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revision 1414, Tue Aug 22 17:25:43 2006 UTC revision 2051, Tue Aug 14 22:23:53 2007 UTC
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1    2007-08-14 13:07  Douglas Bates <bates@stat.wisc.edu>
2    
3            * [r4730] src/Mutils.h: declare alloca
4            * [r4734] NAMESPACE, R/AllGeneric.R, R/Csparse.R, R/HBMM.R, R/Tsparse.R,
5              R/dgCMatrix.R, R/dgTMatrix.R, R/dsCMatrix.R, R/dsTMatrix.R,
6              man/externalFormats.Rd, src/Csparse.c, src/Csparse.h, src/DEPS.mkf,
7              src/HBMM.c, src/HBMM.h, src/Mutils.h, src/SOURCES_C.mkf, src/init.c,
8              src/mmio.c, src/mmio.h: Remove deprecated function writeHB and its
9              methods; switch writeMM to use CHOLMOD code; repair readMM
10    
11    2007-08-14  Martin Maechler  <maechler@stat.math.ethz.ch>
12    
13            * R/nearPD.R, man/nearPD.Rd (nearPD): new function built on Jens
14            Oehlschlaegel's ... result type still to be discussed!
15    
16    2007-08-10  Martin Maechler  <maechler@stat.math.ethz.ch>
17    
18            * man/image-methods.Rd: new, combining all image() methods
19    
20    2007-08-09  Martin Maechler  <maechler@stat.math.ethz.ch>
21    
22            * R/dgCMatrix.R: define qr() and lu() methods for "sparseMatrix"
23            to work via dgC...
24    
25            * R/Matrix.R (Matrix): special treatment for "table" (S3)
26    
27    2007-08-07  Martin Maechler  <maechler@stat.math.ethz.ch>
28    
29            * R/dgTMatrix.R (image): change defaults to
30                    aspect = "iso", colorkey = FALSE
31    
32    2007-08-06  Martin Maechler  <maechler@stat.math.ethz.ch>
33    
34            * src/dsyMatrix.c (dsyMatrix_matrix_mm): 'b' might be matrix;
35            must copy its *expanded* x slot before LAPACK call.
36    
37            * tests/matprod.R: test the last days' changes.
38    
39    2007-08-06 16:43  Douglas Bates <bates@stat.wisc.edu>
40    
41            * [r4712] inst/include/Matrix_stubs.c: Change R_cholmod_printf in stubs
42              as well as in sources
43            * [r4713] src/dsyMatrix.c: Duplicate the contents of the RHS before
44              Lapack call
45    
46    2007-08-03  Martin Maechler  <maechler@stat.math.ethz.ch>
47    
48            * R/Matrix.R (%*%, crossprod, tcrossprod): add method for
49                    ("Matrix", "matrix") which is needed in some cases.
50            Ditto for solve().
51    
52            * R/colSums.R (.as.dge.Fun): need ddenseMatrix methods to avoid
53            infinite recursion in dispatch for some cases.
54    
55    2007-08-02 08:48  Martin Maechler <maechler@stat.math.ethz.ch>
56    
57            * [r4693] src/chm_common.c: R_cholmod_printf() instead of Rprintf() just
58              so pointers match
59    
60    2007-08-02  Martin Maechler  <maechler@stat.math.ethz.ch>
61    
62            * DESCRIPTION (Date): set ready for release -- 0.999375-1
63    
64    2007-08-01 15:44  Douglas Bates <bates@stat.wisc.edu>
65    
66            * [r4686] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
67              src/chm_common.c, src/chm_common.h: Change API for
68              numeric_as_chm_dense and N_AS_CHM_DN
69    
70    2007-08-01  Martin Maechler  <maechler@stat.math.ethz.ch>
71    
72            * src/dtrMatrix.c (dtrMatrix_matrix_mm): fix dimensionality check (!)
73            * tests/matprod.R: regr.test for it
74    
75    2007-07-20  Martin Maechler  <maechler@stat.math.ethz.ch>
76    
77            * R/dMatrix.R: fix from Brian for   Math2(., digits = "missing")
78            * tests/group-methods.R: and regression-test it
79    
80    2007-07-19 19:45  Douglas Bates <bates@stat.wisc.edu>
81    
82            * [r4642] inst/include/Matrix.h, inst/include/Matrix_stubs.c,
83              inst/include/cholmod.h, src/chm_common.c, src/init.c: Export
84              triplet_to_sparse, documentation, use typedefs
85    
86    2007-07-18  Martin Maechler  <maechler@stat.math.ethz.ch>
87    
88            * man/dpoMatrix-class.Rd: added 'corMatrix' example
89    
90            * src/dsyMatrix.[ch] (dsyMatrix_as_matrix): new 'keep_dimnames' arg
91            * src/dtrMatrix.[ch] (dtrMatrix_as_matrix): ditto
92            * src/init.c, R/dsyMatrix.R, R/dtrMatrix.R, R/lgTMatrix.R: ditto
93    
94            * R/lsparseMatrix.R: bug fix in "all" method
95            * R/Ops.R (.do.Logic.lsparse): "|" bug in borderline case
96    
97            * R/dsyMatrix.R (coerce->dsTMatrix): (i,j) slots should *not* have names
98            * R/ngTMatrix.R (coerce->ngTMatrix): ditto;
99                    + matrix |-> nMatrix coercion
100            * R/pMatrix.R: + setAs()  to dMatrix and from nMatrix
101            * man/pMatrix-class.Rd: ditto
102    
103            * R/Matrix.R (Summary): method for non-dMatrix
104    
105            * tests/Class+Meth.R (extraValid): new check about "dirty" slots
106            * tests/Class+Meth.R (tstMatrixClass): test norm(.);
107                    test all Summary methods.
108    
109    2007-07-16  Martin Maechler  <maechler@stat.math.ethz.ch>
110    
111            * R/dgeMatrix.R (norm, rcond): methods for 'matrix'
112    
113    2007-07-14  Martin Maechler  <maechler@stat.math.ethz.ch>
114    
115            * R/sparseMatrix.R (norm): simple methods for sparseMatrix
116    
117            * R/pMatrix.R (t?crossprod): methods for pMatrix
118    
119    2007-07-10  Douglas Bates  <bates@stat.wisc.edu>
120    
121            * src/dgeMatrix.c (dgeMatrix_colsums): Get the logic straight.
122    
123    2007-07-09 20:45  Douglas Bates <bates@stat.wisc.edu>
124    
125            * [r4579] src/dgeMatrix.c: Untangle horrible code in dgeMatrix_colsums
126              trying to fix a subtle bug - which has been somewhere else.
127    
128    2007-07-09 19:43  Martin Maechler <maechler@stat.math.ethz.ch>
129    
130            * [r4578] src/dgeMatrix.c: "cleaned" dgeMatrix_colsums() - but did not
131              solve the bug
132    
133    2007-07-08  Martin Maechler  <maechler@stat.math.ethz.ch>
134    
135            * src/dgCMatrix.c (compressed_to_TMatrix):
136    
137    2007-07-07  Martin Maechler  <maechler@stat.math.ethz.ch>
138    
139            * src/Csparse.c (Rsparse_validate): new, to have some validity
140            checking for RsparseMatrix
141            * src/dgCMatrix.c (xRMatrix_validate): ditto
142            * src/dtCMatrix.c (tRMatrix_validate): ditto
143    
144    2007-07-07  Douglas Bates <bates@stat.wisc.edu>
145    
146            * [r4567] R/AllClass.R: Slots already in RsparseMatrix were redefined in
147              lgRMatrix
148            * [r4568] DESCRIPTION: Prepare for bug-fix release
149            * [r4570] src/CHOLMOD/Check/cholmod_write.c: Include cholmod_matrixops.h
150              for declaration of cholmod_symmetry
151    
152    2007-07-06  Martin Maechler  <maechler@stat.math.ethz.ch>
153    
154            * DESCRIPTION (Version): 0.999375 merged into the trunk; ready for
155            release.
156    
157    2007-07-06 14:11  Douglas Bates <bates@stat.wisc.edu>
158    
159            * [r4559] src/iohb.c, src/iohb.h: Remove Harwell-Boeing input/output
160              functions - no longer used
161            * [r4560] src/HBMM.c, src/Mutils.c, src/dgTMatrix.c, src/dgeMatrix.c,
162              src/dspMatrix.c, src/dsyMatrix.c, src/dtCMatrix.c,
163              src/factorizations.c, src/sparseQR.c: Replace most calls to Calloc by
164              Alloca
165    
166    2007-07-06 13:14  Martin Maechler <maechler@stat.math.ethz.ch>
167    
168            * [r4558] inst/doc/Comparisons.Rnw, src/CHMfactor.c, src/Csparse.c,
169              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dense.c,
170              src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c, src/sparseQR.c,
171              src/t_gCMatrix_colSums.c: more R_CheckStack()s
172    
173    2007-07-05 18:12  Douglas Bates <bates@stat.wisc.edu>
174    
175            * [r4550] inst/include/Matrix.h: Add the macro N_AS_CHM_DN to "alloca"
176              the required amount of memory then call M_numeric_as_chm_dense.
177            * [r4556] src/Mutils.h, src/dgCMatrix.c: Define and use the Alloca macro
178              (like Calloc but calling alloca)
179    
180    2007-07-05  Martin Maechler  <maechler@stat.math.ethz.ch>
181    
182            * R/sparseMatrix.R (printSpMatrix): renamed from prSpMatrix()
183            and extended with more sophisticated 'col.names' option.
184            * NAMESPACE: export  printSparseMatrix()
185            * man/printSpMatrix.Rd: document, incl. examples
186    
187    2007-07-04 16:21  Douglas Bates <bates@stat.wisc.edu>
188    
189            * [r4543] src/cs_utils.c, src/cs_utils.h, src/dgCMatrix.c,
190              src/dtCMatrix.c, src/sparseQR.c: CSP typedef for *cs and macro
191              AS_CSP. API change - pass the empty structure to Matrix_as_cs.
192    
193    2007-07-04  Martin Maechler  <maechler@stat.math.ethz.ch>
194    
195            * DESCRIPTION (Version): 0.99875-4
196    
197            * tests/Class+Meth.R (tstMatrixClass): add dimnames, and hence test
198            some dimnames perservation.
199    
200            * R/dsTMatrix.R (t-method): keep dimnames
201            * R/dtTMatrix.R:  ditto
202    
203            * R/sparseMatrix.R (prSpMatrix): print colnames when non-trivial
204            and ncol(.) < 10
205    
206            * src/cs_utils.c: drop check_class() and use Matrix_check_class()
207            from Mutils.h
208    
209            * src/lgCMatrix.c ([ln]csc_to_matrix): no longer lose dimnames,
210            e.g. in as(<ngCMatrix>, "matrix")
211    
212    2007-07-01 13:27  Douglas Bates <bates@stat.wisc.edu>
213    
214            * [r4529] .: Create a branch for the API changes from the 0.99875
215              series to the 0.999375 series
216            * [r4530] DESCRIPTION, inst/include/Matrix.h,
217              inst/include/Matrix_stubs.c, src/CHMfactor.c, src/Csparse.c,
218              src/Mutils.h, src/Tsparse.c, src/chm_common.c, src/chm_common.h,
219              src/dense.c, src/dgCMatrix.c, src/dsCMatrix.c, src/dtTMatrix.c,
220              src/t_gCMatrix_colSums.c: API change - pass the empty structure to the
221              as_cholmod_x functions
222    
223    2007-06-30 09:05  Martin Maechler <maechler@stat.math.ethz.ch>
224    
225            * [r4527] trunk/Matrix/DESCRIPTION, trunk/Matrix/NAMESPACE,
226              trunk/Matrix/inst/doc/Comparisons.Rnw: add session- and hardware-info
227              to Comparisons
228    
229    >>>>>>> .merge-right.r4561
230    2007-06-29  Martin Maechler  <maechler@stat.math.ethz.ch>
231    
232            * DESCRIPTION (Version): 0.99875-3 ready to be released.
233    
234            * R/sparseMatrix.R (spMatrix): make spMatrix(3,4) working
235    
236            * R/AllGeneric.R: set "Math" (and "Math2") group generics in a way
237            that should also work in a future version of R.
238    
239    2007-06-21  Martin Maechler  <maechler@stat.math.ethz.ch>
240    
241            * NAMESPACE, R/AllClass.R: "xsparseVector" class union.
242    
243            * R/sparseVector.R: more *sparseVector coercions, notably for
244            non - double ones.
245    
246    2007-06-19  Martin Maechler  <maechler@stat.math.ethz.ch>
247    
248            * R/colSums.R: new file for all (col|row)(Sums|Means) methods,
249              notably the new ones building on the new .Call(.)s:
250    
251            * src/dgCMatrix.c (DEF_gCMatrix_COLSUMS): use to define
252            all 4 of [dlin]gCMatrix_colSums().
253    
254    2007-06-18 16:12  Douglas Bates <bates@stat.wisc.edu>
255    
256            * [r4472] src/Syms.h, src/init.c: Added Matrix_lengthSym
257            * [r4473] src/dgCMatrix.c: Modified dgCMatrix_colSums for sparseVector
258              result
259    
260    2007-06-16  Martin Maechler  <maechler@stat.math.ethz.ch>
261    
262            * R/kronecker.R: fix typo (could lead to inf.recursion)
263            * test/simple.R: testing that
264    
265            * R/sparseMatrix.R (prSpMatrix): change to be used as print()
266            method as well (which can have arguments, show() can't).
267    
268    2007-06-16 15:52  Douglas Bates <bates@stat.wisc.edu>
269    
270            * [r4466] R/dgCMatrix.R, src/dgCMatrix.c, src/dgCMatrix.h, src/init.c:
271              added dgCMatrix_colSums for [col,row][Sums,Means]
272    
273    2007-06-15 23:15  Douglas Bates <bates@stat.wisc.edu>
274    
275            * [r4460] R/sparseMatrix.R, man/dgCMatrix-class.Rd, src/dgCMatrix.c,
276              src/dgCMatrix.h, src/init.c: added lm.fit.sparse (unexported),
277              coercion of "factor" to "dgCMatrix" and dgCMatrix_cholsol
278            * [r4461] R/AllClass.R, man/sparseMatrix-class.Rd: draft "indicators"
279              class
280            * [r4463] R/sparseMatrix.R, man/dgCMatrix-class.Rd,
281              man/sparseMatrix-class.Rd: Don't need an "indicators" class - use the
282              row names to store the levels - duh!  Added an example.
283    
284    2007-06-14  Martin Maechler  <maechler@stat.math.ethz.ch>
285    
286            * src/Csparse.c (Csparse_validate): check for *repeated* entries
287            thanks to example from Christian Buchta; with a test here:
288            * tests/simple.R:
289    
290    2007-06-07  Martin Maechler  <maechler@stat.math.ethz.ch>
291    
292            * R/Auxiliaries.R (callGeneric): another fix, needed for some cases
293            of colSums(*, sparseResult = TRUE)
294    
295    2007-06-06  Martin Maechler  <maechler@stat.math.ethz.ch>
296    
297            * R/lsparseMatrix.R, R/ldenseMatrix.R (all, any): change default to
298            'na.rm = FALSE' as "everywhere" else in R.
299    
300    2007-06-05 Douglas Bates <bates@stat.wisc.edu>
301    
302            * [r4421] src/CSparse_install.sh: Modify for new organization of
303              CSparse package
304            * [r4425] src/UFsparse_download.sh: Update to version 3.0.0 of
305              SuiteSparse
306            * [r4426] src/Makefile: add ./UFconfig to the include path for
307              compilation
308            * [r4427] src/cs.[ch]: update to CSparse version 2.2.0
309            * [r4428] inst/doc/UFsparse/* src/{AMD,CHOLMOD,COLAMD}/*
310              src/UFconfig/UFconfig.h: Update to version 3.0.0 of SuiteSparse
311    
312    2007-06-05  Martin Maechler  <maechler@stat.math.ethz.ch>
313    
314            * R/Auxiliaries.R (emptyColnames): + argument msg.if.not.empty, used in
315            * R/sparseMatrix.R (prSpMatrix): now gives a message about
316            suppressed column names.
317    
318    2007-06-04 17:13  Douglas Bates <bates@stat.wisc.edu>
319    
320            * [r4418] src/Csparse.c, src/HBMM.c, src/Mutils.c, src/Mutils.h,
321              src/Tsparse.c, src/chm_common.c, src/chm_common.h, src/dgCMatrix.c,
322              src/dgeMatrix.c, src/dpoMatrix.c, src/dpoMatrix.h, src/dppMatrix.c,
323              src/dppMatrix.h, src/dsCMatrix.c, src/dspMatrix.c, src/dspMatrix.h,
324              src/dsyMatrix.c, src/dsyMatrix.h, src/dtpMatrix.c, src/dtrMatrix.c:
325              Remove warnings after change to const char* CHAR
326    
327    2007-06-04 17:11  Douglas Bates <bates@stat.wisc.edu>
328    
329            * [r4417] inst/include/Matrix_stubs.c, inst/include/cholmod.h: Corrected
330              type of M_cholmod_ssmult
331    
332    2007-06-03 14:42  Douglas Bates <bates@stat.wisc.edu>
333    
334            * [r4412] inst/include/Matrix_stubs.c, inst/include/cholmod.h,
335              src/init.c: Yet another cholmod export - cholmod_ssmult
336    
337    2007-05-23  Martin Maechler  <maechler@stat.math.ethz.ch>
338    
339            * NAMESPACE: exported drop0(), since
340            * man/drop0.Rd: I have seen several cases, I really wanted to use
341            it, so our users may want too.
342    
343    2007-05-22  Martin Maechler  <maechler@stat.math.ethz.ch>
344    
345            * man/colSums.Rd: separately document colSums() etc, since these
346            have the extra argument 'sparseResult'.
347    
348    2007-05-21  Martin Maechler  <maechler@stat.math.ethz.ch>
349    
350            * R/sparseMatrix.R (spMatrix): utility (T)sparse Matrix constructor;
351            * man/spMatrix.Rd: docu., including examples
352    
353            * R/Auxiliaries.R (sp.colMeans): etc, using a patched callGeneric(),
354            in order to make colMeans() etc fast *and* correct.
355            * R/sparseVector.R (replSPvec): "[<-" functionality for
356            sparseVectors; tested in
357            * tests/simple.R:
358    
359    2007-05-19  Martin Maechler  <maechler@stat.math.ethz.ch>
360    
361            * R/sparseMatrix.R (print.sparseSummary): and summary() method for
362            (very) sparse Matrices; output similar to Matlab's print().
363    
364    2007-05-17  Douglas Bates  <bates@stat.wisc.edu>
365    
366            * src/HBMM.c (Matrix_writeMatrixMarket): Write 1-based, not
367            0-based, indices (Jose Quesada <quesada@gmail.com>).
368    
369    2007-05-16  Douglas Bates  <bates@stat.wisc.edu>
370    
371            * R/CHMfactor.R: Added solve methods for a CHMfactor object.
372    
373    2007-05-16  Martin Maechler  <maechler@stat.math.ethz.ch>
374    
375            * R/Auxiliaries.R (sparsapply): new utility, much faster than
376            tapply1() for large sparse matrices.
377    
378    2007-05-15  Martin Maechler  <maechler@stat.math.ethz.ch>
379    
380            * R/Matrix.R (dim<-): reshape now via sparseVector.
381    
382            * R/sparseVector.R: methods and function for
383            * R/AllClass.R: new "sparseVector" class and daughters.
384            * NAMESPACE: export new classes
385    
386    2007-05-14  Martin Maechler  <maechler@stat.math.ethz.ch>
387    
388            * DESCRIPTION (Version): 0.99875-1
389            * src/Makefile.win: also remove Lapack code from here (cf. 04-25).
390    
391    2007-05-11  Martin Maechler  <maechler@stat.math.ethz.ch>
392    
393            * R/Tsparse.R ([, Tsparse): fix last case: *duplicated*, symmetric
394            indexing
395            * tests/indexing.R: test set for that.
396    
397    2007-05-08  Martin Maechler  <maechler@stat.math.ethz.ch>
398    
399            * R/Tsparse.R (replTmat): fix the case of *duplicated* index
400            entries.
401            * tests/indexing.R(out): add regression test for it
402    
403    2007-04-30  Martin Maechler  <maechler@stat.math.ethz.ch>
404    
405            * R/(l(dense|sparse))?Matrix.R (!): use 'x', not 'e1' as argument
406            name for "!" method definitions.
407    
408    2007-04-26  Martin Maechler  <maechler@stat.math.ethz.ch>
409    
410            * R/Tsparse.R (intI): new utility, used for "[" :
411                    Cleanup up there, and fixes for duplicated indices - more TODO!
412    
413            * tests/indexing.R(out): more tests
414    
415    2007-04-25  Douglas Bates  <bates@stat.wisc.edu>
416    
417            * DESCRIPTION,src/Makefile: require R>= 2.5.0 and remove Lapack
418            code that is now part of the R Lapack library.
419    
420            * src/init.c,inst/include/{Matrix_stubs.c,cholmod.h}:export
421            cholmod_factorize_p (used in lme4 for GLMMs and NLMMs).
422    
423    2007-04-21  Martin Maechler  <maechler@stat.math.ethz.ch>
424    
425            * R/Matrix.R (image): method for all Matrices, not just sparse ones.
426    
427    2007-04-17  Martin Maechler  <maechler@stat.math.ethz.ch>
428    
429            * R/Auxiliaries.R (tapply1): unname(.) -> colSums() etc don't end
430            up with extraneous names '0'...'<n-1>'
431    
432    2007-04-12  Martin Maechler  <maechler@stat.math.ethz.ch>
433    
434            * R/dgTMatrix.R (mat2dgT): care about NAs
435    
436    2007-04-11  Martin Maechler  <maechler@stat.math.ethz.ch>
437    
438            * R/kronecker.R: triangularity preserving methods
439    
440    2007-03-27  Martin Maechler  <maechler@stat.math.ethz.ch>
441    
442            * R/kronecker.R: new file collecting kronecker() methods in one
443                    place.  Goal: become much faster!
444    
445    2007-03-23  Martin Maechler  <maechler@stat.math.ethz.ch>
446    
447            * src/dtCMatrix.c (dtCMatrix_solve): use the new code from Kasper
448            Kristensen based cs_spsolve() instead of _lsolve & _usolve which
449            can be much faster.
450    
451            * tests/matprod.R: add regression tests for these (upper & lower).
452    
453    2007-03-19  Martin Maechler  <maechler@stat.math.ethz.ch>
454    
455            * R/Matrix.R (diff): method for our Matrices.
456    
457            * R/sparseMatrix.R (isDiagonal): check dim()!
458    
459    2007-03-17  Martin Maechler  <maechler@stat.math.ethz.ch>
460    
461            * R/Matrix.R (dim<-): new method for "reshape()" built on a
462            proposal from Tamas Papp.
463    
464    2007-03-16  Martin Maechler  <maechler@stat.math.ethz.ch>
465    
466            * R/AllGeneric.R: remove all  if(!isGeneric(.))  clauses
467    
468            * R/zzz.R (.onLoad, .onUnload): do *not* leave bind_activation(TRUE);
469            rather define and export  cBind() and rBind() only.
470            --> useRs *must* change code that used to have cbind()/rbind() !!
471    
472            * R/bind.R: change tests from cbind() to cBind() and similarly to rBind()
473            * R/bind.Rout.save: ditto
474    
475    2007-02-16  Douglas Bates  <bates@r-project.org>
476    
477            * DESCRIPTION (Date, Version): 0.9975-11 with new date
478            * src/dgCMatrix.c (R_to_CMatrix, compressed_to_TMatrix): remove
479            const modifier on declaration of the array 'valid'
480    
481    2007-02-12  Douglas Bates  <bates@stat.wisc.edu>
482    
483            * R/CHMfactor.R: Add image method (coercion to sparseMatrix).
484    
485    2007-02-05  Martin Maechler  <maechler@stat.math.ethz.ch>
486    
487            * DESCRIPTION (Date, Version): 0.9975-10 with new date.
488    
489            * R/Ops.R (Arith): make sure Csparse o Csparse also works for e.g. ntCMatrix
490            * tests/simple.R: test the above and some of these coercions:
491    
492            * R/nsparseMatrix.R: coercing "Csparse" to "lsparseMatrix";
493                    be careful to avoid infinite recursion, using new coercions in
494            * R/ngCMatrix.R and nsC... and ntC...
495            * R/lsparseMatrix.R: ditto
496    
497            * R/SparseM-conv.R: more conversion, notably for triplet matrices.
498    
499            * src/dgCMatrix.c (R_to_C_Matrix): port Doug's fix and
500            * R/Rsparse.R: reactivate .Call()s
501    
502            * tests/Class+Meth.R: a bit more on actual classes
503    
504    2007-02-04  Douglas Bates  <bates@stat.wisc.edu>
505    
506            * src/dgCMatrix.c (compressed_to_TMatrix): fix memory bug using strdup()
507    
508    2007-02-03  Martin Maechler  <maechler@stat.math.ethz.ch>
509    
510            * DESCRIPTION (Version): 0.9975-10 to upload
511    
512            * tests/Class+Meth.R (tstMatrixClass): require coercions to
513            specific classes less unconditionally.
514    
515            * R/Auxiliaries.R: get rid of as_Tsparse() and as_Rsparse()
516    
517            * R/Tsparse.R (triu): etc, use as(*, "TsparseMatrix") instead of as_Tsparse()
518    
519            * R/Rsparse.R (.R.2.T): R-level workaround using compressed_to_TMatrix.
520            * R/Rsparse.R (.R.2.C): R-level workaround since C-level
521            R_to_CMatrix segfaults on one platform.
522            Eliminate most coercion method to *specific* classes, and replace
523            with virtual classes coercions.
524    
525    
526    2007-02-01  Martin Maechler <maechler@stat.math.ethz.ch>
527    
528            * src/init.c: export the CHM...._validate() placeholders, since
529            they *are* called.
530    
531            * tests/Class+Meth.R (classCanCoerce): and starting to test
532            all as(<from>, <to>)
533    
534    2007-01-30  Martin Maechler  <maechler@stat.math.ethz.ch>
535    
536            * R/Tsparse.R ([): more care when subsetting triangular Tsparse
537            * tests/indexing.R: tested now
538            * tests/indexing.Rout.save: updated
539    
540            * src/Csparse.c (Csparse_to_dense): use Rkind = -1 for PATTERN to
541            * src/chm_common.c (chm_dense_to_SEXP): return "ngeMatrix" when
542            appropriate.
543    
544            * NAMESPACE: export a trivial
545            * R/Matrix.R: drop() Matrix-method
546    
547            * R/AllClass.R: moved all prototypes to virtual super classes.
548    
549            * R/Rsparse.R: many more coercions to have less exceptions in
550            * tests/Class+Meth.R:
551    
552            * R/Ops.R (Compare): tweak for case with NA
553            * tests/simpl.R: hence another 'FIXME' eliminated
554    
555    2007-01-29  Martin Maechler  <maechler@stat.math.ethz.ch>
556    
557            * R/diagMatrix.R (solve): the obvious methods for diagonalMatrix
558            objects.
559    
560            * tests/Class+Meth.R (tstMatrixClass): now testing diag(), nnzero(),
561              and more of "!", "&", "|", all, any; coercions
562    
563            * R/Rsparse.R: many coercions (which enable quite a few other
564            methods), thanks to enhancements in
565            * src/dgCMatrix.c (R_to_CMatrix): new, and
566            * src/dgCMatrix.c (compressed_to_TMatrix): now for (d,l,n) ,
567            symmetric & triangular and ..RMatrix objects.
568    
569            * src/TMatrix_as.c (Matrix_T_as_DENSE,Matrix_T_as_GENERAL):
570            renamed file from src/dsTMatrix.c;
571            now dealing with symmetric and triangular Tsparse coercions, both
572            to dense and general.
573    
574    2007-01-27  Martin Maechler  <maechler@stat.math.ethz.ch>
575    
576            * src/dsTMatrix.c: has now "l" and "n" methods besides the "d" ones.
577    
578            * R/Ops.R (Arith): <dgCMatrix> o <numeric> now remains sparse
579            where sensible when the <numeric> is of length > 1.
580    
581    2007-01-26  Martin Maechler  <maechler@stat.math.ethz.ch>
582    
583            * R/Matrix.R ([<-): for M[] <- value: fix length
584    
585    2007-01-25  Martin Maechler  <maechler@stat.math.ethz.ch>
586    
587            * R/Auxiliaries.R (n2l_Matrix): new, to be used in
588            * R/ndenseMatrix.R: new coercions n* -> l*
589    
590    2007-01-22  Martin Maechler  <maechler@stat.math.ethz.ch>
591    
592            * R/triangularMatrix.R: new file; simple triu() and tril() methods.
593    
594            * R/Ops.R ("Logic"): and other "Ops", many updates
595    
596    2007-01-18  Martin Maechler  <maechler@stat.math.ethz.ch>
597    
598            * src/Mutils.h (SET_DimNames): new utility
599    
600            * R/Auxiliaries.R (nnzero): improved and now exported via
601    
602            * NAMESPACE: + nnzero(); length() == prod(dim(.)) method for all "Matrix" objects
603    
604    2007-01-17  Martin Maechler  <maechler@stat.math.ethz.ch>
605    
606            * R/diagMatrix.R (!): fix typo.
607    
608    2007-01-16  Martin Maechler  <maechler@stat.math.ethz.ch>
609    
610            * R/Auxiliaries.R (as_Csparse): and quite a few others:
611                    allow to pass class definition --> speedup
612            * R/sparseMatrix.R: apply the above
613    
614            * R/Csparse.R: coercion Csparse* to dense* now preserves shape properties.
615    
616            * src/Mutils.h (mMatrix_as_geMatrix): new, based on
617            * src/Mutils.c (dup_mMatrix_as_geMatrix): new; generalization of
618            old dup_mMatrix_as_dgeMatrix), eliminating a long-standing "FIXME".
619    
620            * src/dense.c (dense_to_Csparse): use new mMatrix_as_geMatrix()
621    
622            * R/denseMatrix.R (.dense2C): based on dense_to_Csparse: name it,
623            and use it for "sparse*" as well, since it's faster than the
624            as_Csparse(.) way.
625    
626    2007-01-15  Martin Maechler  <maechler@stat.math.ethz.ch>
627    
628            * R/Ops.R ("Logic"): more methods, notably an  <lgC> o <lgC> one.
629    
630    2007-01-12  Martin Maechler  <maechler@stat.math.ethz.ch>
631    
632            * R/Tsparse.R (.TM.repl.i.2col): new internal function to be used
633            as method for   M[ ij ] <- v
634            * R/Csparse.R:: go via Tsparse for "M[ij] <- v"
635    
636            * R/Ops.R: "Compare" for (C|R)sparse: need pointer slot for all
637            FALSE answer
638    
639            * R/Csparse.R (replCmat): fix the "all non-zero" case with reordering
640            * tests/indexing.R: test it, and some of the above
641    
642    2007-01-05  Martin Maechler  <maechler@stat.math.ethz.ch>
643    
644            * R/Auxiliaries.R (is_duplicatedT): new utility
645    
646    2007-01-05  Douglas Bates  <bates@stat.wisc.edu>
647    
648            * src/init.c (R_init_Matrix): export cholmod_scale
649    
650    2006-12-30  Martin Maechler  <maechler@stat.math.ethz.ch>
651    
652            * R/zzz.R (tmp): for R >= 2.5.0, extend formals of our
653            base::as.matrix to (x, ...)
654    
655    2006-12-28  Martin Maechler  <maechler@stat.math.ethz.ch>
656    
657            * R/Ops.R ("Arith" etc): move almost all "Ops" methods to new R
658            file; start using "Logic", hence
659    
660            * DESCRIPTION (Depends): R >= 2.4.1 (since we want "Logic")
661            * NAMESPACE: import and export "Logic"
662    
663    2006-12-27  Martin Maechler  <maechler@stat.math.ethz.ch>
664    
665            * src/zpotfr.f and dependencies: use LAPACK 3.1 version
666            only needed previously to R version 2.5.0.
667    
668    2006-12-26  Martin Maechler  <maechler@stat.math.ethz.ch>
669    
670            * DESCRIPTION (Date, Version): 0.9975-8, ready for release
671    
672            * R/Tsparse.R (replTmat): fix subassignment of triangular
673            * R/Csparse.R (replCmat): ditto
674            * tests/indexing.R: more tests, incl the above fix
675    
676    2006-12-23  Martin Maechler  <maechler@stat.math.ethz.ch>
677    
678            * R/Auxiliaries.R (drop0): extend for non CSparse
679            * R/Auxiliaries.R (diagU2N): should work for all sparseMatrix
680    
681            * src/Csparse.c (Csparse_to_Tsparse, Csparse_general_to_symmetric):
682                    use uplo correctly (!); other places: use uplo_P() macro
683    
684            * R/Csparse.R (replCmat): call diagU2N() when needed
685            * R/Tsparse.R (replTmat): ditto
686    
687            * src/dtCMatrix.c (tCMatrix_validate): new
688            * src/dtTMatrix.c (tTMatrix_validate): new, used in
689            * R/AllClass.R: for validity of dtC, dsC, and dtT, dsT.
690    
691            * R/diagMatrix.R (replDiag): to use in [<-
692    
693    2006-12-22  Martin Maechler  <maechler@stat.math.ethz.ch>
694    
695            * R/Auxiliaries.R (as_Csparse2, as_geSimpl): new functions;
696                    also more general diagU2N().
697    
698    2006-12-21  Martin Maechler  <maechler@stat.math.ethz.ch>
699    
700            * R/bind2.R: new file for all cbind2(), rbind() methods moved here
701            from R/<foo>Matrix.R files. Better diagonal & improved sparse methods.
702    
703    2006-12-20  Martin Maechler  <maechler@stat.math.ethz.ch>
704    
705            * tests/bind.R: a few more cases
706            * R/Auxiliaries.R (.M.kind): also work for atomic vectors
707    
708            * R/denseMatrix.R (cbind2/rbind2): moved here (and generalized) from
709            * R/ddenseMatrix.R (cbind2/rbind2)
710            * R/Tsparse.R (replTmat): final(?!) fix for "[<-" ..
711            * tests/indexing.R
712            * tests/indexing.Rout.save: updated
713    
714    2006-12-18  Martin Maechler  <maechler@stat.math.ethz.ch>
715    
716            * R/Tsparse.R (replTmat): fixed a remaining "[<-" bug in
717            * tests/indexing.R
718    
719    2006-12-15  Martin Maechler  <maechler@stat.math.ethz.ch>
720    
721            * R/sparseMatrix.R (prSpMatrix): "." alignment much improved:
722            align with proper position of "0", i.e., right for integers.
723            argument 'align' by default is "fancy".
724    
725    2006-12-14  Martin Maechler  <maechler@stat.math.ethz.ch>
726    
727            * R/sparseMatrix.R: delegate "Compare" to "Csparse.."
728            * R/Csparse.R: and fix "Compare" for more cases.
729            * tests/Class+Meth.R: test some of these (m == m, m != m)
730    
731    2006-12-13  Martin Maechler  <maechler@stat.math.ethz.ch>
732    
733            * R/lsparseMatrix.R: all() and any() methods
734            * R/ldenseMatrix.R:      ditto
735            * NAMESPACE, R/Matrix.R: ditto
736    
737            * man/all-methods.Rd: document them minimally
738    
739            * tests/simple.R: add a few examples for these
740    
741    2006-12-11  Martin Maechler  <maechler@stat.math.ethz.ch>
742    
743            * R/Tsparse.R ([): fix long standing typo in symmetric case
744            * man/dsCMatrix-class.Rd: add example exhibiting the above case
745    
746    2006-12-10  Douglas Bates  <bates@stat.wisc.edu>
747    
748            * src/CHMfactor.c (CHMfactor_to_sparse): change LDL factorization
749            to LL before converting to a sparse matrix. (The LDL form can be
750            converted to a sparse matrix but it is implicitly a unit
751            triangular matrix and a diagonal matrix overwritten on the diagonal.)
752    
753    2006-12-09  Douglas Bates  <bates@stat.wisc.edu>
754    
755            * src/chm_common.c (chm_factor_to_SEXP): allocate and fill the Dim slot.
756    
757    2006-12-08  Douglas Bates  <bates@stat.wisc.edu>
758    
759            * DESCRIPTION (Version): updated -> release 0.9975-7
760            * src/{init.c,chm_common.c}, inst/include/*: export cholmod_analyze_p
761    
762    2006-11-30  Martin Maechler  <maechler@stat.math.ethz.ch>
763    
764            * R/diagMatrix.R (%*%): write a direct [diag o Csparse] method
765    
766    2006-11-29  Douglas Bates  <bates@stat.wisc.edu>
767    
768            * src/dgeMatrix.c (dgeMatrix_solve): Check error code from dgetri.
769            * tests/dg_Matrix.R: Add Barry Rowlingson's test of a matrix that
770            is exactly singular.
771    
772    2006-11-07  Martin Maechler  <maechler@stat.math.ethz.ch>
773    
774            * DESCRIPTION (Date): updated -> release 0.9975-6
775    
776    2006-11-06  Martin Maechler  <maechler@stat.math.ethz.ch>
777    
778            * R/Csparse.R (replCmat): symmetric indexing of symmetric matrix
779            now returns symmetric.
780    
781            * R/zzz.R ("diag<-"): replace "diag<-" in base for R <= 2.4.x
782    
783            * R/Matrix.R (.M.sub.i.2col):  new, for  M[ cbind(i,j) ] indexing.
784            * R/Matrix.R (.M.repl.i.2col): new, for  M[ cbind(i,j) ] <- value
785    
786            * R/Auxiliaries.R (.type.kind): added
787    
788    2006-11-04  Martin Maechler  <maechler@stat.math.ethz.ch>
789    
790            * src/cs.[ch]: updated to CSparse Version 2.0.3 by simply
791            running src/CSparse_install.sh
792    
793            * R/denseMatrix.R: "[": keep symmetric on symmetric indexing.
794    
795    2006-11-03  Martin Maechler  <maechler@stat.math.ethz.ch>
796    
797            * src/dsCMatrix.c (dsCMatrix_Csparse_solve): new
798            * R/dsCMatrix.R (solve): "fully-sparse" using the above.
799    
800            * R/AllClass.R: "pMatrix" now also inherits from "generalMatrix"
801    
802            * tests/Class+Meth.R (tstMatrixClass): now assure
803            the (important in method programming) property :
804    
805                    ###>>  Every "Matrix" is either
806                    ###>>  "general*", "symmetric*", "triangular*" or "diagonal*"
807    
808                    (where "*" stands for "Matrix")
809    
810            * R/Auxiliaries.R (diagU2N): now .Call()s Csparse_diagU2N for <Csparse>
811    
812            * R/dMatrix.R (Compare(<dMatrix>,<dMatrix>): update and
813            * tests/validObj.R: checks for "comparison"
814    
815            * R/sparseMatrix.R ([): improved indexing for sparse;
816                    trying to keep <symmetric>[ n, n] symmmetric
817    
818            * tests/indexing.R: indexing for logical sparse now ok
819    
820    
821    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
822    
823            * src/Tsparse.c: use xTsparse_validate() , and hence remove
824    
825            * src/{ltC,lsC,lgT}Matrix.[ch]: removed
826    
827    2006-11-02  Martin Maechler  <maechler@stat.math.ethz.ch>
828    
829            * R/AllClass.R (Matrix-class): check length of dimnames in validity.
830    
831            * tests/simple.R: validObject() checking the above.
832    
833            * src/dgCMatrix.c (xCMatrix_validate): new, small and simple,
834            replacing both dgCMatrix_validate and lgCM*.
835    
836            * src/Csparse.c (Csparse_dense_prod, etc): do not lose dimnames;
837            fix dimnames setting in other places.
838            * src/chm_common.c (chm_dense_to_SEXP): now can pass dimnames
839    
840    2006-11-01  Martin Maechler  <maechler@stat.math.ethz.ch>
841    
842            * R/Csparse.R,src/Csparse.c, etc: tcrossprod(<CsparseM>,<CsparseM>)
843    
844            * R/sparseMatrix.R (isSymmetric): drop 'factors' slot for
845            symmetry test, via
846            * R/Auxiliaries.R (.as.dgC.0.factors):
847    
848    2006-11-01  Douglas Bates  <bates@r-project.org>
849    
850            * R/Csparse.R,src/Csparse.c,tests/matprod.R,
851            man/CsparseMatrix-class.Rd: crossprod(<CsparseMatrix>,
852            <CsparseMatrix>) added
853    
854    2006-10-30  Martin Maechler  <maechler@stat.math.ethz.ch>
855    
856            * tests/matprod.R: add a variation of Harri's example
857    
858            * R/dsparseMatrix.R: fix crossprod(<dsparse>, <dge>) to *not*
859            recursive infinitely.
860    
861            * R/dgCMatrix.R: + solve(<sparse>, <sparse>)
862    
863            * tests/indexing.R: add test for the "<" bug fixed 10-27 in R/dMatrix.R
864    
865    2006-10-28  Martin Maechler  <maechler@stat.math.ethz.ch>
866    
867            * tests/Class+Meth.R (tstMatrixClass): more: use non-trivial
868            matrix if possible; test m+m == 2*m; now test dgRMatrix.
869            * R/dgRMatrix.R (.to.dgR): a few more coercions, in order to
870            satisfy the above test.
871    
872    2006-10-27  Martin Maechler  <maechler@stat.math.ethz.ch>
873    
874            * R/Matrix.R (Ops):  <Matrix> o <matrix>  method added
875    
876            * R/dgCMatrix.R: solve(a, b="missing") based on
877            * src/dgCMatrix.c (dgCMatrix_matrix_solve): extend to work with
878            RHS = NULL.
879    
880            * R/diagMatrix.R (diagdiagprod): extend %*% etc to ldiMatrix;
881            add more (needed) [t]crossprod() methods.
882    
883            * man/ddiMatrix-class.Rd: more info, notably on 'diag'
884    
885            * R/Auxiliaries.R (as_CspClass): cleanup
886            (drop0): internal utility for "Csparse_drop(*, 0)"
887            (.bail.out.2): encourage active feedback
888    
889    2006-10-26  Martin Maechler  <maechler@stat.math.ethz.ch>
890    
891            * R/dMatrix.R(Compare): new(), then slots [no validity check]
892    
893            * src/Csparse.c (Csparse_validate): fixed (and more efficient in
894            non-valid or 'sorted' case).
895    
896            * R/dsparseMatrix.R: add "chol" method.
897            * R/ddenseMatrix.R: ditto
898    
899            * R/diagMatrix.R (Ops): group methods for  <diagonal> o <sparse>
900            * NAMESPACE (Ops)
901            * R/diagMatrix.R (diag2T): simple utility used "higher level"
902            coercion; deprecating direct lower level coercions.
903    
904            * R/*.R (seq): use seq_len() and seq_along() where possible.
905    
906    
907    2006-10-23  Martin Maechler  <maechler@stat.math.ethz.ch>
908    
909            * DESCRIPTION (Version): 0.9975-5 ready for release
910    
911    2006-10-20  Douglas Bates  <bates@stat.wisc.edu>
912    
913            * src/init.c (R_init_Matrix): export more cholmod CCallable functions.
914    
915    2006-10-20  Martin Maechler  <maechler@stat.math.ethz.ch>
916    
917            * R/AllClass.R (corMatrix): add 'validity' check;
918                    comment out unused "LDL" class definition
919            * NAMESPACE: mention, but do not export "LDL" class
920            * R/corMatrix.R: new (simple), needed for R-devel with
921            * tests/Class+Meth.R (tstMatrixClass): 1 exception for corMatrix
922              coerce and t() exceptions for all 5 'Mat.MatFact' classes.
923    
924    2006-10-19  Douglas Bates  <bates@stat.wisc.edu>
925    
926            * src/chm_common.h: Add R_cholmod_start to initialize cholmod to
927            use Rprintf and R's error handling.
928    
929    2006-10-17  Martin Maechler  <maechler@stat.math.ethz.ch>
930    
931            * R/diagMatrix.R (%*%): rep(*, each = .) in Matrix %*% diagonal.
932            * tests/matprod.R: add tests for the bug fixed.
933    
934    2006-10-11  Douglas Bates  <bates@stat.wisc.edu>
935    
936            * src/HBMM.[ch]: remove HarwellBoeing format for writing.
937            * src/SOURCES_C.mkf (SOURCES_C): no longer compile iohb.c
938    
939    2006-10-06  Douglas Bates  <bates@stat.wisc.edu>
940    
941            * R/d[gs]CMatrix.R: deprecate the writeHB function.  Use writeMM instead.
942    
943    2006-10-06  Martin Maechler  <maechler@stat.math.ethz.ch>
944    
945            * DESCRIPTION (Version): 0.9975-3
946    
947            * R/diagMatrix.R (bdiag): new function constructing block diagonal
948            (sparse) matrices.
949            * man/bdiag.Rd: docu + examples
950    
951            * R/Csparse.R (replCmat): calling new Csparse_drop() now.
952    
953            * src/Csparse.c (Csparse_general_to_symmetric, Csparse_drop): new functions
954            * R/lsCMatrix.R: three more coercions to lsC (thanks to the above)
955    
956            * R/diagMatrix.R (Diagonal): '[<-' method for diag.matrices such
957            that result is sparse or diagonal (and not dense).
958    
959            * man/Subassign-methods.Rd: fix examples
960    
961            * R/Matrix.R (Matrix):  Matrix(0, *) or Matrix(*, sparse=TRUE)
962            should always return a sparse (and not sometimes a diagonal) matrix.
963    
964    2006-10-05  Martin Maechler  <maechler@stat.math.ethz.ch>
965    
966            * R/Matrix.R ([<-): also for value "Matrix" or "matrix"
967    
968    2006-10-04  Douglas Bates  <bates@stat.wisc.edu>
969    
970            * DESCRIPTION (Version): 0.9975-2
971    
972            * inst/include/Matrix_stubs.c (M_cholmod_sparse_to_triplet): export more symbols
973    
974    2006-10-02  Douglas Bates  <bates@R-project.org>
975    
976            * tests/dg_Matrix.R: Simplify test taking into account new code.
977    
978    2006-09-29  Martin Maechler  <maechler@stat.math.ethz.ch>
979    
980            * R/Csparse.R (replCmat): improve for missing i / j in non-simple cases
981    
982            * R/lsTMatrix.R: new files w/ missing methods
983            * R/nsTMatrix.R:  "  'for completeness'
984    
985            * tests/Class+Meth.R: a bit less 'not.ok.classes'
986    
987            * R/Tsparse.R (t): generalized "t" method from "dgT*" to "Tsparse*"
988    
989    
990    2006-09-28  Douglas Bates  <bates@R-project.org>
991    
992            * src/dppMatrix.h: Ensure definition of dspMatrix_validate is
993            included.
994    
995            * src/init.c, inst/include/{Matrix.h,Matrix_stubs.h,cholmod.h}:
996            Export C-callable functions used in Zt_create in lme4.
997    
998    2006-09-28  Martin Maechler  <maechler@stat.math.ethz.ch>
999    
1000            * DESCRIPTION (Version): 0.9975-1
1001    
1002            * tests/simple.R: less checks fail; using NA, found that our
1003                    kronecker() is not base-compatible with NA's.
1004    
1005            * R/dMatrix.R: "Compare" method now implemented for all cases
1006    
1007            * R/Auxiliaries.R (indTri): == which([lower/upper].tri( * )) new utility
1008    
1009            * man/dtpMatrix-class.Rd: mention length of 'x' slot
1010    
1011            * src/dtpMatrix.c (dtpMatrix_validate): fix check
1012            * src/dspMatrix.c (dspMatrix_validate): ditto
1013    
1014            * R/dtTMatrix.R (gt2tT): fix ("l" -> "n")
1015              including coercion to [nl]tTMatrix.
1016    
1017            * R/diagMatrix.R (show): print a header line as for other classes.
1018    
1019    2006-09-27  Martin Maechler  <maechler@stat.math.ethz.ch>
1020    
1021            * src/Makefile.win (SUBDIRS): fix typo
1022    
1023    2006-09-19  Martin Maechler  <maechler@stat.math.ethz.ch>
1024    
1025            * DESCRIPTION (Date): ready to release 0.9975-0 to CRAN
1026    
1027    2006-09-18  Douglas Bates  <bates@stat.wisc.edu>
1028    
1029            * R/[CT]sparse.R (crossprod and tcrossprod): Handle the cases for x
1030            symmetric and y missing in R code using %*% (cholmod_aat doesn't
1031            accept a symmetric matrix).
1032            * tests/group-methods.R: Uncomment test of crossprod applied to
1033            lsCMatrix objects.
1034    
1035    2006-09-18  Martin Maechler  <maechler@stat.math.ethz.ch>
1036    
1037            * R/AllClass.R (symmetricMatrix): add validity method (available
1038            in C for a long time). Many "n..Matrix": drop (wrong) validity arg.
1039    
1040            * src/lgCMatrix.c (lgCMatrix_validate): check 'x' slot (!)
1041    
1042            * tests/indexing.Rout.save:
1043            * tests/indexing.R: additions, mainly for 'lsparse'
1044    
1045            * R/diagMatrix.R (Diagonal) & coercion to lgTMatrix: fixes for NA
1046            case.
1047    
1048            * R/Auxiliaries.R (nz.NA): new utility now used in nnzero()
1049    
1050    2006-09-16  Martin Maechler  <maechler@stat.math.ethz.ch>
1051    
1052            * R/sparseMatrix.R (prSpMatrix): print logical NAs "visibly"
1053                    as 'N' (1-letter - Ok?)
1054    
1055            * tests/group-methods.R: add test for logical + NAs
1056    
1057            * R/dMatrix.R ("Compare"): fix to work with NA's
1058    
1059            * R/AllClass.R: "Cholesky" etc now inherit from MatrixFactorization.
1060    
1061            * src/lgCMatrix.c (ncsc_to_matrix): renamed from lcsc_to_matrix()
1062                    which is implemented.
1063    
1064    2006-09-15  Martin Maechler  <maechler@stat.math.ethz.ch>
1065    
1066            * src/chm_common.c: coerce logical <-> double instead of
1067            typecasting;  needed for "l" matrix handling in cholmod.
1068    
1069            * tests/other-pkgs.R (graph): small extension in "graph" checks.
1070    
1071            * R/sparseMatrix.R (graphNEL -> Tsparse): method for weight case.
1072            (Tsp2grNEL): other fixes needed
1073    
1074    2006-09-11  Martin Maechler  <maechler@stat.math.ethz.ch>
1075    
1076            * R/AllClass.R ("nMatrix"): and subclasses for "nonzero pattern"
1077                    Matrices, since "lMatrix", also "lsparseM" can have NA
1078            * R/ndenseMatrix.R, etc: new source files
1079            * man/nsparseMatrix-classes.Rd, etc: new help files
1080            * tests/: adaptions
1081            * src/chm_common.c (chm_dense_to_SEXP): and others:
1082                    new 'Rkind' argument: "l*" and "d*" both use CHOLMOD_REAL
1083            * src/Csparse.c, etc: ditto
1084    
1085    2006-09-11  Douglas Bates  <bates@R-project.org>
1086    
1087            * src/Mutils.[ch],init.c inst/include/*.h: Move the
1088            alloc_d**Matrix functions to the lme4 package.
1089    
1090    2006-09-09  Douglas Bates  <bates@R-project.org>
1091    
1092            * src/dsCMatrix.c (dsCMatrix_Cholesky): igoring LDL = FALSE now
1093            fixed
1094    
1095    2006-09-09  Martin Maechler  <maechler@stat.math.ethz.ch>
1096    
1097            * R/lMatrix.R: new
1098    
1099            * R/sparseMatrix.R (Tsp2grNEL): do not yet use graph::foo()
1100    
1101            * R/dgeMatrix.R: do not define tcrossprod() methods for "matrix"
1102            * man/tcrossprod.Rd: ditto
1103    
1104    2006-09-08  Douglas Bates  <bates@stat.wisc.edu>
1105    
1106            * inst/include/Matrix_stubs.c,Matrix.h: Add declarations and stubs
1107            for exported functions
1108            * src/Makefile, src/CHOLMOD/Lib/Makefile, src/Metis,CAMD,CCOLAMD:
1109            Remove partitioning algorithms for sparse matrix reordering.  The
1110            copyright on the Metis code was problematic and the methods were
1111            rarely used.
1112            * src/triplet_to_col.[ch],MMHB.[ch]: Remove triplet_to_col.  Such
1113            operations are now done entirely in CHOLMOD code.
1114    
1115    2006-09-06  Douglas Bates  <bates@R-project.org>
1116    
1117            * src/Mutils.h: Remove functions that are no longer used.
1118    
1119    2006-09-04  Douglas Bates  <bates@R-project.org>
1120    
1121            * src/dtCMatrix.c (dtCMatrix_validate): rename functions.
1122            * src/DEPS.mkf: update
1123    
1124    2006-09-02  Martin Maechler  <maechler@stat.math.ethz.ch>
1125    
1126            * created branches/Matrix-for-R-2.3.x;  on trunk: do
1127            * DESCRIPTION (Version): 0.9975-0
1128            (Depends): R (>= 2.4.0)
1129    
1130    2006-09-01  Douglas Bates  <bates@R-project.org>
1131    
1132            * R/sparseMatrix.R: Added direct method to CsparseMatrix from graphNEL
1133    
1134    2006-09-01  Martin Maechler  <maechler@stat.math.ethz.ch>
1135    
1136            * R/sparseMatrix.R: add coercion from "ANY" to "sparseMatrix"
1137            * R/denseMatrix.R:  add coercion from "ANY" to "denseMatrix"
1138    
1139            * R/Matrix.R ([): use nargs() to disambiguate M[i] and M[i,]
1140    
1141    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1142    
1143            * R/sparseMatrix.R (Arith): moved Arith group method one-level up
1144            from "dsparse" to "sparse" and now go via "Csparse" instead of "dgC"
1145            * R/dsparseMatrix.R: ditto
1146            * R/Csparse.R: ditto
1147    
1148    2006-08-31  Martin Maechler  <maechler@stat.math.ethz.ch>
1149    
1150            * R/dMatrix.R (Compare): improve availability of "<", etc
1151            * R/Auxiliaries.R (asTuniq): new; also make use of R 2.4.x print(*,max)
1152    
1153    2006-08-30  Martin Maechler  <maechler@stat.math.ethz.ch>
1154    
1155            * R/dgCMatrix.R: aargh: "Arith(<dgC>, numeric)" was wrong because
1156            of a 0-index which was used as 1-index (..hmm)
1157    
1158            * R/sparseMatrix.R (prSpMatrix): fix printing an all-0 sparse Matrix
1159    
1160            * R/Auxiliaries.R (all0, is0): for 0-testing in presence of NA's
1161            * R/Auxiliaries.R (isTriMat): use all0() for 0-testing.
1162            (.is.diagonal): ditto
1163    
1164            * R/lgTMatrix.R: as("matrix", "lgTMatrix"): warn about NA's
1165    
1166            * R/Matrix.R (Matrix): also work for NA data
1167    
1168    2006-08-28  Martin Maechler  <maechler@stat.math.ethz.ch>
1169    
1170            * R/Matrix.R (Matrix): + 'forceCheck' argument; dimnames setting
1171            in all cases.
1172    
1173    2006-08-27  Douglas Bates  <bates@R-project.org>
1174    
1175            * src/dense.[ch],init.c, R/ddenseMatrix.R, man/band.Rd
1176            (ddense_band): Added triu, tril and band for ddenseMatrix objects.
1177    
1178    2006-08-25  Martin Maechler  <maechler@stat.math.ethz.ch>
1179    
1180            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): added all subclasses of
1181            subclasses of "ddenseMatrix"
1182            * src/init.c et al: outcomment dtrM*_as_dge* and dsyM*_as_dge*_
1183            * R/ddenseMatrix.R et al: setAs("ddenseMatrix", "dgeMatrix", ..)
1184            instead of half dozen specialized ones.
1185    
1186    2006-08-25  Douglas Bates  <bates@R-project.org>
1187    
1188            * R/lmer.R (qqmath method): Bug fix provided by Emmanuel Tillard
1189            <tillard@cirad.fr> - ordering standard errors to match effects.
1190    
1191    2006-08-24  Douglas Bates  <bates@R-project.org>
1192    
1193            * src/lsCMatrix.c (lsCMatrix_trans): Remove lsCMatrix_chol based
1194            on R_ldl.
1195            * R/lCholCMatrix.R,
1196            src/[dl]CholCMatrix.[ch],R_ldl.[ch],Metis_utils.[ch]: removed
1197            * src/dsCMatrix.c (dsCMatrix_to_dgTMatrix): use CHOLMOD
1198            * many files in ./R and ./src: Use more general version of
1199            dup_mMatrix_as_dgeMatrix to simplify method definitions.
1200            * src/Mutils.c (dup_mMatrix_as_dgeMatrix): Add ddiMatrix,
1201            dtpMatrix, dspMatrix and dppMatrix conversions.
1202    
1203    
1204    2006-08-23  Douglas Bates  <bates@R-project.org>
1205    
1206            * R/AllClass.R,lCholCMatrix.R,src/SOURCES_C.mkf,init.c,NAMESPACE:
1207            Remove classes lCholCMatrix and dCholCMatrix based on R_ldl code.
1208            * src/dgeMatrix.c: Ensure 'factors' slot exists in result of
1209            dgeMatrix_crossprod (may need to do this in other places).
1210            * R/AllGeneric.R,dsCMatrix.R, src/dscMatrix.[ch]: Add Cholesky
1211            generic and method for dsCMatrix.  Use CHOLMOD for chol().
1212    
1213  2006-08-22  Douglas Bates  <bates@R-project.org>  2006-08-22  Douglas Bates  <bates@R-project.org>
1214    
1215          * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general          * src/Mutils.c (dup_mMatrix_as_dgeMatrix): updated for general
1216          types of classed Matrices, matrices or numeric or logical vectors.          types of classed Matrices, matrices or numeric or logical vectors.
1217          * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.          * src/init.c: register dup_mMatrix_as_dgeMatrix for coercions.
1218            * src/chm_common.c,Mutils.h (as_cholmod_factor): Move check_class
1219            to Mutils.h (as an inline) and change name to Matrix_check_class;
1220            fixes in as_cholmod_factor and chm_factor_to_SEXP.
1221            * src/dsCMatrix.[ch]: Use CHOLMOD for dsCMatrix_chol and
1222            dsCMatrix_matrix_solve.  Comment out vestigial functions.
1223            * src/Csparse.c: use diag_P and uplo_P macros.
1224    
1225  2006-08-21  Douglas Bates  <bates@R-project.org>  2006-08-21  Douglas Bates  <bates@R-project.org>
1226    

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