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revision 1368, Sat Aug 12 17:34:00 2006 UTC revision 2018, Wed Aug 1 15:22:05 2007 UTC
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1    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
2    
3            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
4            * tests/matprod.R: regr.test for it
5    
6    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
7    
8            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
9            * tests/group-methods.R: and regression-test it
10    
11    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
12    
13            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
14              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
15              triplet_to_sparse, documentation, use typedefs
16    
17    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
18    
19            * man/dpoMatrix-class.Rd: added 'corMatrix' example
20    
21            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
22            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
23            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
24    
25            * R/lsparseMatrix.R: bug fix in "all" method
26            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
27    
28            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
29            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
30                    + matrix |-> nMatrix coercion
31            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
32            * man/pMatrix-class.Rd: ditto
33    
34            * R/Matrix.R (Summary): method for non-dMatrix
35    
36            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
37            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
38                    test all Summary methods.
39    
40    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
41    
42            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
43    
44    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
45    
46            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
47    
48            * R/pMatrix.R (t?crossprod): methods for pMatrix
49    
50    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
51    
52            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
53    
54    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
55    
56            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
57              trying to fix a subtle bug - which has been somewhere else.
58    
59    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
60    
61            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
62              solve the bug
63    
64    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
65    
66            * src/dgCMatrix.c (compressed_to_TMatrix):
67    
68    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
69    
70            * src/Csparse.c (Rsparse_validate): new, to have some validity
71            checking for RsparseMatrix
72            * src/dgCMatrix.c (xRMatrix_validate): ditto
73            * src/dtCMatrix.c (tRMatrix_validate): ditto
74    
75    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
76    
77            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
78              lgRMatrix
79            * [r4568] DESCRIPTION: Prepare for bug-fix release
80            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
81              for declaration of cholmod_symmetry
82    
83    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
84    
85            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
86            release.
87    
88    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
89    
90            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
91              functions - no longer used
92            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
93              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
94              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
95              Alloca
96    
97    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
98    
99            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
100              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
101              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
102              src/t_gCMatrix_colSums.c: more R_CheckStack()s
103    
104    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
105    
106            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
107              the required amount of memory then call M_numeric_as_chm_dense.
108            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
109              (like Calloc but calling alloca)
110    
111    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
112    
113            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
114            and extended with more sophisticated 'col.names' option.
115            * NAMESPACE: export  printSparseMatrix()
116            * man/printSpMatrix.Rd: document, incl. examples
117    
118    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
119    
120            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
121              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
122              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
123    
124    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
125    
126            * DESCRIPTION (Version): 0.99875-4
127    
128            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
129            some dimnames perservation.
130    
131            * R/dsTMatrix.R (t-method): keep dimnames
132            * R/dtTMatrix.R:  ditto
133    
134            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
135            and ncol(.) < 10
136    
137            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
138            from Mutils.h
139    
140            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
141            e.g. in as(<ngCMatrix>, "matrix")
142    
143    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
144    
145            * [r4529] .: Create a branch for the API changes from the 0.99875
146              series to the 0.999375 series
147            * [r4530] DESCRIPTION, inst/include/Matrix.h,
148              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
149              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
150              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
151              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
152              as_cholmod_x functions
153    
154    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
155    
156            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
157              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
158              to Comparisons
159    
160    >>>>>>> .merge-right.r4561
161    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
162    
163            * DESCRIPTION (Version): 0.99875-3 ready to be released.
164    
165            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
166    
167            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
168            that should also work in a future version of R.
169    
170    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
171    
172            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
173    
174            * R/sparseVector.R: more *sparseVector coercions, notably for
175            non - double ones.
176    
177    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
178    
179            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
180              notably the new ones building on the new .Call(.)s:
181    
182            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
183            all 4 of [dlin]gCMatrix_colSums().
184    
185    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
186    
187            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
188            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
189              result
190    
191    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
192    
193            * R/kronecker.R: fix typo (could lead to inf.recursion)
194            * test/simple.R: testing that
195    
196            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
197            method as well (which can have arguments, show() can't).
198    
199    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
200    
201            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
202              added dgCMatrix_colSums for [col,row][Sums,Means]
203    
204    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
205    
206            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
207              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
208              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
209            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
210              class
211            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
212              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
213              row names to store the levels - duh!  Added an example.
214    
215    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
216    
217            * src/Csparse.c (Csparse_validate): check for *repeated* entries
218            thanks to example from Christian Buchta; with a test here:
219            * tests/simple.R:
220    
221    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
222    
223            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
224            of colSums(*, sparseResult = TRUE)
225    
226    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
227    
228            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
229            'na.rm = FALSE' as "everywhere" else in R.
230    
231    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
232    
233            * [r4421] src/CSparse_install.sh: Modify for new organization of
234              CSparse package
235            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
236              SuiteSparse
237            * [r4426] src/Makefile: add ./UFconfig to the include path for
238              compilation
239            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
240            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
241              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
242    
243    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
244    
245            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
246            * R/sparseMatrix.R (prSpMatrix): now gives a message about
247            suppressed column names.
248    
249    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
250    
251            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
252              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
253              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
254              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
255              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
256              Remove warnings after change to const char* CHAR
257    
258    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
259    
260            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
261              type of M_cholmod_ssmult
262    
263    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
264    
265            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
266              src/init.c: Yet another cholmod export - cholmod_ssmult
267    
268    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
269    
270            * NAMESPACE: exported drop0(), since
271            * man/drop0.Rd: I have seen several cases, I really wanted to use
272            it, so our users may want too.
273    
274    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
275    
276            * man/colSums.Rd: separately document colSums() etc, since these
277            have the extra argument 'sparseResult'.
278    
279    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
280    
281            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
282            * man/spMatrix.Rd: docu., including examples
283    
284            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
285            in order to make colMeans() etc fast *and* correct.
286            * R/sparseVector.R (replSPvec): "[<-" functionality for
287            sparseVectors; tested in
288            * tests/simple.R:
289    
290    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
293            (very) sparse Matrices; output similar to Matlab's print().
294    
295    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
296    
297            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
298            0-based, indices (Jose Quesada <quesada@gmail.com>).
299    
300    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
301    
302            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
303    
304    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
305    
306            * R/Auxiliaries.R (sparsapply): new utility, much faster than
307            tapply1() for large sparse matrices.
308    
309    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
310    
311            * R/Matrix.R (dim<-): reshape now via sparseVector.
312    
313            * R/sparseVector.R: methods and function for
314            * R/AllClass.R: new "sparseVector" class and daughters.
315            * NAMESPACE: export new classes
316    
317    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
318    
319            * DESCRIPTION (Version): 0.99875-1
320            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
321    
322    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
323    
324            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
325            indexing
326            * tests/indexing.R: test set for that.
327    
328    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
329    
330            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
331            entries.
332            * tests/indexing.R(out): add regression test for it
333    
334    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
335    
336            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
337            name for "!" method definitions.
338    
339    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
340    
341            * R/Tsparse.R (intI): new utility, used for "[" :
342                    Cleanup up there, and fixes for duplicated indices - more TODO!
343    
344            * tests/indexing.R(out): more tests
345    
346    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
347    
348            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
349            code that is now part of the R Lapack library.
350    
351            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
352            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
353    
354    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
355    
356            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
357    
358    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
359    
360            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
361            up with extraneous names '0'...'<n-1>'
362    
363    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
364    
365            * R/dgTMatrix.R (mat2dgT): care about NAs
366    
367    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
368    
369            * R/kronecker.R: triangularity preserving methods
370    
371    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
372    
373            * R/kronecker.R: new file collecting kronecker() methods in one
374                    place.  Goal: become much faster!
375    
376    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
377    
378            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
379            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
380            can be much faster.
381    
382            * tests/matprod.R: add regression tests for these (upper & lower).
383    
384    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
385    
386            * R/Matrix.R (diff): method for our Matrices.
387    
388            * R/sparseMatrix.R (isDiagonal): check dim()!
389    
390    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
391    
392            * R/Matrix.R (dim<-): new method for "reshape()" built on a
393            proposal from Tamas Papp.
394    
395    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
396    
397            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
398    
399            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
400            rather define and export  cBind() and rBind() only.
401            --> useRs *must* change code that used to have cbind()/rbind() !!
402    
403            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
404            * R/bind.Rout.save: ditto
405    
406    2007-02-16  Douglas Bates  <bates@r-project.org>
407    
408            * DESCRIPTION (Date, Version): 0.9975-11 with new date
409            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
410            const modifier on declaration of the array 'valid'
411    
412    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
413    
414            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
415    
416    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
417    
418            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
419    
420            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
421            * tests/simple.R: test the above and some of these coercions:
422    
423            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
424                    be careful to avoid infinite recursion, using new coercions in
425            * R/ngCMatrix.R and nsC... and ntC...
426            * R/lsparseMatrix.R: ditto
427    
428            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
429    
430            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
431            * R/Rsparse.R: reactivate .Call()s
432    
433            * tests/Class+Meth.R: a bit more on actual classes
434    
435    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
436    
437            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
438    
439    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
440    
441            * DESCRIPTION (Version): 0.9975-10 to upload
442    
443            * tests/Class+Meth.R (tstMatrixClass): require coercions to
444            specific classes less unconditionally.
445    
446            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
447    
448            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
449    
450            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
451            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
452            R_to_CMatrix segfaults on one platform.
453            Eliminate most coercion method to *specific* classes, and replace
454            with virtual classes coercions.
455    
456    
457    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
458    
459            * src/init.c: export the CHM...._validate() placeholders, since
460            they *are* called.
461    
462            * tests/Class+Meth.R (classCanCoerce): and starting to test
463            all as(<from>, <to>)
464    
465    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
466    
467            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
468            * tests/indexing.R: tested now
469            * tests/indexing.Rout.save: updated
470    
471            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
472            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
473            appropriate.
474    
475            * NAMESPACE: export a trivial
476            * R/Matrix.R: drop() Matrix-method
477    
478            * R/AllClass.R: moved all prototypes to virtual super classes.
479    
480            * R/Rsparse.R: many more coercions to have less exceptions in
481            * tests/Class+Meth.R:
482    
483            * R/Ops.R (Compare): tweak for case with NA
484            * tests/simpl.R: hence another 'FIXME' eliminated
485    
486    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
487    
488            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
489            objects.
490    
491            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
492              and more of "!", "&", "|", all, any; coercions
493    
494            * R/Rsparse.R: many coercions (which enable quite a few other
495            methods), thanks to enhancements in
496            * src/dgCMatrix.c (R_to_CMatrix): new, and
497            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
498            symmetric & triangular and ..RMatrix objects.
499    
500            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
501            renamed file from src/dsTMatrix.c;
502            now dealing with symmetric and triangular Tsparse coercions, both
503            to dense and general.
504    
505    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
506    
507            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
508    
509            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
510            where sensible when the <numeric> is of length > 1.
511    
512    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
513    
514            * R/Matrix.R ([<-): for M[] <- value: fix length
515    
516    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
517    
518            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
519            * R/ndenseMatrix.R: new coercions n* -> l*
520    
521    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
522    
523            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
524    
525            * R/Ops.R ("Logic"): and other "Ops", many updates
526    
527    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
528    
529            * src/Mutils.h (SET_DimNames): new utility
530    
531            * R/Auxiliaries.R (nnzero): improved and now exported via
532    
533            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
534    
535    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
536    
537            * R/diagMatrix.R (!): fix typo.
538    
539    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
540    
541            * R/Auxiliaries.R (as_Csparse): and quite a few others:
542                    allow to pass class definition --> speedup
543            * R/sparseMatrix.R: apply the above
544    
545            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
546    
547            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
548            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
549            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
550    
551            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
552    
553            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
554            and use it for "sparse*" as well, since it's faster than the
555            as_Csparse(.) way.
556    
557    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
558    
559            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
560    
561    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
562    
563            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
564            as method for   M[ ij ] <- v
565            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
566    
567            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
568            FALSE answer
569    
570            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
571            * tests/indexing.R: test it, and some of the above
572    
573    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
574    
575            * R/Auxiliaries.R (is_duplicatedT): new utility
576    
577    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
578    
579            * src/init.c (R_init_Matrix): export cholmod_scale
580    
581    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
584            base::as.matrix to (x, ...)
585    
586    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
587    
588            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
589            file; start using "Logic", hence
590    
591            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
592            * NAMESPACE: import and export "Logic"
593    
594    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
595    
596            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
597            only needed previously to R version 2.5.0.
598    
599    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
600    
601            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
602    
603            * R/Tsparse.R (replTmat): fix subassignment of triangular
604            * R/Csparse.R (replCmat): ditto
605            * tests/indexing.R: more tests, incl the above fix
606    
607    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
608    
609            * R/Auxiliaries.R (drop0): extend for non CSparse
610            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
611    
612            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
613                    use uplo correctly (!); other places: use uplo_P() macro
614    
615            * R/Csparse.R (replCmat): call diagU2N() when needed
616            * R/Tsparse.R (replTmat): ditto
617    
618            * src/dtCMatrix.c (tCMatrix_validate): new
619            * src/dtTMatrix.c (tTMatrix_validate): new, used in
620            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
621    
622            * R/diagMatrix.R (replDiag): to use in [<-
623    
624    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
625    
626            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
627                    also more general diagU2N().
628    
629    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
630    
631            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
632            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
633    
634    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
635    
636            * tests/bind.R: a few more cases
637            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
638    
639            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
640            * R/ddenseMatrix.R (cbind2/rbind2)
641            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
642            * tests/indexing.R
643            * tests/indexing.Rout.save: updated
644    
645    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
646    
647            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
648            * tests/indexing.R
649    
650    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
653            align with proper position of "0", i.e., right for integers.
654            argument 'align' by default is "fancy".
655    
656    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
657    
658            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
659            * R/Csparse.R: and fix "Compare" for more cases.
660            * tests/Class+Meth.R: test some of these (m == m, m != m)
661    
662    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
663    
664            * R/lsparseMatrix.R: all() and any() methods
665            * R/ldenseMatrix.R:      ditto
666            * NAMESPACE, R/Matrix.R: ditto
667    
668            * man/all-methods.Rd: document them minimally
669    
670            * tests/simple.R: add a few examples for these
671    
672    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
673    
674            * R/Tsparse.R ([): fix long standing typo in symmetric case
675            * man/dsCMatrix-class.Rd: add example exhibiting the above case
676    
677    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
678    
679            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
680            to LL before converting to a sparse matrix. (The LDL form can be
681            converted to a sparse matrix but it is implicitly a unit
682            triangular matrix and a diagonal matrix overwritten on the diagonal.)
683    
684    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
685    
686            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
687    
688    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
689    
690            * DESCRIPTION (Version): updated -> release 0.9975-7
691            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
692    
693    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
696    
697    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
698    
699            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
700            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
701            is exactly singular.
702    
703    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * DESCRIPTION (Date): updated -> release 0.9975-6
706    
707    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
708    
709            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
710            now returns symmetric.
711    
712            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
713    
714            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
715            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
716    
717            * R/Auxiliaries.R (.type.kind): added
718    
719    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
722            running src/CSparse_install.sh
723    
724            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
725    
726    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
727    
728            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
729            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
730    
731            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
732    
733            * tests/Class+Meth.R (tstMatrixClass): now assure
734            the (important in method programming) property :
735    
736                    ###>>  Every "Matrix" is either
737                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
738    
739                    (where "*" stands for "Matrix")
740    
741            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
742    
743            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
744            * tests/validObj.R: checks for "comparison"
745    
746            * R/sparseMatrix.R ([): improved indexing for sparse;
747                    trying to keep <symmetric>[ n, n] symmmetric
748    
749            * tests/indexing.R: indexing for logical sparse now ok
750    
751    
752    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
753    
754            * src/Tsparse.c: use xTsparse_validate() , and hence remove
755    
756            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
757    
758    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
759    
760            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
761    
762            * tests/simple.R: validObject() checking the above.
763    
764            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
765            replacing both dgCMatrix_validate and lgCM*.
766    
767            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
768            fix dimnames setting in other places.
769            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
770    
771    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
772    
773            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
774    
775            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
776            symmetry test, via
777            * R/Auxiliaries.R (.as.dgC.0.factors):
778    
779    2006-11-01  Douglas Bates  <bates@r-project.org>
780    
781            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
782            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
783            <CsparseMatrix>) added
784    
785    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
786    
787            * tests/matprod.R: add a variation of Harri's example
788    
789            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
790            recursive infinitely.
791    
792            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
793    
794            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
795    
796    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
797    
798            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
799            matrix if possible; test m+m == 2*m; now test dgRMatrix.
800            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
801            satisfy the above test.
802    
803    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
804    
805            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
806    
807            * R/dgCMatrix.R: solve(a, b="missing") based on
808            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
809            RHS = NULL.
810    
811            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
812            add more (needed) [t]crossprod() methods.
813    
814            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
815    
816            * R/Auxiliaries.R (as_CspClass): cleanup
817            (drop0): internal utility for "Csparse_drop(*, 0)"
818            (.bail.out.2): encourage active feedback
819    
820    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
821    
822            * R/dMatrix.R(Compare): new(), then slots [no validity check]
823    
824            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
825            non-valid or 'sorted' case).
826    
827            * R/dsparseMatrix.R: add "chol" method.
828            * R/ddenseMatrix.R: ditto
829    
830            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
831            * NAMESPACE (Ops)
832            * R/diagMatrix.R (diag2T): simple utility used "higher level"
833            coercion; deprecating direct lower level coercions.
834    
835            * R/*.R (seq): use seq_len() and seq_along() where possible.
836    
837    
838    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
839    
840            * DESCRIPTION (Version): 0.9975-5 ready for release
841    
842    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
843    
844            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
845    
846    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
847    
848            * R/AllClass.R (corMatrix): add 'validity' check;
849                    comment out unused "LDL" class definition
850            * NAMESPACE: mention, but do not export "LDL" class
851            * R/corMatrix.R: new (simple), needed for R-devel with
852            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
853              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
854    
855    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
856    
857            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
858            use Rprintf and R's error handling.
859    
860    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
861    
862            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
863            * tests/matprod.R: add tests for the bug fixed.
864    
865    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
866    
867            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
868            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
869    
870    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
871    
872            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
873    
874    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
875    
876            * DESCRIPTION (Version): 0.9975-3
877    
878            * R/diagMatrix.R (bdiag): new function constructing block diagonal
879            (sparse) matrices.
880            * man/bdiag.Rd: docu + examples
881    
882            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
883    
884            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
885            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
886    
887            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
888            that result is sparse or diagonal (and not dense).
889    
890            * man/Subassign-methods.Rd: fix examples
891    
892            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
893            should always return a sparse (and not sometimes a diagonal) matrix.
894    
895    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
896    
897            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
898    
899    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
900    
901            * DESCRIPTION (Version): 0.9975-2
902    
903            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
904    
905    2006-10-02  Douglas Bates  <bates@R-project.org>
906    
907            * tests/dg_Matrix.R: Simplify test taking into account new code.
908    
909    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
910    
911            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
912    
913            * R/lsTMatrix.R: new files w/ missing methods
914            * R/nsTMatrix.R:  "  'for completeness'
915    
916            * tests/Class+Meth.R: a bit less 'not.ok.classes'
917    
918            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
919    
920    
921    2006-09-28  Douglas Bates  <bates@R-project.org>
922    
923            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
924            included.
925    
926            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
927            Export C-callable functions used in Zt_create in lme4.
928    
929    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * DESCRIPTION (Version): 0.9975-1
932    
933            * tests/simple.R: less checks fail; using NA, found that our
934                    kronecker() is not base-compatible with NA's.
935    
936            * R/dMatrix.R: "Compare" method now implemented for all cases
937    
938            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
939    
940            * man/dtpMatrix-class.Rd: mention length of 'x' slot
941    
942            * src/dtpMatrix.c (dtpMatrix_validate): fix check
943            * src/dspMatrix.c (dspMatrix_validate): ditto
944    
945            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
946              including coercion to [nl]tTMatrix.
947    
948            * R/diagMatrix.R (show): print a header line as for other classes.
949    
950    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
951    
952            * src/Makefile.win (SUBDIRS): fix typo
953    
954    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
955    
956            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
957    
958    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
959    
960            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
961            symmetric and y missing in R code using %*% (cholmod_aat doesn't
962            accept a symmetric matrix).
963            * tests/group-methods.R: Uncomment test of crossprod applied to
964            lsCMatrix objects.
965    
966    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
967    
968            * R/AllClass.R (symmetricMatrix): add validity method (available
969            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
970    
971            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
972    
973            * tests/indexing.Rout.save:
974            * tests/indexing.R: additions, mainly for 'lsparse'
975    
976            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
977            case.
978    
979            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
980    
981    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
982    
983            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
984                    as 'N' (1-letter - Ok?)
985    
986            * tests/group-methods.R: add test for logical + NAs
987    
988            * R/dMatrix.R ("Compare"): fix to work with NA's
989    
990            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
991    
992            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
993                    which is implemented.
994    
995    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
996    
997            * src/chm_common.c: coerce logical <-> double instead of
998            typecasting;  needed for "l" matrix handling in cholmod.
999    
1000            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1001    
1002            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1003            (Tsp2grNEL): other fixes needed
1004    
1005    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1006    
1007            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1008                    Matrices, since "lMatrix", also "lsparseM" can have NA
1009            * R/ndenseMatrix.R, etc: new source files
1010            * man/nsparseMatrix-classes.Rd, etc: new help files
1011            * tests/: adaptions
1012            * src/chm_common.c (chm_dense_to_SEXP): and others:
1013                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1014            * src/Csparse.c, etc: ditto
1015    
1016    2006-09-11  Douglas Bates  <bates@R-project.org>
1017    
1018            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1019            alloc_d**Matrix functions to the lme4 package.
1020    
1021    2006-09-09  Douglas Bates  <bates@R-project.org>
1022    
1023            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1024            fixed
1025    
1026    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1027    
1028            * R/lMatrix.R: new
1029    
1030            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1031    
1032            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1033            * man/tcrossprod.Rd: ditto
1034    
1035    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1036    
1037            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1038            for exported functions
1039            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1040            Remove partitioning algorithms for sparse matrix reordering.  The
1041            copyright on the Metis code was problematic and the methods were
1042            rarely used.
1043            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1044            operations are now done entirely in CHOLMOD code.
1045    
1046    2006-09-06  Douglas Bates  <bates@R-project.org>
1047    
1048            * src/Mutils.h: Remove functions that are no longer used.
1049    
1050    2006-09-04  Douglas Bates  <bates@R-project.org>
1051    
1052            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1053            * src/DEPS.mkf: update
1054    
1055    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1056    
1057            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1058            * DESCRIPTION (Version): 0.9975-0
1059            (Depends): R (>= 2.4.0)
1060    
1061    2006-09-01  Douglas Bates  <bates@R-project.org>
1062    
1063            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1064    
1065    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1066    
1067            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1068            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1069    
1070            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1071    
1072    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1073    
1074            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1075            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1076            * R/dsparseMatrix.R: ditto
1077            * R/Csparse.R: ditto
1078    
1079    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1080    
1081            * R/dMatrix.R (Compare): improve availability of "<", etc
1082            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1083    
1084    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1085    
1086            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1087            of a 0-index which was used as 1-index (..hmm)
1088    
1089            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1090    
1091            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1092            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1093            (.is.diagonal): ditto
1094    
1095            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1096    
1097            * R/Matrix.R (Matrix): also work for NA data
1098    
1099    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1100    
1101            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1102            in all cases.
1103    
1104    2006-08-27  Douglas Bates  <bates@R-project.org>
1105    
1106            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1107            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1108    
1109    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1110    
1111            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1112            subclasses of "ddenseMatrix"
1113            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1114            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1115            instead of half dozen specialized ones.
1116    
1117    2006-08-25  Douglas Bates  <bates@R-project.org>
1118    
1119            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1120            <tillard@cirad.fr> - ordering standard errors to match effects.
1121    
1122    2006-08-24  Douglas Bates  <bates@R-project.org>
1123    
1124            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1125            on R_ldl.
1126            * R/lCholCMatrix.R,
1127            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1128            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1129            * many files in ./R and ./src: Use more general version of
1130            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1131            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1132            dtpMatrix, dspMatrix and dppMatrix conversions.
1133    
1134    
1135    2006-08-23  Douglas Bates  <bates@R-project.org>
1136    
1137            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1138            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1139            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1140            dgeMatrix_crossprod (may need to do this in other places).
1141            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1142            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1143    
1144    2006-08-22  Douglas Bates  <bates@R-project.org>
1145    
1146            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1147            types of classed Matrices, matrices or numeric or logical vectors.
1148            * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1149            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1150            to Mutils.h (as an inline) and change name to Matrix_check_class;
1151            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1152            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1153            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1154            * src/Csparse.c: use diag_P and uplo_P macros.
1155    
1156    2006-08-21  Douglas Bates  <bates@R-project.org>
1157    
1158            * src/lmer.c (internal_mer_RZXinv): Fix memory leak caught by
1159            valgrind.
1160            * tests/matprod.R: Add tests to verify that 'solve' and '%*%' are
1161            inverses.
1162            * src/sparseQR.c (sparseQR_validate): add new validation test, fix
1163            -Wall warnings.
1164            * src/dppMatrix.c,dtrMatrix.c,dgCMatrix.c,dgeMatrix.c,dspMatrix.c:
1165            Use dup_mMatrix_as_dgeMatrix.
1166    
1167    2006-08-20  Douglas Bates  <bates@R-project.org>
1168    
1169            * src/sparseQR.c: Fix thinko in sparseQR_resid_fitted.
1170            * tests/sparseQR.R: Added
1171            * man/sparseQR-class.Rd: Document methods for qr.* generics
1172            * R/sparseQR.R: Return correct # of coefs; fix cut-and-paste errors
1173    
1174    2006-08-19  Douglas Bates  <bates@R-project.org>
1175    
1176            * NAMESPACE, R/sparseQR.R, src/init.c,sparseQR.[ch],SOURCES_C.mkf:
1177            Added methods for sparseQR for qr.qy, qr.qty, qr.coef, qr.resid
1178            and qr.fitted.
1179            * src/Mutils.[ch]: Added dup_mMatrix_as_dgeMatrix utility
1180            * src/dgCMatrix.c: Check for ordering before storing q in dgCMatrix_QR
1181    
1182    2006-08-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1183    
1184            * R/AllGeneric.R: add "qr" and "chol" generics; via 'trick' since
1185            the base version has no "..." argument.
1186    
1187            * R/sparseMatrix.R (prSpMatrix): fix the triangular unit diagonal case.
1188    
1189            * R/Matrix.R: define and
1190            * NAMESPACE: export as.numeric() and as.logical() methods.
1191                    Let's hope these do not badly slow down something...
1192            Finally export the zapsmall() method.
1193    
1194    2006-08-17  Douglas Bates  <bates@R-project.org>
1195    
1196            * src/dgCMatrix.[ch] (dgCMatrix_matrix_solve), src/init.c,
1197            R/dgCMatrix.R: solve methods for dgCMatrix and dense RHS.
1198            * src/dtCMatrix.c :Remove code that is no longer used
1199            * R/dtCMatrix.R: Use C code for diagU2N in CsparseMatrix classes
1200    
1201    2006-08-14  Douglas Bates  <bates@R-project.org>
1202    
1203            * src/Csparse.[ch],init.c (Csparse_to_logical): Added utilities
1204            Csparse_to_logical and Csparse_symmetric_to_general.
1205            * R/dgCMatrix.R,dsCMatrix.R,Csparse.R : Consolidate general
1206            coercion methods between CsparseMatrix and TsparseMatrix.
1207    
1208    2006-08-14  Douglas Bates  <bates@R-project.org>
1209    
1210            * R/dtCMatrix.R,dgCMatrix.R,Csparse.R src/init.c,dgCMatrix.[ch],
1211            Csparse.[ch],chm_common.c,dense.c : Use CHOLMOD code and methods
1212            for CsparseMatrix, TsparseMatrix, denseMatrix or matrix when
1213            possible.
1214    
1215  2006-08-12  Douglas Bates  <bates@R-project.org>  2006-08-12  Douglas Bates  <bates@R-project.org>
1216    
1217          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,          * src/chm_common.[ch],Csparse.[ch],Tsparse.[ch],CHMfactor.c,dtTMatrix.c,

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