "0", i.e., right for integers.
591            argument 'align' by default is "fancy".
592    
593    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
594    
595            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
596            * R/Csparse.R: and fix "Compare" for more cases.
597            * tests/Class+Meth.R: test some of these (m == m, m != m)
598    
599    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * R/lsparseMatrix.R: all() and any() methods
602            * R/ldenseMatrix.R:      ditto
603            * NAMESPACE, R/Matrix.R: ditto
604    
605            * man/all-methods.Rd: document them minimally
606    
607            * tests/simple.R: add a few examples for these
608    
609    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
610    
611            * R/Tsparse.R ([): fix long standing typo in symmetric case
612            * man/dsCMatrix-class.Rd: add example exhibiting the above case
613    
614    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
615    
616            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
617            to LL before converting to a sparse matrix. (The LDL form can be
618            converted to a sparse matrix but it is implicitly a unit
619            triangular matrix and a diagonal matrix overwritten on the diagonal.)
620    
621    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
622    
623            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
624    
625    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
626    
627            * DESCRIPTION (Version): updated -> release 0.9975-7
628            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
629    
630    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
633    
634    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
635    
636            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
637            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
638            is exactly singular.
639    
640    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
641    
642            * DESCRIPTION (Date): updated -> release 0.9975-6
643    
644    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
645    
646            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
647            now returns symmetric.
648    
649            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
650    
651            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
652            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
653    
654            * R/Auxiliaries.R (.type.kind): added
655    
656    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
659            running src/CSparse_install.sh
660    
661            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
662    
663    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
666            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
667    
668            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
669    
670            * tests/Class+Meth.R (tstMatrixClass): now assure
671            the (important in method programming) property :
672    
673                    ###>>  Every "Matrix" is either
674                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
675    
676                    (where "*" stands for "Matrix")
677    
678            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
679    
680            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
681            * tests/validObj.R: checks for "comparison"
682    
683            * R/sparseMatrix.R ([): improved indexing for sparse;
684                    trying to keep <symmetric>[ n, n] symmmetric
685    
686            * tests/indexing.R: indexing for logical sparse now ok
687    
688    
689    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
690    
691            * src/Tsparse.c: use xTsparse_validate() , and hence remove
692    
693            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
694    
695    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
696    
697            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
698    
699            * tests/simple.R: validObject() checking the above.
700    
701            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
702            replacing both dgCMatrix_validate and lgCM*.
703    
704            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
705            fix dimnames setting in other places.
706            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
707    
708    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
709    
710            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
711    
712            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
713            symmetry test, via
714            * R/Auxiliaries.R (.as.dgC.0.factors):
715    
716    2006-11-01  Douglas Bates  <bates@r-project.org>
717    
718            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
719            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
720            <CsparseMatrix>) added
721    
722    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
723    
724            * tests/matprod.R: add a variation of Harri's example
725    
726            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
727            recursive infinitely.
728    
729            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
730    
731            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
732    
733    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
734    
735            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
736            matrix if possible; test m+m == 2*m; now test dgRMatrix.
737            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
738            satisfy the above test.
739    
740    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
741    
742            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
743    
744            * R/dgCMatrix.R: solve(a, b="missing") based on
745            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
746            RHS = NULL.
747    
748            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
749            add more (needed) [t]crossprod() methods.
750    
751            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
752    
753            * R/Auxiliaries.R (as_CspClass): cleanup
754            (drop0): internal utility for "Csparse_drop(*, 0)"
755            (.bail.out.2): encourage active feedback
756    
757    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
758    
759            * R/dMatrix.R(Compare): new(), then slots [no validity check]
760    
761            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
762            non-valid or 'sorted' case).
763    
764            * R/dsparseMatrix.R: add "chol" method.
765            * R/ddenseMatrix.R: ditto
766    
767            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
768            * NAMESPACE (Ops)
769            * R/diagMatrix.R (diag2T): simple utility used "higher level"
770            coercion; deprecating direct lower level coercions.
771    
772            * R/*.R (seq): use seq_len() and seq_along() where possible.
773    
774    
775    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
776    
777            * DESCRIPTION (Version): 0.9975-5 ready for release
778    
779    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
780    
781            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
782    
783    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
784    
785            * R/AllClass.R (corMatrix): add 'validity' check;
786                    comment out unused "LDL" class definition
787            * NAMESPACE: mention, but do not export "LDL" class
788            * R/corMatrix.R: new (simple), needed for R-devel with
789            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
790              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
791    
792    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
793    
794            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
795            use Rprintf and R's error handling.
796    
797    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
798    
799            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
800            * tests/matprod.R: add tests for the bug fixed.
801    
802    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
803    
804            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
805            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
806    
807    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
808    
809            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
810    
811    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
812    
813            * DESCRIPTION (Version): 0.9975-3
814    
815            * R/diagMatrix.R (bdiag): new function constructing block diagonal
816            (sparse) matrices.
817            * man/bdiag.Rd: docu + examples
818    
819            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
820    
821            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
822            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
823    
824            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
825            that result is sparse or diagonal (and not dense).
826    
827            * man/Subassign-methods.Rd: fix examples
828    
829            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
830            should always return a sparse (and not sometimes a diagonal) matrix.
831    
832    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
833    
834            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
835    
836    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
837    
838            * DESCRIPTION (Version): 0.9975-2
839    
840            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
841    
842    2006-10-02  Douglas Bates  <bates@R-project.org>
843    
844            * tests/dg_Matrix.R: Simplify test taking into account new code.
845    
846    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
849    
850            * R/lsTMatrix.R: new files w/ missing methods
851            * R/nsTMatrix.R:  "  'for completeness'
852    
853            * tests/Class+Meth.R: a bit less 'not.ok.classes'
854    
855            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
856    
857    
858    2006-09-28  Douglas Bates  <bates@R-project.org>
859    
860            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
861            included.
862    
863            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
864            Export C-callable functions used in Zt_create in lme4.
865    
866    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
867    
868            * DESCRIPTION (Version): 0.9975-1
869    
870            * tests/simple.R: less checks fail; using NA, found that our
871                    kronecker() is not base-compatible with NA's.
872    
873            * R/dMatrix.R: "Compare" method now implemented for all cases
874    
875            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
876    
877            * man/dtpMatrix-class.Rd: mention length of 'x' slot
878    
879            * src/dtpMatrix.c (dtpMatrix_validate): fix check
880            * src/dspMatrix.c (dspMatrix_validate): ditto
881    
882            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
883              including coercion to [nl]tTMatrix.
884    
885            * R/diagMatrix.R (show): print a header line as for other classes.
886    
887    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
888    
889            * src/Makefile.win (SUBDIRS): fix typo
890    
891    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
892    
893            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
894    
895    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
896    
897            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
898            symmetric and y missing in R code using %*% (cholmod_aat doesn't
899            accept a symmetric matrix).
900            * tests/group-methods.R: Uncomment test of crossprod applied to
901            lsCMatrix objects.
902    
903    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
904    
905            * R/AllClass.R (symmetricMatrix): add validity method (available
906            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
907    
908            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
909    
910            * tests/indexing.Rout.save:
911            * tests/indexing.R: additions, mainly for 'lsparse'
912    
913            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
914            case.
915    
916            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
917    
918    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
919    
920            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
921                    as 'N' (1-letter - Ok?)
922    
923            * tests/group-methods.R: add test for logical + NAs
924    
925            * R/dMatrix.R ("Compare"): fix to work with NA's
926    
927            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
928    
929            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
930                    which is implemented.
931    
932    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
933    
934            * src/chm_common.c: coerce logical <-> double instead of
935            typecasting;  needed for "l" matrix handling in cholmod.
936    
937            * tests/other-pkgs.R (graph): small extension in "graph" checks.
938    
939            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
940            (Tsp2grNEL): other fixes needed
941    
942    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
943    
944            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
945                    Matrices, since "lMatrix", also "lsparseM" can have NA
946            * R/ndenseMatrix.R, etc: new source files
947            * man/nsparseMatrix-classes.Rd, etc: new help files
948            * tests/: adaptions
949            * src/chm_common.c (chm_dense_to_SEXP): and others:
950                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
951            * src/Csparse.c, etc: ditto
952    
953    2006-09-11  Douglas Bates  <bates@R-project.org>
954    
955            * src/Mutils.[ch],init.c inst/include/*.h: Move the
956            alloc_d**Matrix functions to the lme4 package.
957    
958    2006-09-09  Douglas Bates  <bates@R-project.org>
959    
960            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
961            fixed
962    
963    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
964    
965            * R/lMatrix.R: new
966    
967            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
968    
969            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
970            * man/tcrossprod.Rd: ditto
971    
972    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
973    
974            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
975            for exported functions
976            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
977            Remove partitioning algorithms for sparse matrix reordering.  The
978            copyright on the Metis code was problematic and the methods were
979            rarely used.
980            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
981            operations are now done entirely in CHOLMOD code.
982    
983  2006-09-06  Douglas Bates  <bates@R-project.org>  2006-09-06  Douglas Bates  <bates@R-project.org>
984    
985          * src/Mutils.h: Remove functions that are no longer used.          * src/Mutils.h: Remove functions that are no longer used.
# Line 28  Line 1010 
1010    
1011          * R/sparseMatrix.R (Arith): moved Arith group method one-level up          * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1012          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"          from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1013          * R/dsparseMatrix.R: dito          * R/dsparseMatrix.R: ditto
1014          * R/Csparse.R: dito          * R/Csparse.R: ditto
1015    
1016  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>  2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1017    
# Line 45  Line 1027 
1027    
1028          * 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
1029          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.          * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1030          (.is.diagonal): dito          (.is.diagonal): ditto
1031    
1032          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's          * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1033    

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